O. C. Sarmento et al. / TAJST—Vol. 3 (2020)
Effect of Diagenesis on the Microstructure of Fossil Coral
Skeletons from Atauro Island, Timor-Leste
Osvaldo da Cruz Sarmentoa, Aquiles Tomas Freitasa, Bhencao Natália M.Monteiroa, Vital
Cruz M. Vilanovaa, Elizario Moniza, Aniceta de Araújoa, Cornélio Cardoso Moniza, Atsuko
Yamazakib
a) Department of Geology and Petroleum Engineering, National University of Timor Lorosa’e,
Hera-Dili, Timor-Leste
b) Department of Earth and Planetary Science, Faculty of Science, Kyushu University, Fukuoka,
Japan
E-mail: osvaldosarmento1512@gmail.com
Abstract: The diagenesis effects on carbonate sediments are possible to affect the coral
proxy recording climatic variations. We report the diagenesis effect on the microstructure
of fossil coral skeletons and a Tridacna shell from Pleistocene reef terraces in Atauro Island,
Timor-Leste. We use three methods with observation using Feigl’s solution
staining, scanning electron microscope, and thin sections. The fossil Porites coral skeletons
suffer diagenetic changes, mainly growing aragonite filling pore spaces in the
microstructure. On the other hand, Goniastrea coral fossil shows a minimal diagenetic
alteration, even Goniastrea fossils 100ka older than Porites fossils. The fossil giant clam
shell (Tridacna Gigas) from Terrace II is still well preserved very dense aragonite shell and
daily band microstructure. These results suggest that the diagenetic processes accelerate not
only age but also the buried environment of the fossils and microstructure of biogenic
skeletons.
Keyword: diagenesis, fossil coral skeleton, reef terrace, pleistocene, porites, tridacna
Paleoclimate reconstruction in the tropics has
emerged as an important tool for exploring the
natural bounds of climate variability. Long
lived, massive corals provide valuable natural
archives of environment and fossil corals
provide ‘windows’ into climates of the past [2,
7, 10].
The process of diagenesis in coral reef
terraces refers to the precipitation of secondary
aragonite or calcite in skeletal voids, or the
1. Introduction
Uplifted coral reef terraces locally compose
the coast of Timor and around Islands [1, 4].
Millions of hectares of coral reef dominate
much of the world tropical coastline. These
massive structure
results
from
the
accumulation and cementation of skeleton
innumerable corals over thousands of years.
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O. C. Sarmento et al. / TAJST—Vol. 3 (2020)
Atauro Island. The highest elevation of Atauro
Island is 950 m above sea level, and the coral
terrace raised up to 450 m above sea level.
We visited the south part, Berau and Nametan,
and Acrema area in the north of the island
(Fig.1A). The fieldwork conducted on coral
reef terrace indicted on the Figure 1B the
samples collected with special consideration
from beachrock terraces, coral reef and
stratigraphic relationship of the strata. Totally
20 samples were collected to assess the
diagenetic effect history (Table 1).
To observe the diagenesis effects, we choose
the coral specimens from the outcrop of the
cliff on the edge of Terrace I (~100ka) named
[1]. Figure 2 shows the sketch drawing at the
terraces located at south of Atauro Island
(Nametan Beach). The Reef complex cover
the base of the lithology is volcanic rock. At
the outcrop of sampling site, facies classified
three small-scale facies based on their
lithology
(Fig.2).
The
changes
in
sedimentation patterns might be created by
minor sea level fluctuation. The older facies
have been made up of lithified Grainstone
including Porites fossils (ATR10-P3). The
subsequent facies consist in bound stone
(ATR10-C). The middle facies made up of
lithic fragments and it overlies in the older
facies and faunas (ATR10-P1, ATR10-P2 and
ATR10-G).
Fig. 1 Location of the studied area (A) and
sampling points on the south of Atauro
Island (B).
replacement of skeletal aragonite. During this
alteration, the composition of coral terrace are
covered particles by transgression and
regression and diagenesis effects on carbonate
sediments are possible to affect the coral
geochemical proxies [3, 6]. Understanding
diagenetic processes is essential for carbonate
sedimentology and paleoclimate studies.
In this study, we observe microstructure of
fossil coral skeletons and shells to examine the
methods for detecting diagenesis effects and to
understand the diagenetic processes depending
on ages and biogenic carbonate types.
3. Method
3.1. SEM (Scanning Electron Microscope)
SEM is the kind of electron microscope that
produces images of a sample by scanning the
surface with a focused stream of light
by electrons. The technical procedure work of
this machine is very complexity utility and the
specially using by coral research analyses in
the following steps; The firstly sample
2. Sample Site
The sample sites are located in the part of
north and south of Atauro Island, Timor-Leste
(S08°07'45.28",E125°37'48.66",S08°18'24.94
", E125°34'30.00"°,). The coral fringing reef
uplift occurs around the volcanic rocks in
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O. C. Sarmento et al. / TAJST—Vol. 3 (2020)
Feigl’s solution staining, scanning electron
microscope (SEM), and thin section.
preparation, Label for each sample code,
cutting sample to small portion, use SEM
equipment to analyses in the microscope and
take image in SEM for sample analyses with
the magnification of 200 and 1000.
This material of Feigl’s solution is consist
such as; NaCl 100ml, 5Wt% MnSO4, 1Wt%
Ag2SO4, Distilled water 94g (consist in one (1)
boil), This filter to remove the remaining
things, add 1-2 drops NaOH, Filter again to
keep solution black coloured solution and
finally analysis by Stereo Microscope
Analyses. Feigl solution is one of the methods
used to identified the fossil coral mineral and
define the characteristics feature indicate by
colour calcite is the white and aragonite is
black.
3.3. Thin Section Analyses
Thin sections made for all samples at
National University of East Timor, Faculty
Engineering sciences
and
Technology
department geology and Petroleum. There are
nineteen sample for thin sections made by
corals sample found in outcrop (ATR1ATR10, ATR10-C, ATR10-T, ATR10-G, and
ATR-M1 until ATR-M3). These thin sections
used to verify the mineralogy of the corals,
examine the growth banding, and assess
diagenetic changes, cementation, and
alteration of microstructure fossil coral
skeleton.
Fig. 2 Stratigraphy column in the field and
sketch or drawing coral terrace at
outcrop in the field.
Examination of the samples in this
manner allowed microscale assessment of the
fabrics and determination of any diagenesis
that had affected in the fossil corals
microstructure. In this study, we use SEM;
Phenom G2 pure installed in KIKAI institute
for Coral Reef Sciences, Japan. SEM images
were taken under the following conditions: a
7.8 nm pixel resolution; voltage, 5 kV; and
exposure time, 8 s.
4. Result
The coral reef terrace in Acrema North of
Atauro Island exhibits variable degrees of
skeletal preservation. Although mostly devoid
of cement, some corals from in this local
contain minor amounts of fibrous and/or finely
crystalline cement in some of their pores.
Other corals in this area as South of Atauro
Island (Nametan) with well preserved and
another portion have altered, the external
skeletons extensively replaced by coarse
3.2. Feigl’s Solution Staining
There are two ways for examination in
laboratory to determine the mineral
composition for each sample. To examine the
diagenesis effects on fossil coral skeletons and
Tridacna shells, we observe the samples using
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O. C. Sarmento et al. / TAJST—Vol. 3 (2020)
particles (Fig.3). Although these corals have
recrystallized, most pores are open and contain
only minor finely crystalline cement. Massive
coral reef limestone in reef flat zone, beach
conglomerate deposit is well rounded, and
carbonate cemented. Bioturbated muds and
sand in the back reef often with fossil mollusks
(Tridacna), much of the limestone sequence
forms a series of terrace level, where presents,
the reef crest facies mark the highest elevation
of each terrace. The terrace often has a thin
regressive beach conglomerate deposit
overlying the reef and sediment facies. The
limestone surface weathers to pale grey and is
hard cavernous. The development of a
limestone terrace corresponds to sea-level
high, with the oldest terrace occurring at the
highest elevation.
Table 1 Details of Coral Sample list, Fieldwork in Atauro Island Calcite or effect diagenesis rating.
Sample
Name
ATR1
Latitude
Longitude
-8.129244444
125.63018
33
ATR2
-8.128938889
125.62978
06
ATR3
-8.303847222
125.56311
39
ATR4
-8.304377778
125.56257
78
ATR5
-8.305138889
125.56195
ATR6
-8.305302778
ATR7
-8.305547222
ATR8
-8.304736111
125.56145
ATR9
-8.305077778
125.56145
ATR10-G
-8.306927778
125.575
125.56209
17
125.56198
61
Sampling
Location
Acrema
(Atauro_nor
th)
Acrema
(Atauro_No
rth)
Nametan
(Atauro_So
uth)
Nametan
(Atauro_So
uth)
Atauro_Sou
th
Atauro_Sou
th
Atauro_Sou
th
Nametan
Beach
Nametan
Beach
Nametan
(Atauro_So
uth)
4
Genus
(Sampl
e type)
Sample
Field
size
Terrace
((X,Y,Z
Outcrop
cm))
(Coral)
11.11.2
0
(Coral)
9.5.13
Goniast
rea sp.
15.6.5
(Tridac
na)
14.1
Tridacn
a Gigas
Porites
sp.
Porites
sp.
Porites
sp.
Porites
sp.
Goniast
rea sp.
Age
Terrace
(chapel&
Veeh
1978)
-
-
IIIa
230Ka
II
200Ka
I
100Ka
7.14.3
15.5.10
12.8.11
11.9.9
9.11.5
30.21.1
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O. C. Sarmento et al. / TAJST—Vol. 3 (2020)
Tridacn
a
28.22
Porites
sp.
16.13.1
1
Porites
sp.
30.14.1
4
Porites
sp.
23.29.1
0
(Coral)
14.30.6
Nametan
Beach
Porites
sp.
9.7.8
125.575
Nametan
Beach
(Coral)
8.8.3
125.575
Nametan
Beach
(Coral)
16.19.5
ATR10-T
-8.306927778
125.575
ATR10P1
-8.306927778
125.575
ATR10P2
-8.306927778
125.575
ATR10P3
-8.306927778
125.575
ATR10-C
-8.306927778
125.575
-8.306927778
125.575
-8.306927778
-8.306927778
ATR
MODER
N1
ATR
MODER
N2
ATR
MODER
N3
Nametan
(Atauro_So
uth)
Nametan
(Atauro_So
uth)
Nametan
(Atauro_So
uth)
Nametan
(Atauro_So
uth)
Nametan
(Atauro_So
uth)
Fossil porites corals (ATR10-P1, ATR10P2) of the terrace I are investigated by SEM
image, stained Feigl’s solution, and thin
section to observe on
the fossil coral
microstructure with diagenesis changes. On
SEM images of the fossil Porites specimen,
ATR10-P1, on Figure 3 (b,c), fiber-like
crystals are growing on theca wall as
secondary aragonite. On thin section image of
coral skeleton (e,d), microstructure of theca
wall and dissepiment are altered. SEM images
of another Porites coral fossil (g,h), ATR10P2, shows that theca wall has smooth surface,
however, high magnification image suggests
some portion covered by secondary aragonite
crystals. Fiegl’s solution stained specimens
Beach
-
shows small part of calcite and almost part
surrounded by aragonite. Thin section images
(l, m) show the texture on theca wall,
dissepiment, and septa is surrounded by
secondary aragonite crystals.
Fossil coral skeleton, Goniastrea sp.
(ATR3) from Terrace IIIa is investigated by
SEM (Figure 4 (b, c)). The skeletal
dissepiment and theca wall structure are
smooth and well preserved. Fiegl’s solution
stains whole part of aragonite skeleton (d). The
thin section image also suggests theca wall and
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Fig. 3 Figure 4. Observation on ATR10-P1 and ATR10-P2 sample from Terrace I. The SEM images
on the surface of ATR10-P1 with a magnifying power of 200 (b) and 1000 (c). The polarized image
of thin section (d, e). The SEM images on the surface of ATR10-P2 with a magnifying power of 200
(g) and 1000 (h). The coral skeleton stained by Feigl’s solution shows distinguish the part of
aragonite (stained gray) and calcite (stained white) (k). The polarized image of thin section (l, m).
dissepiment structure is well preserved. The
SEM images of fossil Tridacna shell (ATR5)
have no secondary crytals (Fig. 5b, 5c). The
fine growt lines are observed on thin section
images (Fig. 5d, 5e).
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O. C. Sarmento et al. / TAJST—Vol. 3 (2020)
Fig. 4 Observation on ATR3 sample. The SEM images on the surface of skeletons
dissepiment observed with a magnifying power of 200 (b) and 1000 (c). The coral skeleton
stained by Feigl solution shows distinguish the part of aragonite (stained gray to yellow)
and calcite (stained white) in between the theca walls and dissepiment (d). The polarized
image of thin section (e, f) indicated the diagenesis dissepiment and theca wall well
preserved.
Fig. 5 Observation on ATR5 sample. The SEM images on the surface of skeletons observed
with a magnifying power of 200 (b) and 1000 (c). The coral skeleton stained by Feigl solution
shows distinguish the part of aragonite (stained gray ) and calcite (stained blue) in between
surface skeleton (d). The polarized image of thin section (e) well preserved.
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O. C. Sarmento et al. / TAJST—Vol. 3 (2020)
section and scanning electron microscopy to
detect diagenesis changes). Diagenesis, even
at low levels, has the potential to distort the
primary chemistry of coralline aragonite.
Detecting and avoiding diagenesis is of utmost
importance to coral paleoclimate research, and
thin section analysis should play an essential
role in that endeavor.
5. Outlook
The coral reef framework and associated
around Atauro Island provide a remarkably
favorable for marine cement (figure 2). Marine
cementation and diagenetic effect alter fossil
coral manifest as secondary aragonite or
calcite crystal filling inter-skeletal pore spaces
[7, 9, 11].
Quaternary uplifted of marine terraces in
Atauro Island form by the combined effects of
sea-level change (caused primarily by
changing glacial ice volume) and tectonic
uplift on coastlines [1, 4]. Atauro Island is
suitable to understand the diagenesis processes
on coral and shell species in different ages.
This study examines the utility of three ways
methods, SEM analysis, Feigl’s solution, and
thin section. The combination of these three
ways will provide detailed information about
diagenetic effects on biogenic carbonate.
The Porites and Goniastrea corals, and
Tridacna shell from Terraces I and Terraces
IIIa around southern Atauro Island are
compared in terms of the diagenesis effect on
their microstructure (Figs. 3,4,5). The fossil
Porites samples (ATR10-P1, ATR10-P2) are
more influenced by diagenesis than the fossil
Goniastrea samples (ATR3) (fig.4). Fossil
Goniastrea samples (ATR3) shows minimal
evidence of physical diagenetic alteration
(fig.4). These results might be responsible for
1) coral microstructure such as pore spaces and
complex, and 2) the buried environment of
fossils. Diagenesis results in mineral phases,
secondary aragonite, or calcite, depending on
the zone [5, 8]. The growth of secondary
aragonite on the coral skeletal structure
typically occurs within marine phreatic and
marine vadose zones. Secondary calcite,
growing on the skeletal structure or replacing
the original organic aragonite, occurs during
subaerial exposure in the marine or freshwater
vadose zones or can occur in freshwater
phreatic environments.
Finally, we aware that this research paper
was not perfect, including its fossil coral
skeleton and among others, so we hope to have
appropriate cooperation with the readers to be
able and successfully of article paper in the
adjacent future research.
Acknowledgement
The authors are thankful for this research was
made possible by funding from JICA
CADEFEST Project Phase II for providing
financial support. We are deeply indebted to
numerous colleagues from the Kyushu
University. We are thankful for KIKAI
institute for providing SEM facilities to carry
out this work.
The fossil giant clam shell (Tridacna
Gigas) from Terrace II is still well preserved
very dense aragonite shell and daily band
microstructure.
Feigl’s solution is instant methods for
detecting the diagenesis process. Ideally,
Feigl’s solution should be used in combination
with a suite of other methods such as a thin
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