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 Volume - 1

Chief Editor
Dr. Yogendra Singh

A DVA N C E S i n
BIOLOGICAL SCIENCES
ISBN 9788194578741 AND BIOTECHNOLOGY
9 788194 578741

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 ADVANCES in
Biological Sciences
AND BIOTECHNOLOGY
Volume - 1

Chief Editor
Dr. Yogendra Singh
Assistant Professor (Senior Scale)-Biotechnology
Jawaharlal Nehru Krishi Vishwa Vidyalaya
Jabalpur, Madhya Pradesh, India

Integrated Publications
New Delhi
Published By: Integrated Publications

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© Integrated Publications
Publication Year: 2020
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 Contents

Chapters Page No.

1. Metagenomics: Perspectives, Methods and Applications in
Biotechnology 01-18
(Abhinav Kumar Srivastava, Sparsh Phutela, Gaurav Jaiswal, Durg Vijai Singh
and Udai Pratap Singh)

2. Gene Transfer Methods in Plants 19-42

(Shivangi Rahangdale, Yogendra Singh, Deepak Katkani and Naveen Surjaye)

3. Potential of Germplasm Conservation & Cryopreservation 43-62

(Rakesh Mehta, Ankita Pandey and Diksha Patel)

4. Plastivor, Galleria mellonella, as a Bio-Control Agent of

Polythene and Plastics 63-73
(Neelima Painkra and Ashvani Kumar)

5. Coral Reef Ecosystem 75-104

(Ambo Tuwo and Joeharnani Tresnati)

6. Ecosystem and Sustainable use of Mangrove Forests 105-136

(Joeharnani Tresnati, Risal Aprilianto and Ambo Tuwo)

7. Molecular Mechanism of Transgenerational Epigenetic

Inheritance through Paramutation 137-157
(Piyusha Singh, Akanksha Tiwari and Vimlesh Kumar)

8. Potential of Bioethanol as Future Fuel 159-190

(Vinod Kumar Sahu, Yogendra Singh, Sushma Tiwari and Akanksha Tiwari)

9. Next Generation Sequencing: An Emerging Tool 191-217

(Shweta Tiwari, Shivangi Rahangdale, Yogendra Singh and Suneeta Sharma)
 Chapter - 5
Coral Reef Ecosystem
Ambo Tuwo and Joeharnani Tresnati

Abstract
Coral reefs are the most diverse ecosystems on the Earth. They are
habitat for many species of marine organisms, and offer a plethora that
benefit to human life. Coral reef brings in enormous funds to coastal
countries through tourism, fishing, and discoveries of new biochemical and
drugs. Coral reef, together with mangrove ecosystems and seagrass
ecosystems, provide natural coastal protection. Ecologically, coral reefs are
the feeding, nursery and spawning ground for many marine organisms. Coral
reef are sensitive to physical and chemical environmental factors, that can
become limiting factors. Physical environmental factors that have significant
role in the development of coral reefs are temperature, depth, salinity, and
turbidity. Coral reef is a habitat for many species of aquatic microflora and
macrophyta, and many other species of marine flora. Coral communities
consist of coral animals that are reef makers or hermatypics. The Scleractinia
is the most dominant reef makers. Population diversity in the coral reef
ecosystems is very high. Primary productivity of coral reef is higher than
other ecosystems, such as seagrass and tropical forest ecosystems. Coral
reefs suffer from a lot of pressure, about 75 percent of the world’s reefs face
threats from pollution, habitat destruction, overfishing and, increasingly, a
changing climate that increases temperatures, sea level, and acidity in the
oceans. Degradation of coral reef can be caused by anthropogenic and
natural disturbance. Anthropogenic disturbance are coral rock extraction,
sedimentation, waste, eutropication, and fisheries. Coral reef are also suffer
by natural pressure. The natural pressure are disease, acanthaster outbreak,
coral bleaching, and global climate change. Some previous studies showed
that rising global temperatures, increasing oceanic CO2, and other impact of
climate change were affecting coral reef health in a negative way, and if CO2
emissions continue to increase at the current rate, there will most certainly
reductions in the area and diversity of coral reefs in the future.

Page | 77
Keywords: coral reefs, distribution, limiting factors, productivity,
biodiversity, current condition, global warming
1. Introduction
Coral reefs are a unique ecosystem in the tropical ocean that formed by
massive deposits of calcium carbonate produced by hermatipic coral that live
in symbiosis with zooxanthellae [1, 2]. Zooxanthellae can produce organic
material through photosynthesis, which is then secreted in large part to its
host (coral animal) [2-4].
There are four terms that sound same but their meanings are different,
namely coral reefs, corals, hard coral, and rock coral. Coral reefs are large
limestone structures formed and produced by coral animals and other
calcareous organisms that forming a compact ecosystem as a habitat for
marine organism [2, 4, 5]. Corals are a group of organisms from the phylum
Coelenterata, the class of Anthozoa, especially from the order Scleractinia
which forms hard and soft corals [6, 7]. Hard coral are calcareous corals,
usually referred to as hermatypic corals [2, 6]. While rock coral is dead coral
in the form of limestone [2].
Economically, coral reefs can provide at least five benefits, namely:
1) As a fishing ground, various species of fish, ornamental fish and
other marine organism can be consumed or reared in an aquarium;
12% of the world's marine catches come from coral reef areas; and
Southeast Asian reef fisheries generated US $2.4 billion
2) As job provider, Maldives fisheries contributed 25% of the total
available employment
3) As a tourist attraction, world diving tourism contributes 4.5 billion
dollars per year obtained from 4,726 dive centers and resorts
4) As a producer of active ingredients for drugs and cosmetics
5) As natural laboratory for research and education [2, 4, 7-9]
And ecologically, coral ecosystems, especially fringing reefs and barrier
reefs, play an important role as:
1) Primary producer, coral reefs can produce 15 to 35 C tons Ha-1 year-1
2) Coastal areas abrasion protector due to waves and strong currents
3) As a habitat, coral reefs are the feeding ground, nursery ground, and
spawning ground of marine organisms
4) As an excellent nutrient recycler [2-4, 10]

Page | 78
2. Coral reef dynamics
Coral reefs dynamics are so complex and have a unique ecological
process. Coral reefs develop parallel to the reef evolution. According to
Darwin's evolution theory, the island sinking produces four types of coral
reefs [11, 12]. First is the fringing reef which is the coral reefs located at the
coast of the main land or small islands, fringing reefs are frequently found in
Indonesian sea [3]. Second is the barrier reef, which is the coral reef that
stretches outside the main land or small islands. Third is a circular atoll,
where in the middle there are deeper waters. Fourth is the patch reefs which
is a coral reefs that does not appear on the surface of the water, separate from
land or islands, patch reefs are frequently also found in Indonesian sea [3].
Each of these reef patterns grows and develops depending to the coral
species as the lime formation. The lime formation rate varies depend on reef
area and active period of corals, the day or night [2]. The lime formation rate
is slow, the highest rate is found at Acropora species with a growth rate of 4
to 17 cm year-1 [4].
Coral reefs can form zoning or vertical and horizontal distribution.
Vertical distribution of coral reefs depends on the coral reefs slopes profile,
deeper, and speed of coral growth. Vertical distribution depend also on the
depth, light intensity, sedimentation, oxygen, and coral species [4, 13]. On
certain coral reefs such as in Jamaica where the coral reef population is rich
and diverse, corals can form reefs to a depth of 70 meters, and even some
coral species can form reefs at a depth of 100 meters [14].
Horizontal distribution can form a kind of zone. Formation of this zone
depends on five factors. First, is direction of the coming wind or waves. In
the area where the wind comes in, on the surface, the waves are so strong
that they are only overgrown by algae from the genus Lithothamnion [13, 14].
Coral is abundant in parts that are rather deep to a depth of 50 cm. On atolls,
corals are very abundant in the rear wind area (leeward). In the wobbly areas
of the atoll, corals also grow in areas facing the sea, but are not too dense.
Second is the depth of the waters; coral reefs are abundant at the depth of
three to 10 meters. Third is the waters temperature, coral reefs are abundant
in areas where temperature changes due to solar radiation is not too large.
Fourth is the waters salinity, coral reefs are abundant in areas where changes
in salinity due to rain are not too large. Fourth is biological factors, coral
reefs are abundant in areas that are optimal for biological processes and
ecological interactions [4, 15].

Page | 79
3. Limiting factors and coral distribution
Coral reefs development is very sensitive to physical and chemical
environmental factors and both of them can be a limiting factor. The
physical environment factors are temperature, depth, salinity, and turbidity.
Corals can live in water temperatures above 18 ºC with optimal temperatures
between 23 ºC and 25 ºC. The maximum temperature that can be tolerated by
corals are ranges between 36 ºC and 40 ºC. Coral can grow well in water
depths of less than 50 m, but the optimal depth is 25 m or less. Coral are
stenohalin organisms or can only tolerate a low range of salinity fluctuation,
which is between 32 and 35 permil [16]. Coral need sunlight for the
photosynthesis of zooxanthellae [2]. The distribution of coral reefs in the
world is strongly influenced by limiting factors; the good condition of
Indonesia's marine environment has caused coastal waters and small islands
in Indonesia to have a high diversity of coral reefs [17].
Tomascik et al. (1997) estimate that:
1) The area of coral reefs in world waters is around 617,000 km-2
2) The area of coral reefs in the Indonesian Archipelago around 85,707
km-2, consisting of 50,223 km-2 of barrier reefs, 19,540 km-2 atolls,
14,542 km-2 fringing reefs and 1,402 km-2 of patch reef
According to Tomascik et al. (1997), to live, grow and develop
properly, corals require the following environmental condition factors:
1) Coral cannot tolerate water temperatures below 20 ºC, the range of
water temperatures that can be tolerated by corals are 20 to 30 ºC.
The optimal water temperatures for corals are 23 to 25 ºC. Changes
of more than 3 ºC from normal coral temperature, can cause stress
to the coral
2) Coral needs high water brightness, the optimal intensity for corals
growth is 15 to 20 of the surface light intensity; lights are needed by
corals for photosynthesis
3) Coral cannot tolerate high salinity fluctuations and too fluctuating,
coral can live well in the salinity range of 32 to 36 ppt, with optimal
temperatures of 32 to 35ppt
4) Coral can tolerate pH fluctuations between 7.5 and 8.5
5) Coral requires good oxygen concentration
6) Certain currents and waves are needed by corals because currents
and waves can improve nutrients supply, increase oxygen solubility,
and refresh or change water

Page | 80
 7) Corals need water with a low solid content; suspended fine particles
can cover the coral surface of the and interfere with photosynthesis
of zooxanthella which is symbiotic with coral
8) Coral likes waters with hard bottom substrates, hard substrates are
needed to adhere
9) Coral likes uncontaminated waters, pollution can kill coral
10) Coral wants a low concentration or nutrient supply, if the nutrients
are abundant, then phytoplankton will develop rapidly so that it
disrupts the penetration of light into water
11) Coral does not want the presence of high phytoplankton biomass, if
the phytoplankton biomass is high, the coral will not get enough
light, so that its growth is disrupted, or even die [3, 4, 16, 18-20]
4. Coral ecosystem organisms
Coral ecosystem is a habitat for many species of aquatic flora, such as
algae, seaweed, coralin algae, calcareous green algae and seagrass. In coral
reef ecosystems also live many species of aquatic fauna, such as:
1) Invertebrates, i.e. crustaceans, snails, shellfish, and echinoderm,
such as sea urchins, sea anemones, sea cucumbers, sea stars and sea
lilies
2) Fish, i.e. opportunistic carnivorous, herbivorous, omnivorous, and
planktovorous fishes
3) Reptiles, i.e. sea snakes and sea turtles
Organism, especially coral fish populations have different daily
distribution patterns between day and night. Planktovorous fish or plankton
feeder are widely scattered around the reef during the day, hiding or
sheltering in crevices of the reef at night. Foraging fish are generally benthic
feeder. Biota diversity and balance of coral ecosystems are highly dependent
on food webs. Excessive extraction of certain species can cause an explosion
of excessive prey populations, which can disturb the balance of the
ecosystem [4, 21, 22].
In Indonesian coral reef there are at least 452 species of coral animals
belonging to 80 genera and 15 families. The fifteen families are:
Acroporidae, Agariciidae, Astrocoeniidae, Caryophylliidae,
Dendrophylliidae, Faviidae, Fungiidae, Merulinidae, Mussidae, Oculinidae,
Pectiniidae, Pocilloporidae, Dendrophylliidae, Faviidae, Fungiidae,
Merulinidae, Mussidae, Oculinidae, Pectiniidae, Pocilloporidae,
Dendrophylliidae, Faviidae, Fungiidae, Merulinidae, Mussidae, Oculinidae,

Page | 81
Pectiniidae, Pocilloporidae, Poritidae, and Siderastreidae. In the coral
ecosystems, up to 2,000 reef fish species can be found [16, 17, 22].
5. Biotic and abiotic components
Coral reef ecosystems have diverse components of biotic and abiotic.
The biotic component consists of producers, consumers and decomposers.
The main producer in coral reef ecosystem is algae from a class of
dinophyceae named zooxanthelae that live in symbiosis with coral animals.
Other producers are several species of algae that live together in coral reef
ecosystems [23-25]. The consumers that live in the ecosystem of coral reefs are
reef fish, molluscs, sponges, echinoderms etc. Decomposers are
decomposing bacteria. Abiotic components are elements and compounds of
organic and inorganic. The environmental parameters are temperature,
oxygen, nutrients and other physical factors that can be a limiting factor if it
is outside the tolerance threshold of an organism.
Biotic and abiotic components interact each another so that the changes
in one component can effect on the ecosystem balance. Ecosystem balance
will be constant if existing components remain in dynamic equilibrium. The
dynamic equilibrium indicated by high biodiversity value of biotic elements
in coral reef ecosystems. In stable ecosystems there is a consistent
interaction between species and populations, especially in the case of food
webs. If the food web is disturbed due to the extinction of one of the
population, it can result in disruption or inconsistency in the flow of energy
or food in the food web. Imbalance occurs due to the missing one or more
food chains that can simplifie the food web of the ecosystem [25-27].
Simplification or food webs will reduce the diversity or biodiversity. Low
biodiversity indicates an imbalance in the ecosystem. High imbalance causes
low elasticity or resilience, so ecosystems become fragile or sensitive to
shocks
6. Coral communities
Coral communities consist of corals that are reef makers or hermatypics
and non reef makers or ahermatypics. The Scleractinia is the most dominant
reef makers. The Scleractinian community that occupies coral reefs in the
world's oceans is very high diverse. The total number of Scleractinian taxa is
around 800 species devided in 110 genera. Scleractinian diversity varies
depending on the condition of the area and region. The total number of
Scleractinian genera reaches a maximum in the Philippines, Indonesia and
North Australia [4]. Until 1998, the number of Scleractinian coral species
recorded in all Indonesian waters was estimated at 364 species of the 76
genera [28].

Page | 82
 There is three life strategy of Scleractinian hermatypic taxa, namely "r"
strategy, "k" strategy and "intermediate" strategy (between "r" and "k"). "r"
strategy is an opportunistic corals that living in small or medium sized
colonies; limited growth; reach sexual maturity early; spend most of their
energy for breeding; annual reproductive cycle; short life time; survival
enhancement by intensive reproduction; high growth rate; can increase
ability to compete and fight over the substrate by recruitment and vegetative
propagation; and can survive under various types of environmental stresses,
such as low salinity, pollution, turbidity, and high temperatures in shallow
water. The "r" strategy coral are Stylopohra pistillata, Psammocora
contigua, Pocillopora damicornis, Seriatipora histrix, and several species of
genera Montipora, Acropora and Pavona [4].
The "k" strategy coral are conservative coral that use most of their
energy for growth and metabolism [4]. Conservative coral has unlimited
growth, colony size can reach diameters from one to three meters; uses a
small part of their energy for breeding; have a long life, it can live for tens or
hundreds of years; and have annual reproductive cycle. The "k" strategy
coral are Porites and Montastrea genera.
Most coral species are the "intermediate" strategy, life strategy between
the "r" strategy and the "k" strategy. "Intermediate" strategy corals are able
to adapte differences environmental conditions and various hard substrates.
Phenotically, corals in this strategy are unstable, because the colonies are
formed in a variety of reef environment conditions that emerge many forms
of ecomorphological adaptation. "intermediate" strategy are the genus
Acropora, Faviid, Pavona, Hydronophora, Galaxea and Goniopora.
Alcyoniina family is Scleractinian that has "Intermediate" strategy [4].
Besides hermatypic corals, there are ahermatypic 173 species of ahermatypic
corals (27 genera) found in Indonesian waters [3].
In Indonesian waters, there are at least 450 species of hard coral which
are divided into 15 families with 72 genera. The 15 families are:
1) Pocilloporidae (Pocillopora, Madracis, Seriatopora, Stylophora
and Palauastrea)
2) Acroporidae (Acropora, Anacropora, Montipora and Astreopora)
3) Fungiids (Cycloseris, Lithophyllon, Herpolitha, Polyphyllia,
Halomitra, Sandalolitha, Fungia, Heliofungia, Diaseris, Zoopilus,
Ctenaciis and Podabacea)
4) Agariciidae (Gardinoseris, Pavona, Leptoseris, Coeloseris and
Pachyseris)

Page | 83
 5) Astrocoeniidae (Stylocoeniella)
6) Poritidae (Porites, Alveopora and Goniopora)
7) Faviidae (Caulastrea, Plesiastrea, Favia, Favites, Oulophyllia,
Goniastrea, Platygyra, Leptoria, Montastrea, Diploastrea,
Leptasrea, Cyphastrea, Oulastrea and Echinopora)
8) Trachyphyllidae (Trachylhyllia and Wellsophyllia)
9) Oculinidae (Archelia and Galaxea)
10) Merulinidae (Hydnophora, Merulina and Scapophyllia)
11) Mussidae (Acanthastrea, Symphyllia, Lobophyllia, Scolyma,
Cynarina and Blastomusa)
12) Pectinidae (Pectinia, Echinophyllia, Oxypora, and Mycedium)
13) Caryophylliidae (Euphyllia, Catalaphyllia, Plerogyra and
Physogyra)
14) Rhizangiidae (Culicia)
15) Dendrophylliidae (Turbinaria, Tubastrea and Dendrophyllia) [3].
In Indonesia waters, there are also three families of soft corals, namely
Alcyonacea, Helioporacea, and Pennatulacea [3].
7. Coral reef biodiversity
Biodiversity is a representation of the complexity of energy flow and
material cycles in an ecosystem. Higher biodiversity make higher
complexity; higher complexity make higher ecosystem stability. Ecosystem
stability is represented by the ability of populations in the communities of an
ecosystem to survive (stability of resistance) from outside disturbances, for
example decrease of oceanographic conditions that cause reduction in
producers number. Ecosystem stability is also represented by the ability of
the population to recover (resilience stability) after outside disturbances have
passed, for example improving oceanographic conditions that cause a
gradual increase in producers number. These two stabilities determine the
ecosystem carrying capacity, higher stability make higher carrying capacity.
High biodiversity means there are a complex food webs in the
ecosystem. Complex food webs make the organisms in certain ecosystem
have many food alternative, so that if a food chain is disturbed or broken due
to interference from outside the ecosystem, then there are still other food
chains that can be utilized. High biodiversity provides an opportunity for all
species in a community to recover their conditions progressively. An
ecosystem that have diverse producers or consumers will have diverse

Page | 84
responses to external disturbances. Producers or consumers will recover
themselves at different timescale after the external disturbances. passed.
Coral communities consist of reef makers corals or hermatypic corals
and non reef makers or ahermatypic corals; the Scleractinia are the most
dominant reef makers. Scleractinian have around 800 species devided in 110
genera [3, 4]. Marine life diversity in the coral reef ecosystems are very high,
around the world, there are about 33,000 to 60,000 species of flora and
fauna. At least 30 animal and algae phyla are associated in coral reef
ecosystems [29]. The algae that are often found in coral reef ecosystems is
seaweed. In the Eastern Indonesian waters are found about 765 species of
seaweed, consisting of 179 species of green algae, 134 species of brown
algae and 452 species of red algae [15]. Molluscs are also very diverse. In the
Raja Ampat Papua coral reef ecosystem, there are about 699 mollusc species
[30]
. It is reported 3,000 species of sponge were found during the Sibolga
expedition; and 1,500 species during the Snellius II expedition [3]. About 736
species of reef fish of 254 genera were found in Komodo Island waters [3].
There are about 970 species of reef fish found in the Raja Ampat Islands [21].
This high biodiversity is the product of long evolutionary process that allows
many species to coexist in limited apace and high density life in the coral
reef ecosystems. Some fishes species adapt to the limited space by sharing
use of space periodically, some reef fishes optimize the use of space by
alternating day and night. There are reef fish species that are active during
the daytime, and other species are active at nighttime. During the daytime,
some reef fishes looking for food actively in the water column, at the same
time, some other reef fishes use the empty space in the coral crevices to rest
or take shelter; and vice versa, at nighttime, some reef fishes go out from
coral crevices to look for food actively in the water column, at the same
time, some fish that are active during the day come into the empty space in
the coral crevices to rest or take shelter [2]. This space sharing use reduce
interspecific competition in coral reef ecosystem. Reef fish also adapt to
reduce predation risk by shape adaptations of mouth, color, disguise, and
thorns [2]. High biodiversity in the coral reef ecosystem shown by the
involvement of numerous organisms communities in material cycle and
energy flow that is in the ecosystem. There are four groups communities in
coral reef ecosystems, namely plankton, microphytes and macrophytes,
benthos, and reef fishes [4].
7.1 Plankton
Plankton consists of bacterioplankton, phytoplankton and zooplankton.
Bacterioplankton is considered as important producers in the coral reef

Page | 85
ecosystem [4, 31-33]. Filter animals, namely sponges, ascidians, and oysters,
control Bacterioplankton abundance. Sponge (Toxadocea) can use up
bacterioplankton biomass within two hours. Ascidian (Ascidia nigra) and
oysters (Crassostrea) can prey or filter bacterioplankton more effectively
than filters with a 3 mm mesh. Bacterioplankton predation rate depends on
the biomass; predation rate can reaches 100% when the bacterioplankton
concentration is above 300 cells m-1 liter-1 water. Bacterioplankton biomass
is influenced by the tidal period, which is low at beginning and peak of tide.
Bacterioplankton biomass is also affected by season, abundant in February to
March. Bacterioplankton biomass varies from one coral reef to another and
from one location to another within a reef area.
Phytoplankton is an important producer in the coral reef ecosystem [4, 34-
36]
. Phytoplankton biomass varies according to season, maximum in February
to March, and minimum in June to August. The phytoplankton number and
species varies from a coral reef to another. For Diatoms, the volume varies
between 16 to 1.672 thousand cells liter-1, Dinoflagellates between 0 to 28
thousand cells liter-1, and Cyanobacteria between 0 to 2,475 thousand cells
liter-1. Phytoplankton primary production varies according to the coral reef
type. The productivity of atolls and semi-circular coral reefs are between 0.5
to 250 mg C m-3 day-1 or 0.02 to 1.0 g C m-2 day-1, while the productivity of
fringing reef and barrier reefs is 3 to 700 mg C m-3 day-1 or 0.01 to 6.0 g C
m-3 day-1. Phytoplankton biomass in coral reef ecosystem is relatively
smaller than in the open sea; and phytoplankton biomass is higher in atolls
compared to other type of coral reefs. Phytoplankton predation by filter
feeder is very intensive in coral reef ecosystem [4].
Zooplanktons are important heterotrophs in the coral reef ecosystem; its
abundance is related to period and space [4, 37, 38]. Zooplankton in the lagoon
area is relatively more abundance than in the open sea area, and zooplankton
abundance during the daytime is less than at nighttime, the maximum
abundance is at 18 to 20 at night, and the minimum during the daytime.
Zooplankton abundance varies also by season, abundant in January to May,
and minimum in June to July. The abundance and biomass variation of
zooplankton is not too big within at a coral reef area.
7.2 Microphytes and Macrophytes
Microphytes and macrophytes are other important primary producers in
coral ecosystems. Their productivity is related to period and space [2, 4, 39-41].
Benthic microphyte productivity in coral reef areas is around 0.06 to 3.2 g C
m-2 day-1. In coral reef areas, there is a seasonal succession of macrophytes.
Sargassum dentifolium is abundant in January to April, succeeded by

Page | 86
Styropodium zonale in April to June, and Turbinaria eilatensis in May to
June. Macrophytes are abundant in slightly sheltered reef areas and in the
middle of the lagoon, in areas where the wind comes or windward, the
percentage of coral cover is low. Benthic plants, especially seagrass, are
generally more abundant in lagoon areas compared to other parts of the reef.
Algae and seagrass biomass in coral areas between 0.2 to 21.0 kg m-2 of wet
weight. Aquatic plant production at many coral reefs area is around 0.8 to
13.6 C m-2 day-1.
Benthic microphyte is another primary producer in the coral reef
ecosystems. Its production is around 0.06 to 3.2 g C m-2 day-1. In coral reef
ecosystem there is a seasonal succession of macrophytes. Sargassum
dentifolium is abundant in January to April, followed by Styropodium zonale
from April to June, and Turbinaria eilatensis from May to June [4]. The
spatial distribution of benthic chlorophyll a is affected by a combination of
several parameters such as depth (and therefore light), sediment type and
macrophyte interactions [42]. Benthic microalgae have been identified as a
highly productive component of coral reef ecosystems. Its productivity were
23 to 1153 mg Chl a m–2 [43]. Macrophytes are abundant in the sheltered
areas in the middle part of the lagoon. In areas where the wind comes, the
percentage of cover is low. Benthic plants, especially seagrass, are generally
abundant in lagoon areas, while in other parts of the reef are lacking, algae
and seagrass biomass in coral reef ecosystem are between 0.2 to 21 kg Wet
Weight m-2. Aquatic plant production at the coral reef ecosystems in many
locations around 0.8 to 13.6 C m-2 day-1 [4]. Thirty-seven species of marine
algae, belonging to 31 genera were recorded from Minicoy Atoll. The
predominant seaweeds observed were Enteromorpha clathrata, Caulerpa
species, Ulva lactuca, Halimeda gracilis, Padina pavonia, Dictyota
dichotoma, Dictyurus purpurescens, Kappaphycus alvarezii and
Acanthophora delilei [40, 44].
7.3 Benthos
Benthic communities in the coral reef ecosystem are molluscs, sponges,
polychaeta, benthic crustaceans, echinoderms, tunicates, bryozoans,
foraminifera and other protozoa [4, 15]. Molluscs consist of gastropods and
bivalves. Certain Gastropod density, such as Chiton Acanthopleura gemata,
can reach 10 to 15 specimens m-2. Bivalve communities consist of small to
large sizes. Large bivalves are Tridacna gigas whose size can reach one
meter with a weight of 300 kg. Smaller sized bivalves are T. maxima and T.
squamosa whose size can reach 40 cm; and T. crocea 20 cm. The role of
molluscs in coral reef ecosystems is as a filter feeder of microplankton and

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other suspended organic matter, as well as predators of coral reefs and soft
corals (Oliva, Cyphoma, Heliacus, Ephithonium, Drupa, etc.). The
composition of trophic gastropod levels in coral ecosystems is as
omnivorous and phytovorous (30 to 40%), predator and coralovorous (40 to
50%), and filter feeder (10 - 20%) +. The size, growth rate and longevity of
some molluscs on coral reefs on Heron Island vary greatly, depending on
species and substrate conditions [45].
Sponge is the second most important organism after coral animals in the
coral reef ecosystem. Sponge can produce organic material by symbiosis like
as coral. Sponge is able to produce 56 to 331 mg O2 g-1 weight-1 of body wet
each day. The three main classes of sponges are Demospongia that can
present 90 to 95%, Calcarea 4 to 8%, and Sclerospongia 1%. Of the three
sponge classes, more than 500 species live as benthic organisms in the coral
reef ecosystems. Digging sponges are another important component of coral
communities. The digging sponge reaches 25% of the total sponge in the
coral area. The most dominant genera are Cliona, Mycale, and
Anthosigmella [4]. Sponges are an important structural and functional
component of coral reef ecosystems, it is indispensable when characterizing,
assessing, or monitoring a coral reef. Sponges have at least six biological and
ecological properties that make them an influential part of coral reef
ecosystems: high diversity, higher than all coral groups combined; high
abundance and biomass (weight, volume), it may more abundance than all
other reef epibenthos in many areas and reef zones; capacity to mediate non-
animal processes such as primary production and nitrification through
complex symbioses; chemical and physical adaptation for successful space
competition; the ability to strengthen the carbonate skeleton through
calcification and cementation; and able to influence life condition in the
water column by high water filtration capabilities and respiratory secondary
metabolites [46].
The polychaeta community that lives in coral reefs is formed by two
sub-orders, namely Errantia and Sedentaria. Errantia is an organism that
lives freely, whereas Sedentaria is an organism that lives as sedentary or
permanent. Errantia has a round or flat body shape, has legs (parapodia or
cirrae) measuring 2 mm to 10 cm. The errantia family that lives on coral is
Nereidae, Eunicidae, Syllidae, Polynoidae, and Amphinomidae. Trophic
errantia levels are carnivores that prey on meiobenthos and other worms
(Eunice aphroditois), as well as algae and periphyton predators (Eunice
viridis) [4, 47, 48]. Sedentaria is species of polychaeta that lives in a tube.
Sedentaria generally eat bacterioplankton, phytoplankton and suspended

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organic matter (suspensivora). Families that live on coral are Serpulidae,
Sabellidae, Spionidae, Terebellidae, Capilellidae, and Chaetopteridae [4, 49, 50].
Benthic crustaceans are very abundant in coral reef ecosystem. In Indo-
Pacific, there are more than 1,200 species, of which 800 are decapods
(including 500 species of crabs). Decapods are demersal crustaceans that
swim in the water column at nighttime, hiding in sediments, rocks, algae and
holes during the daytime to avoid predators. In addition, there are
crustaceans that inhabit soft sediments and rocks that are covered by
seagrass and macrophytes. Other crustaceans are cryptofauna crustaceans,
and commensal and symbiotic crustaceans of many species of organisms [4,
51-54]
.
Echinoderms are mostly found in coral reef ecosystems; in Indo-Pacific,
more than 1,000 species are found. Echinoderms present at all trophic levels,
namely filter feeders (Ophiura and Crinoida), detritivorous (Holothuria and
Ophiura), herbivorous (Seaurchin), predators (Seastar and some Ophiura and
Seaurchin) [4, 55-64]. Seaurchin has four main families inhabit in coral reef
ecosystems, namely regular seaurchin (Diadematidae and Echinometridae)
and irregular seaurchin (Clypeasteridae and Brissidae). In Indo-Pacific, there
are around 140 species of Seaurchin. Their density can reach 20 to 70
specimens m-2 with an average of 5 to 10 specimen’s m-2. Most of seaurchins
are nocturnal, mostly herbivorous and omnivorous which eat seagrass,
periphyton, corals, microbials and sediments. Seastars that live in the coral
reef ecosystems are found in more than 250 species, most of them are
omnivorous that prey on sessile, detritus, vagile and gastropod organisms.
Some of them are predators, such as Pteraster and Asterina who prey on
sponges, hydroids and ascidians. Others are corallivore that prey on coral,
such as Acanthaster planci. Ophiura is a nocturnal animal that hides under
the rock or seagrass during the daytime. Its density can reach 50 to 70
specimens m-2. In Indo-Pacific there are around 300 species with different
tropic levels; Ophiotrix is a detritivore that lives in areas overgrown with
seagrass and algae; Ophiocoma is a filter that lives on the edge of coral reef;
Ophiothela is a commensal that lives in a coral colony; and Ophiocomella
that live on sponges. Crinoids that live in the coral reef ecosystem in Indo-
Pacific are found about 280 species, generally are nocturnal which at night
they come out of hiding holes and swim in the water to find the right
position to cling to, after which they begin to filter. In areas outside the
slope, the density can reach 50 specimens m-2. The number of arms varies
from 10 (Tropiometra and Oligometra) to 200 (Comanthus), with an average
number of arms of 20 to 40. Holothuria that live in the coral reef ecosystem

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in Indo- Pacific have about 140 species. It is the main macrobenthos in the
lagoon on a shallow and sandy bottom of coral reef ecosystems. Some
species measuring one to two kg. Biomass between 50 to 500 grams m-2. The
density is between 0.2 to 40 specimens m-2. The highest density ever found
was 200 specimens m-2 for Holothuria difficilis on Eniventok Atoll [4].
Tunicate are filter-feeder organisms that prey on phytoplankton,
bacteria, and detritus particles [65, 66]. There is a symbiosis with algae in the
skin tissue, for example at the family Didemnidae. More than 200 species are
found in Indo-Pacific. Tunicate is prey by many demersal fishes, gastropod
predators, crabs, polychaeta and echinoderms [4].
Bryozoa are filter feeder that filters detritus, phytoplankton or
zooplankton. Bryozoa are prey by shrimp, crabs and many species of fish. In
dark areas, bryozoans can live on the surface of mollusc shells, dead corals
and rocks. Bryozoa has a temporal and spatial distribution [4]. Steginoporella
sp was abundant in November at a depth of 10 m. Stylopoma spongites are
most commonly found at a depth of 21 m. Whereas Reptadeonella such as
Plagioporus are more commonly found at a depth of 10 m than at a depth of
21 m [67].
Foraminifera are a bioindicator in assessment and monitoring of coral
reef health [68-71]. Foraminifera and other Protozoa are very important
community in the coral reef ecosystem. They prey on bacteria, algae, eggs
and meiobenthic larvae. Some species of foraminifera symbiotic with algae.
Protozoa produce 50% of total carbon material production of sand in coral
areas [4]. Foraminifera is an important food source for reef fish such as
planktivorous and herbivorous grazers [72]. Protozoa have caused coral
disease on some Indo-Pacific reefs. Coral disease is caused by eukaryotes,
specifically Halofolliculina covallasia, ciliate heterotrich, and folliculinid.
These protists kill coral and damage the skeleton when it settles in living
coral tissue and releases lorica. This disease was first recorded in 1988 and
has since been known to have infected branched and massive corals in
several locations in the Indo-Pacific [73].
7.4 Coral reef fishes
Reef fishes were the principal bioindicator in assessment and monitoring
of coral reef health. Coral reef fishes are vertebrate organisms that living in
water, breathing with gills, and moving using fins. The tropical structure of
coral reef fishes are herbivorous, planktovorous, benthovorous, Piscivorous
(carnivorous), coralovorous, omnivorous and multivorous. The most
abundance fish species in coral reef ecosystem is opportunistic carnivorous

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(about 50 to 70% of the fish species). The second are herbivorous and
coralovorous (about 15% of existing species) i.e. Scaridae and Acanthuridae
families. The rest are omnivorous and multivorous, i.e. families
Pomacentridae, Chaetodontidae, Pomacanthidae, Monochantidae,
Ostractiontidae and Tetraodontidae. Only a few species are zooplankton
feeder, i.e. Clupeidae and Atherinidae. Coral reef ecosystem is a habitat for
many species of reef fish. Coral reef ecosystem is a comfortable living place
for more than 350 species of coral and 2,000 species of reef fishes [4, 74-77].
In Wallace line at Spermonde Islands, Makassar Strait, 34 species of
Parrotfishes were found, namely Bolbometopon muricatum; Calotomus
carolinus; C. spinidens; Cetoscarus ocellatus; C. bleekeri; C.
capistratoides; C. frontalis; C. japanensis; C. microrhinos; C. sordidus;
Hipposcarus longiceps; Leptoscarus vaigiensis; Scarus altipinnis; S.
caudofasciatus; S. chameleon; S. dimidiatus; S. festivus; S. flavipectoralis;
S. forsteni; S. frenatus; S. ghobban; S. hypselopterus; S. niger; S. oviceps; S.
prasiognatos; S. psittacus; S. quoyi; S. rivulatus; S. rubroviolaceus; S.
scaber; S. schlegeli; Scarus sp; S. spinus; and S. tricolor [74]. In the same
area, 30 species of wrasses were found, namely: Anampses
caeruleopunctatus; A. geographicus; A. meleagrides; Cheilinus chlorourus;
C. fasciatus; C. trilobatus; Cheilinus sp.; Cheilio inermis; Choerodon
anchorago; C. rubescens; C. schoenleinii; C. zosterophorus; Coris cuvieri;
C. gaimard; Epibulus insidiator; Halichoeres chrysus; H. hortulanus; H.
scapularis; Hemicoris schroederi; Hemigymnus fasciatus; H. melapterus;
Hemitautoga hortulana; Hologymnosus oxyrhinchus; Iniistius dea;
Novaculichthys taeniourus; Oxycheilinus bimaculatus; O. celebicus; O.
digramma; Pseudodax moluccanus; and Thalassoma hardwicke [77].
Reef fishes are divided into three groups. First is the indicator fishes,
this fishes species are known as an indicator for the coral reef health
condition, such as Chaetdontidae (114 species). Second are the fishes that
play a role in the food chain such as Pomacentridae, Scaridae, Acanthuridae,
Caesionidae, Siganidae, Muliidae, and Apogonidae. The third is reef fishes
that interact each other and form very complex food webs. In the coral reef
ecosystem, there are three forms of interaction between reef fishes. First is
direct interaction as a protection from predators, especially for young fish.
Second is the interaction in looking for food that includes the relationship
between reef fishes and other organisms that live on coral reef ecosystems
including algae. Third is indirect interaction as a result of coral structure and
hydrological and sedimentary condition [3, 4, 15].

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 The high diversity of coral fishes in the coral reef ecosystem is the result
of the reef fish adaptation process that produces the high specification and
specific ecological niche. On coral reefs, 130 to 2,200 species of reef fish
can be found. This species of diversity can only occur if there is a complex
ecological control and regulation system [2, 4]. This complexity can be
explained through two theories. First is the classic hypothesis that assumes
that reef fish can coexist is the result of a high level of specialization where
each species has a special adaptation obtained from competition occur in the
coral reef ecosystem. In this hypothesis, reef fishes are assumed to have
narrow or specific ecological niches so that the coral reef ecosystem can
accommodate more species. Second is the Lottery hypothesis where reef
fishes are assumed to not have special characteristics, many similar species
have the same needs, and there is active competition. It is not yet known
which theory is the most correct, but it seems that reef fishes compete
indirectly; and each species of fish must specialize or adapt to its
environmental conditions in order to survive. To survive, reef fishes can do
one or more of the following four things. First, the fish regulates the use of
space by regulating different active periods (daytime and nighttime),
regulating the use of space by making optimal the space use [2]. Second, reef
fish specializes in feeding and eating to avoid or reduce direct food
competition. The third is to disguise the color of the body with the color of
its environment, for example in sharks that live in the bottom area will have
a back color similar to the bottom color of the waters. Sharks that live on the
surface have bright belly colors that are difficult to recognize from the
bottom by their predators. Underwater camouflage has a back or body color
that is similar to the bottom of the water so it is not easily recognized by
predators. Third is symbiosis to get food, protection and other mutualistic
benefits [2].
8. Coral reef productivity
The main primary producer of coral reef ecosystems is zooxanthellae,
which is in mutual symbiosis with coral animals. Zooxanthellae transfers
98% of the energy produced by photosynthesis to coral, whereas coral
provide protection and access to light and nutrients to zooxanthellae [4].
During the photosynthesis process, zooxanthellae fixes a large part of
nutrients and carbon present in coral. This carbon is mostly glycerol,
including glucose and alanine. This energy is used by coral for metabolic
functions or build protein, fat and carbohydrate molecules, and to coral
enhance the ability of coral to produce calcium carbonate [78].

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 High primary production places the coral reef ecosystem as the most
productive ecosystem. The primary production of coral ecosystems is up
from 1,500 to 3,500 g C m-2 year-1 [16]. This production shows that the
primary production of coral reef ecosystems is higher than the primary
production of other productive ecosystems, such as seagrass ecosystems
which have primary production around 500 g C m-2 year-1 and tropical forest
ecosystems that have primary production around 800 g C m-2 year-1 [4].
Productivities of a windward coral reef community on Eniwetok Atoll
were 0.016-0.135 g cm-2 dry weight, with the mean of all corals (33
specimens, 12 species) was 0.063 g cm-2 dry weight; and more details were
0.056 g cm-2 dry weight for mean of Massive Scleractinia; 0.060 g cm-2 dry
weight for mean of Branching Scleractinia; 0.067 g cm-2 dry weight for mean
of Octocorallia and Milleporina [79]. Productivity of some Massive
Scleractinia were 0.033-0.076 g cm-2 dry weight for Leptastres sp.; 0.54-
0.060 g cm-2 dry weight for Favia sp.; 0.116-0.135 g cm-2 dry weight for
Favia green species, 0.040-0.044 g cm-2 dry weight for Porites lobata; 0.016
g cm-2 dry weight for Porites lobata (in deep water); and 0.060 g cm-2 dry
weight for Turbinaria mesenterina; 0.036 g cm-2 dry weight for Acropora
palmerae. Productivity of some Branching Scleractinia were 0.038-0.048 g
cm-2 dry weight for Acropora cymbicyathus; 0.038-0.077 g cm-2 dry weight
for Pocillopora sp.; 0.053-0.124 g cm-2 dry weight for Lobophyllia sp.
Productivity of some Octocorallia and Milleporina were 0.056 g cm-2 dry
weight for Heliopora caerulea; 0.029 g cm-2 dry weight for Millepora
platyphylla (encrusting section); 0.094 g cm-2 dry weight for Millepora
platyphylla (vertical branch); 0.041-0.080 g cm-2 dry weight for Millepora
murrayi (encrusting section); and 0.074-0.117 g cm-2 dry weight for
Millepora murrayi (vertical branch) [79].
9. Current condition of coral reef
Coral reefs suffer due to a lot of pressure as a result of unsustainable
use. Based on the percentage of coral cover, the condition of coral reef
ecosystems can be grouped into four, namely:
1) very good or excellent, when the cover of live coral is 75% to 100
2) good, when the cover of live coral is 50% to 75%
3) fair, when the cover of live coral is 25% to 50%
4) poor, when live coral cover is lower than 0.25% [80]
Based on the four groupings, [81] obtained from his observations on 325
stations spread throughout Indonesia, that only 7% of Indonesia's coral reefs

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were in very good condition. As many as 22% are in good condition, 28%
are in moderate condition and 43% are in poor condition. Indonesia's coral
reefs is in a critical and threatened category [82].
The world's coral condition reefs were:
1) Around 10% is destroyed
2) About 30% is in critical condition and will disappear within 10 to
20 years later if anthropogenic pressure is not reduced
3) About 30 are under threat, and will occur in the next 20 to 40 years,
if anthropogenic pressure continues to increase
4) Only about 30 of the world's coral reefs are in stable condition and
are expected to exist for a very long time [82]
Based on data of Indonesian Ministry of Maritime Affairs and Fisheries,
currently around 70% of coral reefs in the Indonesian sea were in very bad
condition, and only 30% are still relatively good. Specifically in South
Sulawesi, coral reefs have suffered damage of up to 75% which is generally
caused by fishing activities using explosives. Tropical coral reef ecosystem
coverage around the world has declined by 30% to 50% since the 1980s.
Nearly 75 of the world’s reefs face threats from pollution, habitat
destruction, overfishing and, increasingly, a changing climate that increases
temperatures, sea level, and acidity in the oceans [4, 7].
Coral reef ecosystems degradation can be caused by anthropogenic
disturbance and natural disturbance [9]. Anthropogenic disturbance are coral
rock extraction, sedimentation, waste and eutrophication, and coral reef
fisheries. The beauty and uniqueness of corals and reef fishes cause certain
suffer to the coral reefs due to collection of corals and reef fishes as
ornamental corals and fishes; this corals and reef fishes colllection. will be a
serious problem if there is no limitation. The collecting of corals and reef
fishes in large quantity by exporters of sponges is very dangerous for coral
reef ecosystems and has the potential to reduce the diversity of coral species.
Coastal communities also take a lot of coral rock to be used as building
materials. This can disrupt the ecological function of coral reefs. Even now
coral reefs cover only less than one percent of the Earth’s, but the coral reefs
ecosystem is a life space for a significant amount of marine life, including
some 4,000 species of fish [4].
Increased sedimentation in coral reefs can be caused by activities that
occur directly on reef areas, such as port development. Sedimentation can
also be caused by activities that occur indirectly in coral reef ecosystems,

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such as mining, agriculture, and urbanization. The sediments flow to coral
ecosystems can cover the surface of coral polyps, and disrupt the
zooxanthella photosynthesis process. Suspended sediment in coral reefs
increase turbidity and blocking the sunlight fenetration to the waters column
[4, 16]
.
Organic waste in the coral reef ecosystem can cause a decrease in
oxygen dissolve and an increase in the toxic materials concentration. Waste
can contain toxic materials or by-products from pesticides, herbicides,
chlorine, or heavy metals. The use of big quantity of oxygen during the
decomposition of organic waste can cause anoxy conditions, and endanger
the heterotrophic organisms in coral ecosystems. The high economic value
of reef fishes triggers people to catch big quantity of reef fish using
unsustainable fishing gear, such as bombing and the use of cianide poisons.
Massive unsustainable fishing activities can cause imbalance of food web in
coral ecosystem. This time, at least 500 million people rely on coral reefs
ecosystems for food, coastal protection, and their livelihoods. In the U.S.
alone, NOAA estimates the commercial value of fisheries from coral reefs at
more than $100 million annually. Worldwide, reefs generate billions of
dollars per year from fisheries and tourism.
Coral reef ecosystems are also suffer by natural pressure. The natural
pressure are disease, acanthaster, coral bleaching, and global climate change.
There are four categories of diseased coral, namely white band disease, black
band disease, bacterial infection and shut down reaction. White band disease
and black band disease can natural pressure coral tissue. Black band disease
is caused by cyanophyta Phormidium corallyticum. Coral mortality due to
disease can play a role in sustaining the diversity of corals because it can
convert coral species that form large colonies. If black band disease broken
part of a coral colony, then the skeleton left behind will be available to be
occupied by other coral species.
Acanthaster planci is a coral polyp eater or corallivorous. An
acanthaster can destroy 5-6 m2 of coral colony per year. Acanthaster colony
can destroy several km2 per year. Acanthaster has damaged 90% of coral on
the coast of Guam along 38 km and destroyed 80% of coral on Australia's
Green Island [4]. Damage of coral reefs depends on the species of coral
forming coral reefs, Porites and Pocillopora which form the most massive
blocks are not much attacked by Acanthaster.
Coral bleaching is a process where coral colonies lose pigment due to
the release of symbiotic zooxanthellae in coral polyps. Bleaching can occur

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on corals in shallow areas to a depth of 40 m. The bleaching phenomenon
may be a mechanism to provide opportunities for adult corals to exchange
zooxanthella with those in the waters, because bleaching occurs continuously
and relatively regularly. Bleaching allows the continuous replacement of
zooxanthellae in corals. Global coral bleaching are affecting the reefs in the
Atlantic, Pacific and Indian Oceans within the same year. The first
documented global bleaching event occurred from 1997 to 1998; where at
least 15% of reefs worldwide died. A second event happened in 2010 and
another from June 2014 to May 2017. That one affected more than 70% of
the world’s reefs, the longest, most widespread, and most damaging event on
record. It affected reefs that had never bleached before, including the
northernmost part of Australia’s Great Barrier Reef. The Great Barrier Reef
lost half its coral, other locations lost more than 90%.
Climate change can have a negative impact on coral ecosystems. There
are five key factors that can affect coral reefs during periods of climate
change, namely rising sea levels, rising sea water temperatures, changes in
solubility of carbonate minerals, increased ultraviolet radiation, the
possibility of strengthening storm activity and currents. Climate change is
the greatest global threat to coral reef ecosystems. As temperatures rise,
mass coral bleaching events and infectious disease outbreaks are becoming
more frequent. Additionally, carbon dioxide absorbed into the ocean from
the atmosphere has already begun to reduce calcification rates in reef-
building and reef-associated organisms by altering seawater chemistry
through decreases in pH or ocean acidification.
The previous studies show that rising global temperatures, increasing
oceanic CO2 and other consequences of climate change are affecting coral
reef health in a negative way. An increase of 1 to 3 °C in sea surface
temperature will cause widespread mortality and more frequent bleaching
[83]
. The study on coral reefs in Guan show that many of the reefs have
declined in health during the past 40 years, with live coral coverage about
50% in the 1960s and less than 25% in the 1990s [84]. Another negative
impact related to climate change is the increasing levels of CO2 in oceans
that cause ocean acidification that affects the ability of corals to make
calcium carbonate. Globally, when CO2 concentrations are at 560 ppm,
corals will dissolve instead of accumulate calcium carbonate, resulting in
massive die-offs [85]. Research on seaweed exposed to three concentrations of
CO2 (700 ppm, 1000 ppm, and 1300 ppm) and three different water
temperatures (30 °C, 32 °C, 34 °C) showed a significant effect of CO2 on the
performance of carotenoid pigments from seaweed [86]. Other studies show

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that exposed calcifies algae to four different temperatures and four different
CO2 levels; the greater amounts of CO2 caused significant decline in
photosynthetic efficiency, ability to accumulate calcium carbonate, and
growth in all species. The results also showed that after five weeks, in the 34
°C trial under all CO2 levels, all species were edited [87]. The results of
previous studies concluded that if CO2 emissions continue at the rate they are
emitted now, there will most certainly be reductions in the extent and
diversity of coral reefs in the future [82].
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