Egyptian Journal of Aquatic Biology & Fisheries
Zoology Department, Faculty of Science,
Ain Shams University, Cairo, Egypt.
ISSN 1110 – 6131
Vol. 24(2): 427 – 439 (2020)
www.ejabf.journals.ekb.eg


Molecular Identification and Phylogenetic Tree Reconstruction of
Marine Fish from the Essential Wetland Area of Banyuwangi,
Indonesia

Sapto Andriyono
1*
and Suciyono

Suciyono
2

1
Department of Marine, Fisheries and Marine Faculty, C Campus Jl. Mulyorejo Surabaya.
Universitas Airlangga, Surabaya 60115, East Java, Indonesia.
2
Department of Fish Health Management and Aquaculture, Fisheries and Marine Faculty,
PSDKU. Universitas Airlangga, Banyuwangi 68425, East Java, Indonesia
*
[email protected]


INTRODUCTION

Pangpang Bay is in the region of the Banyuwangi Regency, which is directly
bordered by the waters of the Bali Strait and the Indian Ocean. There is a massive
potential in this region, including the capture fisheries, fisheries processing, aquaculture,
and the presence of mangrove ecosystems (Buwono et al., 2015; Kawamuna et al., 2017
and Raharja et al., 2014). However, the pattern of resource utilization that has not been
appropriately managed causes environmental problems such as a decrease in water
quality due to the disposal of organic waste in the fisheries industry without processing
(Anugrah, 2013), overfishing status in the sardine fisheries, deforestation of mangrove
forests for ponds as well as urban development activities, declining pond production, and
coastal area abrasion.
Currently, the Indonesian government is conducting a study by setting several
areas to become the development areas for fishery products as Minapolitan, through the
ARTICLE INFO ABSTRACT
Article History:
Received: March 23, 2020
Accepted: April 11, 2020
Online: April 14, 2020
_______________

Keywords:
Molecular identification,
Marine fish,
Banyuwangi,
Pangpang Bay,
Indonesia

Pangpang Bay is necessary to get serious attention because it is one of
the essential wetlands in Banyuwangi, Indonesia. This area able to generate
income for traditional fishers and ecological supports the surrounding area
because it is possible to be a spawning area and nursery ground for many
estuary fish. The identification of fisheries resources is carried out using a
molecular approach in the Cytochrome oxidase subunit I (COI) region that
is commonly used in barcoding. Identification with this method is expected
to minimize errors in determining the name of the species of species that
exist in Pangpang Bay. Based on molecular identification information in the
COI region, 37 marine fish species were distributed in 25 families, and 4
orders. The results of this study are the initials of molecular information on
fisheries resources in the Pangpang Bay area.

Andriyono and Suciyono, 2020 428
Decree of the Minister of Maritime Affairs and Fisheries No.32/MEN/2010 (Suryawati
and Purnomo, 2017). One of the Minapolitan is the Muncar sub-district, which located
in Banyuwangi. This area is made as one of the most potential minapolitan capture
fisheries locations with consideration in several aspects. Muncar is showing potential
fishery commodities, strategic geographical location, and having production chains
(upstream-downstream) that are already running well. Another hand, Muncar also has
adequate main supporting facilities such as transportation and communication facilities,
as well as environmental feasibility and local government support. Before the Muncar
was established as a minapolitan in 2010, the community had relied on fish resources that
had developed since the mid-'60s (Wiratama, 2012). This condition can be seen from a
number of studies exploring the Muncar area relating to the use of traditional fishing
technologies. In its development, purse-seines were introduced by the Marine Fisheries
Research Institute (BPPL) in the 1972s and continues to be used today (Perkasa et al.,
2016).
In connection with this tremendous potential of water resources, the government
(Ministry of Forestry) has determined the Pangpang bay area to be an essential area that
has synergistic ecological and economic roles (Setyaningrum, 2017). Balanced
management and utilization efforts are expected to facilitate the community around the
Pangpang Bay area, which is almost entirely dependent on the existence of these water
resources. In this study, the initial information in management is the collection of a
database of fisheries resources owned by this region. The morphological approach in
identifying fish and the combination of molecular methods to reduce errors in fish
identification in the Pangpang Bay area has been carried out. Previous studies have not
found data that specifically inventory fish species in this area. Much research has been
done on mangrove vegetation and aquatic fauna that are not specifically on fish species
(Buwono et al., 2015 and Buwono, 2017). Information on the results of this study is
essential for related research to the genetic and biological diversity of fisheries in
economically important marine fish species obtained from this crucial region, as well as
being the basis for formulating policies in sustainable management.
The molecular identification can be called DNA barcoding. This DNA barcoding
method has been agreed globally to ensure the identification of both plant and animal
species, either fresh samples or processed product samples (Pepe et al., 2007 and Giusti
et al., 2017). DNA barcoding efforts on aquatic biota have been carried out and are
currently receiving a lot of attention, especially efforts to increase the database on
GenBank. Compared to the morphological identification method, DNA barcoding has an
accuracy that is close to 100% matched (Meyer and Paulay, 2005). A single region of
mitochondrial DNA Cytochrome C Subunit I gene (COI) that will be deposited in the
Genbank database as central bioinformatics becomes the gene marker that is used as the
basis for DNA barcoding. Scientists have proven their effectiveness in DNA barcoding in
freshwater fish(Hubert et al. 2008), and marine fish (Ward et al., 2005 and Lakra et al.,
2011). Meanwhile, research on DNA barcoding in Indonesia has also begun to develop.
However, it is still limited to several areas such as freshwater fish in Java and Bali
(Dahruddin et al., 2017), freshwater fish Lake Laut Aceh (Ariyanti, 2012 and
Muchlisin et al., 2013), the Pogar River Sulawesi Island (Arai et al., 1999), Lake
Matano Sulawesi (Roy et al., 2004), and Malang (Andriyono et al., 2019b). Whereas
DNA barcoding has done in Indonesia is still limited to certain species such as Shark

429 Molecular Identification of Marine Fish from the Wetland of Banyuwangi, Indonesia



(Prehadi et al., 2014 and Sembiring et al., 2015) and Orange-Spotted grouper (Antoro
et al., 2006). Other researchers studied DNA barcoding of a grouper (Jefri et al., 2015),
seahorse (Lourie and Vincent, 2004), and goby fish species (Winterbottom et al.,
2014). Several scientists concerned on coral reef fish species such as three-spot dascullus
(Bernardi Giacomo et al. 2001), anemone-fishes (Madduppa et al., 2014), and Banggai
cardinalfish (Bernardi and Vagelli, 2004). Due to the limited genetic information of
marine fishes, this research is significant to report of Pangpang Bay fish resources
through molecular approach.

MATERIALS AND METHODS

Sampling Site
Sampling sites for sample collection was performed in Pangpang Bay,
Banyuwangi district of East Java Province (Figure, 1). No specific permit was required
for this study. All samples had been collected from the traditional fishermen in
Wringinputih Village, Muncar, Banyuwangi. That specimens were dead upon purchasing,
and none of the collected specimens were in the endangered category based on the IUCN
Red List database. The digital camera has taken for each individual sample

Fig 1. Map of sampling site distribution around Pangpang Bay, Banyuwangi

DNA extraction
Each sample has been compiled based on the morphological characters. After
collection, it directly preserved in 90% ethanol. Genomic DNA was extracted using an
Accuprep® Genomic DNA Extraction Kit (Bioneer) according to the manufacturer’s
guidelines. The anal fin (1 cm) was dissected and mix with 6X lysis buffer, which was
further homogenized by the TissueLyser II (Qiagen). Quantification of purified genomic
DNA was performed by nanoDrop (Thermofisher Scientific D1000), aliquoted and stored
at the -70
o
C for further analysis.

Andriyono and Suciyono, 2020 430

PCR condition and Data Analysis
The universal fish primer, BCL-BCH (Baldwin et al. 2009, Handy et al. 2011),
used to obtain the partial sequences of cytochrome c oxidase I (COI) region. The PCR
mixture (20µL) contained 11.2 µL ultra-pure water, 1 µL primer forward and reversed
(0.5 µM), 0.2 µL Ex Taq DNA polymerase (TaKaRa, Japan), 2 µL 10X ExTag Buffer, 2
µL dNTPs (1 µM, TaKaRa, Japan). This PCR reaction, we used 2 µL genomic DNA as a
template. The PCR condition was carried out under the following setting: 95
o
C for 5 min
in initial denaturation. After that, denaturation performed at 95
o
C for 30 s in 40 cycles,
followed by 50
o
C for 30 s in annealing and 72
o
C for 45 s in extension step. The final step
of PCR are final extension at 72
o
C for 5 min. The PCR products of COI was purified with
the AccuPrep®Gel purification kit (Bioneer, Korea).

Data Analysis
The pairwise evolutionary distance among the family was determined by the
Kimura 2-Parameter method. The Neighbor-joining (NJ) tree was constructed, and 1000
bootstrap analysis was carried by Mega 7 (Kumar et al., 2016).

RESULTS

Species Identification
In this study, 40 fish samples were identified in 37 marine fish species distributed
in 25 families, and four orders (Table 1). The types of fish are the catch of traditional
fishermen who use fishing gear in the form and a small portion using fishing rods and
fishing nets. In addition to identification based on morphology, molecular identification is
also carried out.

Phylogenetic Reconstruction
The results of the phylogenetic tree reconstruction (Figure, 2) showed that all
Perciformes clustered in large clades, whereas in the Order Pleuronectiformes separated
with Psammoperca waigiensis. This phylogenetic also shows that economically
important Lutjanidae species form a clade. In this study, four species of Lutjanus (L.
indicus, L. carponotatus, L. fulviflamma, dan L. argentimaculatus), were found, two
species of Siganus (S. sutor dan S. vermiculatus), and one species of Sardinella
melanura. Lutjanus genetic information has received the attention of many researchers,
even information about the complete mitochondrial genome is known as Lutjanus vitta
(Andriyono et al., 2018), Lutjanus carponotatus (Kim et al., 2019), and Lutjanus
fulviflama (Andriyono et al., 2019d).
In this study, the Sardinella melanura species (Andriyono et al., 2019c)
identified from Pangpang Bay waters, also supplement the information that not only
Sardinella lemuru is commonly found in the Strait of Bali (Pradini et al., 2017 and
Wujdi et al., 2016). Whereas in the species Siganidae, Siganus sutor and Siganus
vermiculatus are estuary fish groups that can be found throughout the year. This species
is also reported to be found in Sulawesi waters, and even the S. sutor species is the first
record found in Sulawesi waters (Burhanuddin et al., 2014). Information in the study
also complements previous research that S. sutor was also found in Pangpang Bay waters.

431 Molecular Identification of Marine Fish from the Wetland of Banyuwangi, Indonesia




Table 1. List of online BLASTN results through NCBI database from marine fish
specimens of Pangpang Bay, Banyuwangi
No.
Sampel
ID
Order Family Species Name
Query
Cover
(%)
Identity
(%)
1 bw32 Clupeiformes Clupeidae Sardinella melanura 100% 99%
2 bw38 Engraulidae Thryssa baelama 96% 99%
3 bw42

Thryssa baelama 97% 99%
4 bw45 Perciformes Ambassidae Ambassis sp. 97% 99%
5 bw33 Apogonidae Jaydia novaeguineae 98% 99%
6 bw44 Archamia bleekeri 99% 99%
7 bw18 Carangidae Scomberoides tala 96% 100%
8 bw31 Carangoides chrysophrys 99% 100%
9 bw23 Eleotridae Butis amboinensis 97% 99%
10 bw28 Gerreidae Gerres filamentosus 100% 99%
11 bw29 Gerres filamentosus 100% 99%
12 bw43 Gobiidae Acentro gobiuscaninus 95% 100%
13 bw21 Oxyurichthys ophthalmonema 98% 92%
14 bw9 Haemulidae Diagramma pictum 97% 99%
15 bw12 Plectorhinchus lineatus 97% 100%
16 bw27 Pomadasys kaakan 98% 99%
17 bw10 Labridae Choerodonan chorago 99% 99%
18 bw11 Cheilinus fasciatus 98% 99%
19 bw1

Latidae Psammoperca waigiensis 95% 99%
20 bw26 Leiognathidae Leiognathus equulus 100% 99%
21 bw15 Lethrinidae Lethrinus lentjan 100% 99%
22 bw6 Lutjanidae Lutjanus fulviflamma 100% 99%
23 bw7 Lutjanus carponotatus 97% 99%
24 bw16 Lutjanus argentimaculatus 100% 100%
25 bw25 Lutjanus indicus 99% 100%
26 bw17 Perciformes Mugilidae Planiliza macrolepis 98% 100%
27 bw5 Mullidae Parupeneus heptacanthus 98% 100%
28 bw20 Upeneus sulphureus 94% 99%
29 bw8 Nemipteridae Pentapodus bifasciatus 98% 100%
30 bw14 Scaridae Scarus vetula 97% 99%
31 bw22 Scatophagidae Scatophagus argus 100% 99%
32 bw4 Serranidae Cephalopholis miniata 100% 100%
33 bw34 Epinephelus coioides 100% 100%
34 bw13 Siganidae Siganus sutor 94% 99%
35 bw39 Siganus vermiculatus 98% 99%
36 bw36 Terapontidae Terapon jarbua 100% 100%
37 bw37 Terapon jarbua 100% 100%
38 bw40 Trichiuridae Trichiurus lepturus 99% 99%
39 bw41 Pleuronectiformes Cynoglossidae Cynoglossus cf. cynoglossus 96% 99%
40 bw19 Scorpaeniformes Platycephalidae Platycephalus indicus 92% 99%

Andriyono and Suciyono, 2020 432


Fig 2. Phylogenetic reconstruction of COI gene sequences of marine fish from Pangpang
Bay using Neighbor-Joining algorithm using Mega7

Water quality parameters
The physical condition of the waters and the water's quality are vital components
forming the habitat of a living thing. The results of measurements of some physical and

433 Molecular Identification of Marine Fish from the Wetland of Banyuwangi, Indonesia



chemical parameters of the seawaters carried out in situ included six chemical parameters
and three physical parameters (Table 2).

Table 2. The measurements of physico-chemical parameters in Pangpang Bay waters.
No. Parameter unit
Station
1 2 3 4 5 6 7
Chemical
1 DO mg/L 6,2 12,2 8,4 10,7 6,2 8 6,7
2 Salinity PSU 30 31 30 30 34 30 19
3 pH 6,5 7,5 7 7,5 7,5 7,5 7
4 Nitrate mg/L 0,05 0,07 0,03 0,03 0,02 0,03 0,03
5 Nitrite mg/L 0,12 0,2 0,2 0,11 0,11 0,09 0,02
6 Phosphate mg/L 0,11 0,79 0,3 0,04 0,12 0,39 1,56
Physical
7 Brightness m 30 45 60 80 100 100 60
8 Depth m 1 1,5 2 3 6 10 6
9 Temperature
o
C 32 31,9 32,6 31,8 31,6 31 31

DISCUSSION

Indonesia has committed to protecting biodiversity by signing international
treaties since 1992. The government also realized the commitment by enacting Law No. 5
of 1994 concerning the ratification of the Convention on Biological Diversity two years
after ratifying the international treaty, as a continuation of the responsibilities undertaken
in Brazil in 1992. The Indonesian government uses two approaches in protecting
biodiversity, namely conservation of the area and preservation of species, including their
genetic resources (Gunawan and Sugiarti 2015).
Slightly different from the conservation area, the Pangpang Bay, Banyuwangi
Regency, has been designated by the Ministry of Forestry as an essential ecosystem. This
determination was motivated by the Republic of Indonesia Presidential Instruction
Number: 03 of 2010 concerning Equitable Development, namely the Millennium
Development Goals (MDGs) program, the focus of its activities is the guarantee of
Environmental Sustainability (Lundine et al., 2013). The uniqueness of Pangpang Bay,
which is determined as an essential area, is a determination based on many things, one of
which is excellent mangrove potential (Raharja et al., 2014; Buwono, 2017 and
Kawamuna et al., 2017;). Based on field visit results, fact-finding and group and plenary
discussions from participants in the preparation of the Pangpang Bay Banyuwangi Bay
Wetland/Mangrove Action Plan, there are 6 (six) main issues in the management of
Pangpang Bay mangroves. These issues are environmental aspects, improving
community welfare, regulation, and law enforcement, increasing capacity and human
resources, improving infrastructure, and developing institutional management of the area.
One of the environmental aspects that can be conveyed is the availability of accurate
information about fisheries resources owned by Pangpang Bay, Banyuwangi, presented in
this study.

Marine fish identification

Andriyono and Suciyono, 2020 434
Based on the type of fish caught on the static fishing gear (banjang) fishing gear,
the size and species identified are quite diverse. The dominant fish caught were the
Perciformes (89.2%), followed by the Cluperiformes (5.4%), Pleuronectiformes (2.7%),
and Scorpaeniformes (2.7%). Although the Perciformes dominates from the results of
identification, species from other orders also become a common catch of traditional
fishermen. In the Perciformes, relevant economic groups include the Carangidae,
Lutjanidae, and Serranidae families, have been identified in this report. Carangid fish
species caught are species of Scomberoides tala and Carangoides chrysophrys (Table 1).
Many research reports found this type in Pangpang Bay waters throughout the year with
varying sizes. Apart from being the primary source of income for the traditional fishing
community of Pangpang Bay, it is estimated that this area will become a hidden area that
stores a high diversity of aquatic biota. Pangpang bay area is located near the Alas Purwo
National Park area. The national park at the eastern end of the island of Java is a
biodiversity reserve in the region. Previous studies mention that mangrove areas that live
in the National Park are recorded to have a diversity of potential nekton (fish), including
Lutjanus fulviflamma and Ephinephelus gibbonus, even though the Gobiidae
(Acentrogobius caninus) dominates in that region (Ainullah et al., 2015).
Pangpang Bay area is believed to be a nursery ground and also feeding zone, both
at the juvenile stage and in the fingerling of several economic marine fish species. The
catch shows that the fish are mostly young fish, which are likely feeding and growing in
this area. With the condition of waters protected from waves (because they are bays),
non-pelagic and small pelagic fish are commonly found (Table 1). In addition to these
fish groups, due to the substrate waters that tend to be mud, demersal fish that were
foraging in the bottom are also found, such as goby fish, Acentrogobius caninus, and
Trypauchen vagina (Andriyono et al., 2019a).
In the type of Clupeiformes, Sardinela melanura was identified in this study
although many reports mention that Sardinella lemuru is a species of Clupeidae that has
habitat in this region (Sartimbul et al., 2010 and Pradini et al., 2017). The identified
Sardinela melanura is the first recorded of the complete mitochondrial genome isolated
from fish in the Indonesian region (Andriyono et al., 2019c). In Indonesia, several
Sardinella species have been reported to have habitats, such as Sardinella fimbricita
(Rahardjo and Simanjuntak 2017), Sardinella jussieu (Sektiana et al., 2017),
Sardinella fijiensis (Wang et al., 2019). Among some species of Sardinella, S. albella, S.
fimbricata and S. gibbosa have received less attention in taxonomy (Stern et al., 2016).
The economic value of sardine fish is sufficiently taken into account in the global
fisheries market (Genisa 1999) in particular as a processed product and to obtain fish oil
that contains essential fatty acids such as DHA (17.07%) and EPA (13.82%) (Andriyani
et al., 2017). Fisheries processing companies in Indonesia that make processed sardine
(fish cane) as a significant commodity are also entirely developed and become a mainstay
in increasing export revenues.
Although Pangpang bay waters have high fishery potential, fishery activities
around the area are also one of the biggest threats to the destruction of fisheries resources
in the region. The use of fishing gear that is not environmentally friendly has the potential
to damage fish populations, such as the condition of over-fishing in Pangpang Bay
(Ekawaty, 2015). This situation can be seen with the use of trap net (traditional name)
and chart trap (floating trap net), which are passive and not selective fishing gear by

435 Molecular Identification of Marine Fish from the Wetland of Banyuwangi, Indonesia



using tidal conditions (Cochrane, 2002), which are widely installed on the coast and
mangroves. An intake of fishes is carried out following the tidal system in this area,
which can be done in the morning or evening. This region experiences tidal current
around date 12-19 and 27-6 every month. Meanwhile, the fishermen do not take their
catch when the water from stagnant happens around 20-27 and 5-10 each month. In these
stagnant conditions, aquatic faunas are caught less, so they prefer to repair or clean the
nets and wait when the seawater starts to tide. From the catches obtained, the length of
fish caught varies in size from about 2 cm to around 30 cm in total length, and also, the
number (capacity) of fish found has been decreased from year to year (Ekawaty, 2015).
With this method of fishing, it is expected to further reduce fish resources due to the
pressure of exploitation that is increasingly high by the community (Andriyono et al.,
2019a).

Physical-Chemical Parameters
The sedimentation process in the Pangang bay area is quite high, with some rivers
entering the bay, including the Setail River and several other rivers from the west. With
this high sedimentation, this area has become an ideal habitat for mangrove plants which
were found to be quite dominant in the eastern edge of the Pangpang Bay area of 490 ha
(Radiarta et al., 2017).
The characteristics of the bay waters can be observed from the tidal system, which
is included in the mixed type with two ebb and two tides. Tidal conditions are aquatic
dynamics that significantly affect the oceanographic process in waters. The
characteristics of sea level elevation data are obtained from the Meneng station. The
Meneng Station is a station owned by Deshidros of Indonesia Navy Station, at latitude
08011'00'S; longitude 1140 54 '00' 'T. The data used is the average water level elevation
per hour for one year in 2013. The tidal type at the Meneng station is a mixture leaning to
a Mixed Daily semi-diurnal tidal pattern (Buwono et al., 2015). Besides, the dynamics of
water parameters in the Pangpang bay area are observed to be quite diverse (Table 2) and
overall are still in moderate criteria for marine aquaculture activities if developed in this
area (Radiarta et al., 2017). Nonetheless, waste discharges from several fishing
industries in Muncar (Setiyono and Yudo 2018) allow the accumulation of organic
material and other wastes that increase the burden of waters, especially for the living
needs of aquatic biota. From previous studies, the contaminants of Fe, Pb, Cr, and Zn
have been measured in the Pangpang Bay region with an average concentration of 0.02
mg/L, 0.09 mg/L, 0.03 mg/L, and 0.8 mg/L, respectively (Radiarta et al., 2017).

CONCLUSION

The potential of marine fish diversity in the Pangpag Bay area needs to be
considered, as well as getting a severe threat with the rise of fishing activities that are less
environmentally friendly. The use of "banjang" which produces non-selected catches of
various sizes, is the leading cause of the decline in the biodiversity value of this region.
Based on molecular identification information in the COI region, 37 marine fish species
were distributed in 25 families, and four orders. Based on this identification, we believe
that there are still many other species of marine fish that have not been identified in this
study due to the limitations of fishing gear and the scope of the research conducted.

Andriyono and Suciyono, 2020 436
Environmental DNA metabarcoding can be applied by performing a combination of
traditional surveys with various fishing tools (passive and active) to obtain complete and
useful information in the formulation of conservation policies in this region.

ACKNOWLEDGMENTS

We are grateful to the Ministry of Education and Culture, the Republic of Indonesia.
Besides, we also want to thank Prof Kim Hyun-Woo, the Molecular Physiology
Laboratory, Pukyong National University, Busan, Korea for his suggestions during these
experiments.

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