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All Journal HAYATI Journal of Biosciences PROSIDING SEMINAR NASIONAL JOURNAL OF COASTAL DEVELOPMENT ILMU KELAUTAN: Indonesian Journal of Marine Sciences BULETIN OSEANOGRAFI MARINA Saintek Perikanan : Indonesian Journal of Fisheries Science and Technology Jurnal Ilmu Lingkungan Journal of Marine Research Microbiology Indonesia Jurnal Matematika & Sains Indonesian Journal of Biotechnology Jurnal Kelautan Tropis Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology Marine Research in Indonesia Jurnal Segara ACROPORA: Jurnal Ilmu Kelautan dan Perikanan Papua Jurnal Perikanan

Agus Sabdono

Departemen Ilmu Kelautan, Fakultas Perikanan Dan Ilmu Kelautan, Universitas Diponegoro

Author-ID : 367511

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Education Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology

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PHYLOGENETIC DIVERSITY OF SECONDARY METABOLITE PRODUCING-BACTERIA ASSOCIATED WITH SPONGES FROM BANDENGAN WATERS, JEPARA Ocky Karna Radjasa; Agus Sabdono
JOURNAL OF COASTAL DEVELOPMENT Vol 10, No 1 (2006): Volume 10, Number 1, Year 2006
Publisher : JOURNAL OF COASTAL DEVELOPMENT

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A total of 13 bacterial isolates associated with sponges collected from Bandengan water, Jepara, North Java Sea, Indonesia, was successfully screened for antibacterial activity against pathogenic bacteria Vibrio parahaemolyticus, Aeromonas hydrophila and Staphylococcus aureus. Active bacterial isolates were rapidly grouped by using rep-PCR and a dendrogram was constructed. Six isolates were further selected based on the constructed dendrogram for subsequent DNA sequencings, resulted in the richness of secondary metabolite-producing bacteria associated with sponges from Bandengan having closest similarity to Pseudoalteromonas, Brachybacterium, Vibrio, alpha proteobacterium and uncultured bacterium clones.

MICROBIAL SYMBIONTS IN MARINE SPONGES: Marine natural product factory Agus Sabdono
JOURNAL OF COASTAL DEVELOPMENT Vol 11, No 2 (2008): Volume 11, Number 2, Year 2008
Publisher : JOURNAL OF COASTAL DEVELOPMENT

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Marine sponges (phylum Porifera) are among the oldest multicellular animals (metazoans), the sea’smost prolific producers of bioactive metabolites, and of considerable ecological importance due to theirabundance and ability to filter enormous volumes of seawater. In addition to these important attributes,sponge microbiology is now a rapidly expanding field. Marine sponges produce numerous bioactivecompounds with promising pharmaceutical properties. Sponges are well known to harbor diversemicrobes and represent a significant source of bioactive natural compounds derived from the marineenvironment. Recent studies of the microbial communities of marine sponges have uncovered previouslyundescribed species and an array of new chemical compounds. Microbial symbionts in marine spongesoffer potential sources of marine natural products and serve as marine natural product factory thatsupplies bioactive compounds in a sustainable way.

DIVERSITY OF CULTURABLE BACTERIAL COMMUNITY ASSOCIATED WITH THE CORAL Galaxea fascicularis FROM UJUNG KULON, INDONESIA Agus Sabdono; Ocky Karna Radjasa; Rudiger Stöhr; Elena Zocchi
JOURNAL OF COASTAL DEVELOPMENT Vol 9, No 1 (2005): Volume 9, Number 1, Year 2005
Publisher : JOURNAL OF COASTAL DEVELOPMENT

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Coral reefs are the most diverse marine ecosystems; however, little is known about their microbialdiversity in these ecosystems. The present study is aimed at investigating the general insights into thediversity of the bacterial community associated with the coral Galaxea fascicularis. A culture collectionof 45 bacteria associated with coral G. fascicularis from Ujung Kulon, Indonesia was established byplating on Zobell’s 2214E. Isolates were screened by means of RLFP and sequencing of representative16S rDNAs. Using the restriction enzyme HaeIII, isolates were classified into 8 pattern group. Thesequence results indicated that a high diversity of bacterial phylotypes was present within the coralGalaxea fascicularis. In general, there are three major groups of bacteria: (i) members of the division Firmicutes , (ii) Actinobacteria, and (iii) γ-proteobacteria. Phylogenetic data on microbial communitycomposition in coral G. fascicularis will help in the rational selection of culture conditions to improvethe diversity of bacteria and the knowledge on the physiological, biochemical, genetic, and molecularproperties of coral bacteria.

BIOPROSPECTING OF BACTERIAL SYMBIONT OF Tunicate Didemnum molle FROM SAMBANGAN, KARIMUNJAWA ISLANDS Miftahuddin Majid Khoeri; Ocky Karna Radjasa; Agus Sabdono; Herawati Sudoyo
JOURNAL OF COASTAL DEVELOPMENT Vol 14, No 3 (2011): Volume 14, Number 3, Year 2011
Publisher : JOURNAL OF COASTAL DEVELOPMENT

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Coral reef is a productive ecosystem with high biodiversity in the sea and being targeted to find a useful bioactive compound. However, the serious problem in development of bioactive compounds from marine invertebrate is the supply problem, because to get a small amounts of active compounds a massive numbers of sea organisms are needed. Tunicate is an animal in coral reef ecosystem that produces many bioactive compounds with pharmacological activities, such as, antibacterial, antitumor, and anticancer compounds. It has been reported that bacterial symbionts of coral reef invertebrates may synthesize the same compounds as the host. The purposes of this research are to isolate and to identify microbes which have antibacterial activity against MDR bacteria based PCR 16S rRNA and to detect the existence of PKS and NRPS biosynthetic gene fragments from tunicate bacteria of Didemnum molle. Out of 15 bacterial isolates, one isolate showed antibacterial potential against Escherichia coli and Staphylococcus sp. Molecular identification result showed that TS2A5 bacterium has a homology of 99 % with Virgibacillus sp. strain GSP17 16S ribosomal RNA gene. This isolate was also capable of amplifying NRPS gene fragment.

ANTI-BACTERIAL PROPERTY OF A CORAL-ASSOCIATED BACTERIUM Bacillus sp. AGAINST CORAL PATHOGENIC BBD (BLACK BAND DISEASE) Agus Sabdono; Ocky Karna Radjasa
JOURNAL OF COASTAL DEVELOPMENT Vol 9, No 3 (2006): Volume 9, Number 3, Year 2006
Publisher : JOURNAL OF COASTAL DEVELOPMENT

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Marine organisms such as corals are frequently colonized by bacteria that may be pathogenicto them. One of the means by which they are able to combat microbial attack is by chemical defense. Anumber of metabolites obtained from algae and invertebrates may be produced by associatedmicroorganisms. The purpose of study was to isolate and characterize of coral-associated bacteriahaving antibacterial potency against BBD coral disease. A coral-associated bacterium, KM2 isolate,was successfully screened for antibacteria production against indigenous BBD pathogenic bacteriabased on PCR amplification of the non-ribosomal peptide synthetase gene and was identified as closelyrelated to Bacilus sp based on its 16S rDNA.. KM2 strain was found to inhibit the growth of coralpathogenic BBD bacteria tested Myroides odoratimimus strain BBD1, Bacillus algicola Strain BBD2and Marine Alcaligenes bacterium Strain BBD3. This bacterium was found to inhibit the growth of allthose BBD coral pathogenic bacteria.

Isolasi dan Identifikasi Bakteri Pendegradasi Koprostanol dari Lingkungan Sungai, Muara, dan Perairan Pantai Banjir Kanal Timur Semarang pada Monsun Timur Misbakul Munir; Norma Afiati; Ocky Karna Radjasa; Agus Sabdono; Tonny Bachtiar
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 9, No 2 (2004): Jurnal Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Aktifitas manusia yang terus meningkat di wilayah pesisir, telah menyebabkan terjadinya peningkatan tekanan lingkungan yang berasal dari berbagai macam sumber pencemaran, antara lain limbah industri, pertanian, transportasi, dan limbah domestik. Salah satu sumber pencemar yang cukup dominan di lingkungan perairan pantai adalah pencemaran akibat limbah domestik. Selama ini yang dipakai untuk mengetahui pencemaran lingkungan oleh limbah domestik adalah menggunakan indikator biologi yaitu bakteri coliform. Namunpenggunaan bakteri coliform sebagai indikator pencemaran limbah domestik mempunyai permasalahan antara lain tidak terdeteksinya bakteri coliform tersebut pada perairan pantai, sementara diduga kuat bahwa perairan tersebut tercemar oleh limbah domestik termasuk feces. Oleh karena itu indikator alternatif sangat diperlukan. Salah satu indikator alternatif pencemaran limbah domestik adalah koprostanol, yang mempunyai sifat cukup konservatif, dapat dikuntitatifkan dan dapat dihubungkan dengan sumber pencemar yang spesifik. Namun perlu diingat bahwa di alam, koprostanol mengalami proses degradasi oleh bakteri, sehingga perlu dilakukan penelitian mengenai isolasi dan identifikasi bakteri pendegradasi koprostanol pada lingkungan sungai, muara, dan perairan pantai Banjir Kanal Timur Semarang pada monsun timur. Penelitian dilakukan pada bulan Juli s/d Agustus 2003 pada lingkungan sungai, muara, dan perairan pantai Banjir Kanal TimurSemarang. Isolasi bakteri dari sampel air dan sedimen dilakukan di Laboratorium Mikrobiogenetika, FMIPA Jurusan Biologi UNDIP Semarang dan identifikasi bakteri pendegradasi koprostanol terseleksi dilakukan diLaboratorium Hama dan Penyakit Balai Besar Pengembangan Budidaya Air Payau (BBPBAP) Jepara. Hasil penelitian diperoleh bahwa bakteri pendegradasi koprostanol yang berasal dari lokasi Banjir Kanal TimurSemarang pada berbagai variasi lingkungan dan habitat diperoleh 69 isolat (83,13%) dari 83 isolat yang diuji. Sedangkan hasil identifikasi terhadap 6 isolat terbaik diperoleh 3 (tiga) genus bakteri mampumendegradasi koprostanol, yaitu Achromobacter, Bacillus, dan Branhamella. Dari 3 genus bakteri pendegradasi koprostanol yang didapatkan, ada 2 (dua) genus yang selama ini belum dilaporkan, yaitu genus Achromobacter, dan Branhamella.Kata kunci : Koprostanol, Limbah Domestik, Indikator Pencemar, Isolasi, Identifikasi, BakteriIncreasing human activities in coastal areas have caused an increase of environmental pressures that come from various sources such as industrial disposal, agriculture, transportation, and domestic wastes. One of dominant sources in coastal waters is contamination by domestic wastes. So far to determine environmental contamination by domestic waste is by using biological indicator, coliform bacteria. However the use ofcoliform bacteria have problems for example, they cannot be detected in coastal waters contaminated by domestic waste including faeces. Therefore, an indicator alternative is urgently needed. Alternative indicatorof domestic waste contamination is coprostanol, which is conservative, easy to quantity and related to specific pollutant source. It is important to note coprostanol is naturally degraded by indigenous bacteria.Therefore it is necessary to conduct a study on isolation and identification of coprostanol-degrading bacteria in river, estuarine, and coastal environments of Banjir Kanal Timur Semarang during dry season. The research had been carried out from July to August 2003 at environmental of river, estuarine, and coastal of Banjir Kanal Timur Semarang. Isolation of bacteria from water and sediment samples were conducted atMicrobiogenetics Laboratory, Faculty of Mathematics and Natural Sciences Diponegoro University, meanwhile identificaton of coprostanol-degrading bacteria selected was conducted by at Pest and Diseases Laboratory,Balai Besar Pengembangan Budidaya Air Payau (BBPBAP) Jepara. The result showed that coprostanol-degrading bacteria obtained from Banjir Kanal Timur Semarang at various environments and habitat were 69 bacterial isolates (83,13%) from 83 isolat tested. Identification revealed that (three) genus were found to degrade coprostanol, namely Achromobacter, Bacillus, and Branhamella. From 3 genus of coprostanol-degrading bacteria identified, 2 of them : Achromobacter, and Branhamella have not been reported so far.Key words : Coprostanol, Domestic Waste, Pollution Indicator, Isolation, Identification, Bacteria

Genetik Uniformity of Widely Separated Population of Coral Acropora aspera from Karimunjawa and Panjang Island Waters Revealed by Partial Sequence of Internal Transcribed Spacer-4 Regions Diah P Wijayanti; Chrisna A Suryono; Agus Sabdono
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 9, No 3 (2004): Jurnal Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Telah kita ketahui dengan baik bahwa kaarang hidup tersebar dari daerah tropis sampai subtropis di Indo Pasifik. Namun malangnya informasi tentang hubungan secara genetic antar populasi terumbu karang yang dipisahkan oleh jarak tersebut sangat kurang. Variasi genetic karang Acropora aspera telah dianalisa dengan internal transcribed spancer-4 (ITS-4). Analisa dilakukan terhadap dua pupulasi karang yang berasal dari Karimunjawa dan Jepara. Hasil sequencing dengan ITS-4 menunjukan bahwa diantara meraka terdapat hubungan yang dekat baik yang ada di Karimunjawa dan Jepara. Dari hubungan tersebut dapat diasumsikan bahwa populasi A. aspera yang ada di Jepara berasal dari Karimunjawa bila dillihat sebaran genetis.Kata kunci: Acropora aspera, sebaran genetis, ITS-4 It is well known that coral species are broadly dispersed across the tropical and subtropical Indo Pacific. Unfortunately, there is little information about the genetic connectivity between coral populations separatedby large distance. Variability in the nucleotide sequence of the internal transcribed spacer-4 (ITS-4) of the nuclear ribosomal gene in coral Acropora aspera was analyzed. Two populations of corals from Karimunjawaand Jepara were investigated. Sequencing analysis of ITS region of rDNA gene showed that there is closely related between parental of A. aspera Karimunjawa and Jepara. This relation suggest that presumably A.aspera population in Jepara was originated from Karimunjawa through genetic flow.Key words: Acropora aspera, gene flow, ITS-4

Degradation of Phenylurea Diuron Herbicide by Coral Bacterium Agus Sabdono
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 9, No 1 (2004): Jurnal Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Bakteri yang diisolasi dari permukaan karang mampu menggunakan senyawa herbisida fenilurea diuron sebagai sumber karbon dan energi. Organisme ini mampu menggunakan diuron hingga 125 mg/l. Namunfase lag dan waktu untuk mendegradasi mengalami kelambatan bila berada pada konsentrasi diatas 100 mg/l diuron. Kinetika pertumbuhan bakteri ini dilakukan secara kultur batch. Estimasi laju pertumbuhanmaksimum (ìmax) sebesar 0,46 j-1 diperoleh dari pengukuran turbiditas dan nilai konstanta kejenuhan pertumbuhan (Ks) sebesar 49,5 mg/l diuron. Pengaruh konsentrasi diuron paling tinggi pada laju penggunaansubstrat spesifik (ó) adalah 0,0195 j-1 yang diperoleh pada perlakuan konsentrasi 125 mg/l diuron.Kata kunci: bakteri karang, diuron, kinetika pertumbuhanA bacterium which utilizes phenylurea diuron as a sole source of carbon and energy was isolated from coral surface. The organism utilized diuron up to 125 mg per liter. The lag phase and time for degradation, however, were severely prolonged at diuron concentrations above 100 mg/liter. The growth kinetics of coral bacterium was studied in batch culture. Estimation of maximum growth rates (ìmax), obtained from turbidity measurements, was 0.46 h-1 and half-saturation growth constant (Cs) was 49.5 mg/l diuron. The highest effect of diuron concentration on the specific substrate removal rate (ó) is 0.0195 h-1 obtained from 125 mg/l diuron concentration.Key words : coral bacterium , diuron, growth kinetics

Deteksi Transfer Plasmid Pendegradasi 2,4-D (pPP202) pada Bakteri Escherichia coli dH5α dengan Menggunakan Indikator Media EMBA Agus Sabdono
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 7, No 3 (2002): Jurnal Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Plasmid (pPP202) dari Vibrio natriegens diintroduksi secara laboratoris dengan elektrotransformasi pada inang bakteri Escherichia coli dH5α. Pulsed Field Gel Electrophoresis (PFGE) digunakan untuk mengisolasi plasmid DNA. Plasmid pPP202 mengandung gen yang menyandi degradasi parsial senyawa 2,4-diklorofenosi asetat (2,4-D). Bakteri E. coli dH5α tidak memiliki gen yang diperlukan untuk meneralisasi 2,4-D pada khromosomnya. Asumsi tersebut memungkinkan untuk dilakukannya studi transfergen dengan menyeleksi transconjugant pada media indikator EMBA yang mengandung 2,4-D sebagai sumber karbon. Sehingga isolat yang mengandung plasmid pPP202 pada inang E. coli bisa dideteksi dengan melihat kesamaan warna dengan koloni V. natriegens PP202 yang berwarna merah. Selanjutnya, transconjugant tersebut diuji lagi pada media Zobel 12216E + 200 ppm 2,4-D yang dibandingkan dengan koloni negatif yang berwarna putih.Kata kunci : plasmid; transfergen; transconjugant A plasmid (pPP202) of Vibrio natriegens was introduced on host Escherichia coli dH5α, with electrotransformation Pulsed Field Gel Electrophoresis (PFGE) was used to isolate the DNA plasmid. Genes on this plasmid encode partiaI 2.4-dichlorophenpxyacetic acid (2.4-D) degradation. The E. coli dH5α lacks the chromosomal genes necessary for mineralization of 2.4-D, and this fact allows presumptive transconjugants obtained in gene transfer studies to be selected by plating on EMBA indicator media containing 2.4-D as the carbon source. Use of this approach enabled detection of plasmid pPP202 transfer to E. coli where previously it had not been detected. Thus, all of the 2,4-D-degrading isolates of E. coli that contained a plasmid pPP202 whose red colony colour was similar to the colony colour of V. natriegens Strain PP202, were considered as transconjugants. In addition, transconjugants were observed at distinct times in Zobell 2216E + 200 ppm 2.4-D that supported transconjugant populations compared to controls (white colour) in which no gene transfer was detected.Keywords: plasmid; gene transfer; transconjugant

Arsenic Contamination of the Coastal Aquifers in the North Coast of Java, Indonesia Chrisna Adhi Suryono; Agus Sabdono; Bhaskoro Rochaddi; B. Tyas Susanti
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 13, No 1 (2008): Jurnal Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

A study was conducted to assess the Arsenic (As) metal contamination of the shallow aquifers in Jakarta, Semarang, and Surabaya city of Java and its relation to the highly developed industrial and domestic activities in the coastal region. Arsen was assayed in the waters of 30 wheals throughout the terrestrial cities, in residential zones using Atomic Absorption Spectrophotometer technique. The mean and standard deviation of As in Jakarta, Semarang and Surabaya were 17.19± 19.08, 1.78 ±2.28 and 0.59 ± 0.26 μgL-1, respectively.The r As concentration of groundwate shows in correlation with Fe significantly. The levels of As in some investigated three Indonesian metropolis cities were below the maximum allowable concentrations of metals recommended by Indonesian Drinking &. Domestic Water Quality Standard for Ground Water and WHO's (World Health Organization) Guideline Values for Drinking Wate, except for station 6 of Jakarta were concentration 59,65 μgL-1

Co-Authors Agus Indarjo Agus Trianto Agus Trianto Agus Trianto Agus Triyanto Agustina Agustina Agustina Aiyen Tjoa Aldion Adin Nugroho Ali Djunaedi Ali Djunaedi Ali Ridlo Ambariyanto , Ambariyanto Ambariyanto Angelina Ferawaty Siregar Angelina Ferawaty Siregar Aninditia Sabdaningsih Azizi, Muhammad Faris B Tyas Susanti B. Tyas Susanti Bambang Yulianto Baskoro Rochaddi Bhaskoro Rochaddi Burhan Habibi Yunus Chrisna A Suryono Chrisna A Suryono Chrisna A Suryono Chrisna Adhi Suryono Chrisna Adhi Suryono Delianis Pringgenies Denny Nugroho Sugianto Desy Wulan Triningsih DIAH AYUNINGRUM Diah Ayuningrum, Diah Diah P Wijayanti Diah P Wijayanti Diah Permata Wijayanti Diah Permata Wijayanti Diah Permata Wijayanti Dio Dirgantara Duhita Sinidhikaraning Kencana Elena Zocchi Endang Sri Lestari Erwin Ivan Riyanto Erwin Ivan Riyanto Eunike Dorothea Hutapea Farrastasya Muflihul Azzami Fauziah Shahul Hamid Gina Saptiani Gina Saptiani Hadi Endrawati Haeruddin Haeruddin Hakim, Muhamad Fikri Hudi Nur Hans Arthur Philips HANS- PETER GROSSART Hans-Peter Grossart Herawati Sudoyo Herida, Azalia Puspa Hermin Pancasakti Kusumaningrum Heru Kurniawan Alamsyah Ibnu Pratikto Ida Ayu Putu Sri Widnyani Intan Budi Setiasih Irwani Irwani Irwani Irwani Irwani Irwani Irwanto, Eko Ita Widowati JOEDORO SOEDARSONO Johannes F Imhoff Jusup Suprijanto Jusup Suprijanto Jutta Wiese Larasati, Stefanie Jessica Henny Leenawaty Limantara Mada Triandala Sibero Mada Triandala Sibero Meinhard Simon Miftahuddin Majid Khoeri Misbakul Munir Muchlissin, Sakti Imam Muhamad Fikri Hudi Nur Hakim Muhamad Ziaul Faiz Muhammad Eka Darmawan Rafsanjani Muhammad Zainuri Nadya Cakasana Norma Afiati Norma Afiati Nur Taufiq Syamsudin Putra Jaya Taufiq Syamsudin Putra Jaya Ocky Karna Radjasa Ocky Karna Radjasa ocky radjasa Popi IL Ayer Prastyo Abi Widyananto Puspa Kapinangasih Putut Har Riyadi Raden Ario Rafsanjani, Muhammad Eka Darmawan Ragil Saptaningtyas Raja Aditya Sahala Siagian Ratna Diyah Palupi Retno Hartati Rignolda Djamaludin Rina Setyowati Sulistiyoningrum Rini Pramesti Rivan Novianto Madilana Romadhon Romadhon Rory Anthony Hutagalung Rosa Amalia Rudhi Pribadi Rudiger Stöhr S Sukarmi S. Sulistiyani Sakti Imam Muchlissin Sakti Imam Muchlissin Sakti Imam Muchlissin Setiasih, Intan Budi Setyani, Wilis Ari Sibero, Mada Triandala Slamet Budi Prayitno Sri Achadi Nugraheni Sri Lintang Artono Sri Redjeki Sri Redjeki Stalis Norma Ethica Stefanie Jessica Henny Larasati Subagiyo Subagiyo Subagiyo Subagiyo Subagyo Subagyo Sugiyanto Sugiyanto Sugiyanto Sugiyanto Sugiyanto Sunaryo Sunaryo Suzana Kristy Satriani Fofied Syauqina Nashihi Aufar Thorsten Brinkoff TONNY BACHTIAR Tonny Bachtiar Tony Bachtiar Tony Bachtiar Torben Marten TORBEN MARTENS Tri Yuni Atmojo Tri Yuni Atmojo Ulfah Amalia Wahyuningsih, Candra Widy Febriansyah Wilis Ari Setyani Yeni Sulistiyani Yesaya Putra Pamungkas

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