Vol.3, No.5, 344-350 (2011) Natural Science
Copyright © 2011 SciRes. OPEN ACCESS
Distributions of pigments in reef sediments,
contribution of phytoplankton to organic
matter budget in coral reef
Mohammed Rasheed1*, Tariq Al-Najjar1, Said Damhoureyeh2
1Marine Science Station, University of Jordan and Yarmouk University, Aqaba, Jordan; *Corresponding Author:
2Biology Department, University of Jordan, Amman, Jordan.
Received 22 March 2011; revised 18 April 2011; accepted 27 April 2011.
The temporal distributions of pigment on bio-
genic calcareous and terrigenic reef sediments,
chlorophyll a, chlorophyll b, chlorophyll c, fuco-
xanthin, and porphine concentrations were mea-
sured monthly in two sediment columns (0 - 15 cm)
for one year. Pigment concentrations increased
significantly during winter (November-April) in
both sediment types particularly in the upper
layers of the sediments. Phytoplankton contri-
butions to organic matter were found to be 8 ± 3
and 6 ± 2% in calcareous and terrigenous se-
diments respectively. The accumulation and the
successive degradation of phytoplankton de-
tritus to inorganic nutrients in calcareous sand
may partly sustain the productivity of the coral
reef communities which live in nutrient-poor
Keywords: Pigment; Calcareous Sediments;
Terrigenous Sediments
Organic matter in the water column can be buried into
the sediment through precipitation. Some of these com-
pounds can be degraded in the sediment thorough bio-
chemical reactions [1-7]. Shelf and coastal sediments are
considered the most productive parts of the ocean floor
[8,9]. Most of the organic matter sedimentation occurs in
the shelf sediments [8]. These sediments are exposed to
waves, currents, temperature differences, and nutrient
inputs [10]. Due to this high capacity for organic matter,
and the exposure of these sediments to different physical
and chemical actions, the sediments at coastal regions
may have an important regulatory and buffering function
in the ocean. The main source of organic matter
to the shelf sediments is the deposition of detrital mate-
rial from the local phytoplankton community in the
overlying water which may compromise 20 - 50% of the
produced organic carbon, nitrogen and phosphorous [11].
Some pigments can be found in the living and deceased
phytoplankton as detrital materials as well as in the fecal
pellets of the zooplankton.
Calcareous sediments are those of biogenic origin and
composed mainly of carbonate while terrigenous sedi-
ments are those of land source that have found their way
to the land and composed mainly of silicate. Calcareous
sediments are usually found in tropical and subtropical
environments within coral reef ecosystems. The main
component of these sands are coral fragments, mollusc
fragments, foraminiferans tests, and calcareous red algae
[12]. Due to their different sources, carbonate and sili-
cate sediments have different chemical and physical cha-
racteristics, such as porosity, light attenuation, surface
structure, sorption and desorption characteristics, as well
as different accumulation rate of organic matter [5,12].
The aim of this study was to assess the accumulation
rates of some pigments including chlorophyll a, b, c,
fucoxanthin, and porphine in calcareous and terrigenous
sediments of the Gulf of Aqaba during different seasons
of the year as well as to estimate the contribution of phy-
toplankton-pigment to the total organic carbon in cal-
careous and terrigenous sediments. This work was un-
dertaken to estimate the contribution of phytoplankton
detritus in the total organic matter deposited in calcare-
ous and terrigenous sediments in the coral reef areas,
since organic matter deposited in coral reef sediments
may remineralize to inorganic nutrient and sustain the
coral reef system which live in nutrient-poor water.
2.1. Study Sites
The study was carried out in a marine reserve thriving
M. Rasheed et al. / Natural Science 3 (2011) 344-350
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with coral reef community in the northern Gulf of Aqaba
(Figure 1). This reef is considered as one of the best-
developed reefs in the Red Sea [13] with high rate of
biogenic carbonate production. Two sampling sites at 5 m
water depth were selected for this study; the two sites
were 200 meters apart, first site was located in an area
with calcareous sediments while the second consisted
mainly of terrigenous sediments.
2.2. Sampling
At the beginning of this study, physical and chemical
properties were analyzed. Cores of sediment to about 20
cm sediment depth were sampled monthly for pigment
analysis using cylindrical acrylic pipes (25 cm high, 9.5
cm inner diameter). In the lab, the sediments of the cores
were cut into slices as thin as 1 cm in the first 6 cm of
the sediment and 2 cm subsequently. About 5 cm3 of the
sediment were kept in deep freeze 80˚C for pigment
2.3. Analytical Procedures
2.3.1. Sediment Properties
Grain size distribution of the sediment has been as-
sessed by set of calibrated analytical sieves. Sediment
porosities were calculated from weight loss of wet sedi-
ment after drying at 60˚C for 24 h. The hydraulic con-
ductivity (permeability) of the sediment was measured
with a constant head permeameter as described by Klute
and Dirksen [14]. Calcium carbonate content was deter-
mined by complexometric titration of calcium carbonate
with 0.1 N of HCL according to Muller [15]. Organic
carbon contents in the sediments were measured follow-
ing the method of Sandstrom [16], at which 0.2 g of the
34.79 34.82 34.85 34.88 34.91 34.94 34.973535.03
Longitude (E)
Latitude (N)
Marine Science
0 1 2 3 4 5 km
34 34.5 35
Red Sea
Gulf of Aqaba
Figure 1. Study sit at the northern Gulf of Aqaba, Red Sea.
sediment were treated with concentrated H2SO4 and po-
tassium dichromate and then titrated with ferrous am-
monium sulfate solution.
2.3.2. Pigment Analysis
Pigments were analysed following the method of
Rusch et al. [17]. Accordingly, 90% acetone was used
for pigment extraction and then the extract was obtained
by centrifugation at 4˚C for 15 minutes at 15000 rpm.
The supernatant was filtered through 20 µm syringe-
filter and concentrated using opaque vacuum oven. 20 µl
of the extracted pigment were injected and separated
through a Hypersil ODS C18 column [17,18]. The ana-
lysis was done in duplicates for each sediment sample.
3.1. Sediment Properties
Calcareous sediments have more carbonate content
than terrigenous sediments (about 18 fold, Table 1). This
is expected as the source of calcareous sands is biogenic
with carbonate body. Grain size, porosity, and perme-
ability are obviously higher in the calcareous sands than
in the terrigenous sands which emphasize the different
sources of the two sediments and that the granules of the
calcareous sands are non regular and have more bores.
Although calcareous sands have larger grain size, higher
organic carbon is found in these sands indicating also the
biogenic source of these sediments and higher surface
area [5].
3.2. Pigment Distribution in Sediments
The northern Gulf of Aqaba has usually four specified
conditions which control nutrients, organic matter and
phytoplankton spatial distributions in the coastal water
[5,19-22]. These conditions prevailing in four different
periods are 1) summer months which extend usually from
June to November with low nutrients, organic matter and
phytoplankton level 2) transition month between sum-
mer and winter (December) 3) winter months (Janu-
ary-April) with high nutrient, organic matter concentra-
tions as well as high phytoplankton level 4) transition
month between winter and summer (May). The data
shown in (Figure 2, August, December, March, and May)
is to characterize pigment concentrations. Pigment con-
centrations at all months decline from the upper layer of
the sediments to the bottom layers (Figure 2). Yet, sub-
surface maxima can be observed in some months for
calcareous sediments (e.g. chl b-December at 1 cm sedi-
ment depth). Chlorophyll a profiles showed an increase
in the concentrations from August to March in both se-
diment types (Figure 2). However, a significant in-
M. Rasheed et al. / Natural Science 3 (2011) 344-350
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Figure 2. Pigment concentrations (µg·dm3) in calcareous (triangle) and terrigenous (square) sediments in August, De-
cember, March and May. Complete data sets including the whole year (January - December) are available from the au-
thors. The error bars represent the standard deviation of two measured samples from the same sediment depth.
M. Rasheed et al. / Natural Science 3 (2011) 344-350
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Table 1. Chemical and physical properties of calcareous and terrigenous sediments.
Sediment type CaCO3 (%) Median grain
size (µm)
Mean grain size
(µm) Sorting Porosity (%)Permeability
Organic carbon
Calcareous 70 - 90 605 545 1.3 52 ± 6 135 ± 18 0.41 ± 0.1
Terrigenous 3 - 6 230 258 0.8 35 ± 5 22 ± 6 0.26 ± 0.1
crease in the upper layer of the sediments was observed,
while no change was observed in the bottom layers (Fig-
ure 2). similar trends were noticed for other pigments.
Comparison between the calcareous and terrigenous se-
diments showed that calcareous sediments have higher
concentrations than terrigenous sediments (Figure 2).
This is more pronounced in the middle and deep layer as
indicated by the ratio of individual pigment in calcareous
to terrigenous sediments (Table 2).
The results revealed two important aspects. The sea-
sonal patterns of pigments concentrations in both sedi-
ment types and the elevated pigments concentrations in
calcareous sediments compared to those of terrigenous
silicate sediments.
4.1. Seasonal Pattern
Higher pigment concentrations were measured in the
sediment in winter than the summer (Figure 2). This
was clearly obvious in the upper layers of the sediments
(Table 3). The rates of pigment changes were always
positive in the upper layer (0 - 2) compared to fluctuated
values in the middle and lower layers of the sediments
(Table 3), indicating that the upper layers were impacted
by seasonal pattern existing in the Gulf of Aqaba [19-22].
Low nutrients and chlorophyll a concentration were
found in the water column at coastal and offshore waters
during summer, while in winter, high concentrations
were attributed to intrusion of nutrient and organic mat-
ter rich water from deep water to the shallow and coastal
water [5]. This might impact pigment concentrations
directly by intrusion of organic matter rich in plankton
detritus from deep water [21] and indirectly by primary
productivity enhance and phytoplankton bloom due to
availability of different nutrients [23-26]. Furthermore,
tight coupling between seasonal changes in the water
column and permeable sediments was found [5] in the
northern Gulf of Aqaba and in the North Sea [27].
4.2. Pigment Distributions in Calcareous
and Terrigenous Sediments
The concentrations of different pigments in calcareous
sediments were obviously higher than those of silicate
sediments especially in the upper (0 - 2 cm) and the
middle layers (2 - 8 cm) of the sediments (Figure 2),
where bioturbation and advective process may effect the
transport mechanism in the sediments [28,29]. This im-
plied that organic matter was trapped more in calcareous
sediments which might be caused by different properties
of calcareous and terrigenous sediments such as mineral
structure, surface area, permeability and porosity of the
sediment as well as the benthic fauna that present at both
Although grain sizes of calcareous sediments was
higher than these of terrigenous sediments, higher sur-
face area of calcareous sediments was measured for the
sediment of the Gulf of Aqaba (0.41 and 0.27 m2·g1 for
calcareous, and terrigenous respectively [5]. Calcareous
sediments with a rough surface [5,30] which originated
from skeletal remain of corals, sea urchins, and other
benthic organisms, contained many small pores that in-
crease the surface area of the calcareous grains. The high
surface area then enhanced the ability of the sediment to
accumulate more organic matter [31-33]. Rasheed et al.
[5] using fluoresceine as inert tracer, found higher ac-
cumulation rate (1.3 fold) in calcareous sediment than in
terrigenic sediment and related this to less rounded shape
and rough grain surface of the calcareous sediments. The
in-situ accumulation rate in calcareous and terrigenous
sediments revealed more organic matter accumulated in
the calcareous sediments (factor 1.5) which is attributed
to a higher grain surface area of the calcareous sedi-
ments. The upper layers of the coral sands are well aer-
ated and illuminated and are inhabited by dense popula-
tions of microalgae, bacteria and microzoobenthos [34].
This would increase subsequently pigment concentra-
tions in these sands.
Higher permeability was measured in calcareous se-
diment compared to terrigenous sediments (6 fold, Table
1). This might increase the accumulation rate of the cal-
careous sand as demonstrated by several authors
[5,12,30,35-38]. The in situ incubation to investigate
trapping efficiency of organic particles in sieved carbon-
ate and silicate sediments with different permeability
revealed 2-fold of pigment concentrations were trapped
in the calcareous than in the terrigenous sediments and
pigments penetrated deeper into the these sediment [5].
The high porosity and permeability of carbonate sedi-
ments allow water currents to penetrate and resuspend
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Table 2. Average ratios between pigment concentrations in calcareous and terrigenous sediments from different layer of the sediment.
Surface sediments are represented by 0 - 2 cm layer, middle sediments are represented by 2 - 8 cm layer, and bottom sediments are
represented by 8 - 15 cm layer.
Period Layer (cm) chl a chl b chl c fucoxanthin porphine
0 - 2 1.3 1.7 1.7 1.7 1.7
2 - 8 2.2 4.2 3.1 3.2 4.1
8 - 15 4.5 1.5 4.8 5.1 4.9
0 - 2 1.4 2.1 1.8 2.7 2.3
2 - 8 2.5 3.6 6.3 4.9 6.2
8 - 15 5.1 10.2 5.9 5.4 5.4
0 - 2 0.9 1.4 1.3 1.5 1.3
2 - 8 1.8 1.8 3.9 4.2 6.3
8 - 15 4.6 2.3 1.1 1.0 5.8
0 - 2 1.3 2.0 2.0 2.0 2.0
2 - 8 2.6 3.5 4.0 4.2 7.7
8 - 15 7.3 6.2 1.3 1.2 7.2
Table 3. Rates of pigments changes (mg·dm3·d1) during winter period (November - March) in calcareous and terrigenous sedi-
ments. Rates are calculated from concentration differences between March and November divided by periods.
chl a chl b chl c fucoxanthin porphine
Layer (cm)
0 - 2 5.48 3.38 0.16 0.08 0.37 0.13 1.78 0.08 3.38 0.88
2 - 8 1.05 0.12 0.00 0.06 0.12 0.01 0.56 0.01 5.49 0.26
8 - 15 1.29 1.25 0.01 0.02 0.01 0.10 0.02 0.04 0.07 0.10
sand [39,40], which enhance advective transport through
these sediments. In high permeable sand, advective ex-
change may be dominant which increase the flow of
water with particulate matter into the sediments [5].
Flume experiments showed that the ensuing advective
pore water flows could transport solutes and particulate
matter up to 10 centimeters into the bed within 12 hours
[36,41,42]. In our experiment, the calcareous sand ac-
cumulated pigments deeper than terrigenous sand (e.g.
chlorophyll a was transported to 11 cm and 7 cm into
calcareous and terrigenous sediments respectively). As
calcareous sediments had higher permeability than terri-
genic, organic matter could be transported and accumu-
lated deeper into these sediments. Rasheed et al. (2003 a)
found that organic matter transported 2.5 and 1.5 cm
deep into carbonate and silicate sediments respectively.
This was caused according to the authors by advective
pore water flows. Pilditch and Grant [35] and Huettel
and Rusch [36] demonstrated in flume experiments that
permeable sand beds could filter phytoplankton from the
boundary layer. Horizontal pressure gradients, generated
when the boundary flows interact with small sediment
topography (sand ripples, biogenic structures, shells)
causing water intrusion into the bed which will transport
suspended particles into the sediment.
Benthic fauna might also effect pigment distribution
in the sediment either through bioturbation [29] or by
feeding activities. The distribution of organic matter at
both sediment sites revealed more shells and snails in
calcareous sediments than in terrigenous sediments. This
might increase pigment content in the deep layers of the
calcareous sediments more than those of the terrigenous
sediments [5].
4.3. Phytoplankton Contribution to Total
Organic Matter Budget in Coral Reefs
Calcareous sediments are dominant in the continental
shelves where coral reefs are present [34]. Through
transportation of solute into the sediments through ad-
vective process, calcareous sediments filter these solutes
M. Rasheed et al. / Natural Science 3 (2011) 344-350
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and the trapped particulate matter present. Phytoplank-
ton detritus can be also trapped in the sediments. In or-
der to calculate the contribution of phytoplankton detri-
tus in total organic matter deposited in calcareous and
terrigenous sediments, the conservative calculations us-
ing the accumulative rates of chl a and fucaxanthin in
the sediment and the pigment concentration percentage
for the total phytoplankton in the Gulf of Aqaba during
winter season were 28 and 12% respectively [20], how-
ever, we found phytoplankton contributions of 8 ± 3 and
6 ± 2% of organic matter to calcareous and terrigenous
sediments respectively. The accumulation of phyto-
plankton detritus and the subsequent degradation of
these detritus to inorganic nutrients may partly support
the productivity of the coral reef community which lives
in nutrient-poor environments.
Thanks are due to Khalid Altrabeen for his help in the lab. We would
like to thank Tariq Al-Salaman and Ali Hammad for helping in the
collection of the samples. This work has been funded by the Marine
Science Station, Aqaba-Jordan.
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