Articles

Molecular Phylogeny of Giant Clams Based on Mitochondrial DNA Cytochrome C Oxidase I Gene NURYANTO, AGUS; DURYADI, DEDY; SOEDHARMA, DEDI; BLOHM, DIETMAR
HAYATI Journal of Biosciences Vol 14, No 4 (2007): December 2007
Publisher : Bogor Agricultural University, Indonesia

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Abstract

There is an uncertainty for the relationships among giant clam species of Tridacninae, in particular among species belongs to subgenus Chametrachea i.e. Tridacna crocea, T. maxima, and T. squamosa based on different genetic markers. This study examined the relationships among three species within subgenus Chametrachea compared to the previous studies. Neighbour Joining, Maximum Parsimony and Maximum Likelihood tree were constructed based on 455 bp of the mitochondrial DNA cytochrome c oxidase I gene from T. crocea, T. squamosa, T. maxima, T. gigas, and several sequences derived from Genbank for the outgroups. The results showed that giant clams formed a monophyletic group. Within Tridacna group, T. crocea was more closely related to T. squamosa than to T. maxima and they formed a monophyletic group. T. crocea and T. squamosa were sister taxa and sister group to T. maxima and T. gigas. Close affinity between T. crocea and T. squamosa was also supported by high similarity on nucleotide level (94.30%) and concordant with the results of the previous studies using mitochondrial 16S rRNA and nuclear 18S rRNA. Key words: phylogenetic relationships, Chametrachea, cytochrome c oxidase I
The Oogenesis of Sclerectinian Corals Caulastrea furcata and Lobophyllia corymbosa KAWAROE, MUJIZAT; SOEDHARMA, DEDI; MAULINIA, MAULINIA
HAYATI Journal of Biosciences Vol 14, No 1 (2007): March 2007
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Caulastrea furcata and Lobophyllia corymbosa are corals of order Sclerectinian. Caulastrea furcata is the only species of genus Caulastrea that could be found in Kepulauan Seribu and L. corymbosa is a rare species. The purpose of this research was to study sexual reproduction of the Sclerectinian coral. The result showed that the ovaries of C. furcata and L. corymbosa were developed in the mesentery, inside the mesoglea, and pinched by gastrodermis. Distinctive channel with trophonema like structure was found in both species as well as gamete which was spawned from polyp through distinctive channel. The gamete simply spawned trough gastrodermis, heading from mesentery filament to excretion track. Histological observation showed that there were four stages of gamet maturity level. However, gonad maturity level consisted of three stadia depended on the characteristic of the ovary. Key words: oogenesis, sexual, reproduction, corals Caulastrea, Lobophyllia, Seribu Island
KUALITAS AIR SUNGAI CISADANE, JAWA BARAT - BANTEN Siahaan, Ratna; Indrawan, Andry; Soedharma, Dedi; Prasetyo, Lilik B
JURNAL ILMIAH SAINS Vol 11, No 2 (2011): Volume 11 Nomor 2, Oktober 2011
Publisher : Sam Ratulangi University

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Abstract

KUALITAS AIR SUNGAI CISADANE, JAWA BARAT - BANTEN Ratna Siahaan1), Andry Indrawan2), Dedi Soedharma2), dan Lilik B.Prasetyo2) 1)Mahasiswa S3 Sekolah Pascasarjana IPB, Dosen Universitas Sam Ratulangi; e-mail:ratna245_siahaan@yahoo.com; 2)Dosen Sekolah  Pascasarjana IPB, Bogor ABSTRAK Sungai Cisadane memiliki fungsi dan nilai untuk kesejahteraan manusia dan hidupan liar yang hidup di dalam sungai. Kegiatan manusia yang memanfaatkan air sungai dan membuang sampah/limbah ke Sungai Cisadane dapat menurunkan kualitas air Sungai Cisadane. Penelitian ini bertujuan untuk menganalisis kualitas air S.Cisadane berdasarkan faktor fisika dan kimia air sungai. Penelitian dilakukan di sembilan (9) titik di sepanjang Sungai Cisadane dari hulu hingga hilir pada Agustus-November 2011. Hasil menunjukkan jika air Sungai Cisadane telah tercemar. Secara umum, kualitas air Sungai Cisadane di bagian hulu dan tengah (Stasiun 1-6) masih dapat dipergunakan sebagai air untuk peruntukan Kelas 2 (PP.No.82/2001) dengan kualitas air tercemar ringan. Namun, air Sungai Cisadane di bagian hilir (Stasiun 7-8) hanya untuk peruntukan Kelas 3 dan 4 dan dikategorikan tercemar parah. Kata kunci: kualitas air, sungai Cisadane   WATER QUALITY OF CISADANE RIVER, WEST JAVA-BANTEN ABSTRACT Cisadane River has functions and values for human welfare and wildlife. Human activities in using river water and dumping waste to the river could decrease water quality of Cisadane River. The aim of this research was to analysis water quality of Cisadane River based on physical and chemical factor.  Water sampling was conducted along Cisadane River from up to downstream at nine (9) stations. Result showed that Cisadane River is polluted. Generally, water quality of Cisadane River in up and middle part (Station 1-6) could be used for purposes as in Class 2 (Gov.Reg/PP No.82/2001) and classified into moderately polluted. But, water quality of down Cisadane River (Station 7-9) only for Class 3 and 4 that categorized into heavily polluted. Keywords: Cisadane river, water quality
Seksualitas dan Perkembangan Gamet Sponge Laut Aaptos aaptos Schmidt Haris, Abdul; Soedharma, Dedi; Zamani, Neviaty P.; Pariwono, John I.; ', Rachmaniar
Jurnal Natur Indonesia Vol 14, No 3 (2012)
Publisher : Lembaga Penelitian dan Pengabdian kepada Masyarakat Universitas Riau

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Abstract

This research was aimed to know the characteristics of gamet development of marine sponge Aaptos aaptos living in tropical waters of Barrang Lompo Island, Spermonde Archipelago, South Sulawesi. In order to know gamet development, it was conducted three periods of sample collection at each moon phase. After sample collection, the specimen were put into tissue cassette and then were removed to fixative solution of FAACC (for 100 mL = 10 mL formaldehyde solution of 37–40%: 5 mL glacial acetic acid: 1.3 g calcium chloride dihydrate: 85 mL destilate water) for +48 hours, and then were removed to 70% alcohol for temporary storage before doing histological preparation following standard procedure. Sexuality of marine sponge Aaptos aaptos living in Barrang Lompo Island is gonochoric. Spermatocyt developed in spermatic cyst, while oocyt developed in the mesohyl. Stage of male gamet development was divided into four phases i.e. spermatocyt I phase, spermatocyt II phase, spermatocyt III phase, and spermatocyt IV (spermatid) phase, similarly, female gamet develop- ment was divided into four phases i.e. oocyt I phase, oocyt II phase, oocyt III, oocyt IV phase. Each phase of gamet development had specific characterstics different from among each others.
KONDISI TELUR PADA BERBAGAI BAGIAN CABANG KARANG Acropora nobilis Rani, Chair; Soedharma, Dedi; Affandi, Ridwan; Suharsono, ,
Jurnal Ilmu-Ilmu Perairan dan Perikanan Indonesia Vol 11, No 1 (2004): Juni 2004
Publisher : Institut Pertanian Bogor

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Abstract

Penelitian ini bertujuan untuk mengetahui distribusi telur menurut tingkat perkembangannya, rataan jumlah telur per polip dan proporsi polip yang reproduktif pada berbagai bagian cabang karang A. nobilis. Sebanyak 10 koloni A. nobilis yang berdiameter > 15 cm diambil contohnya secara acak di bagian barat laut perairan terumbu karang Pulau Barrang Lompo, Kepulauan Spermonde, Makassar pada tanggal 27 Januari 2002 (satu hari sebelum bulan purnama). Polip dari tiga bagian cabang (apikal, tengah dan basal) diperiksa jumlah telur yang dikandungnya secara histologis. Terdapat interaksi antara pertumbuhan dan reproduksi terhadap alokasi sumber daya pada berbagai bagian koloni karang. Alokasi sumber daya terhadap fungsi biologi tertentu akan mengorbankan fungsi biologi lainnya. Pertumbuhan karang yang terlokalisasi pada bagian tertentu suatu koloni karang berhubungan dengan rendahnya aktivitas reproduksi. Hasil penelitian menunjukkan adanya perbedaan yang nyata (p < 0.001) distribusi telur menurut tingkat perkembangannya pada berbagai bagian cabang karang. Bagian tengah cabang memiliki proporsi polip karang yang berkaitan dengan lokasi energi untuk pertumbuhan yang lebih reproduktif (100%) dengan kandungan rataan jumlah telur yang lebih tinggi (5.22 butir/potongan polip) dibanding bagian apikal dan basal cabang.Kata kunci: Distribusi, telur, cabang karang, Acropora nobilis
AFINITAS SPESIES PADA KOMUNITAS ENDOPSAMMON DI ZONE INTERTIDAL DALAM KAWASAN TAMAN NASIONAL BALI BARAT Bagus Jelantik Swasta, Ida; Soedharma, Dedi; Boer, Mennofatria; Wardiatno, Yusli
Jurnal Ilmu-Ilmu Perairan dan Perikanan Indonesia Vol 13, No 2 (2006): Desember 2006
Publisher : Institut Pertanian Bogor

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Abstract

Sebagai benthos hewani yang berukuran kecil dan menghuni ruang-ruang interstisial, endopsammon memiliki peranan ekologis yang amat penting dalam ekosistem laut. Karena itu, mengkaji aspek ekologi endopsammon sangat menarik. Afinitas spesies merupakan salah satu aspek ekologi yang amat penting untuk dipelajari. Dua aspek afinitas spesies yang sangat penting untuk dikaji adalah tumpang tindih relung dan asosiasi spesies khususnya dalam kaitannya dengan tingkat kekerabatan spesies dalam komunitas endopsammon.Dua tujuan yang ingin dicapai penelitian ini adalah: 1) untuk mengetahui secara pasti apakah tumpang tindih relung dan asosiasi spesies terjadi dalam komunitas endopsammon dan 2) untuk mengetahui secara pasti apakah tingkat tumpang tindih relung dan tingkat asosiasi spesies dipengaruhi oleh tingkat kekerabatan di antara spesies endopsammon. Beberapa lokasi yang digunakan dalam penelitian ini adalah pantai Teluk Terima, pantai Labuhan Lalang, dan pantai Teluk Banyuwedang yang berada dalam kawasan Taman Nasional BaliBarat. Di semua lokasi ini dibuat 25 stasiun penelitian, dan di setiap stasiun contoh substrat diambil pada tiga tingkat kedalaman yaitu 0-5 cm, 5-10 cm, dan 10-15 cm. Contoh substrat diambil dengan menggunakan core, sedangkan ekstraksi contoh dilakukan dengan metode Uhlig, metode pembasuhan dan metode pengapungan. Spesimen yang didapat diawetkan dengan menggunakan larutan formalin 10 %, dan diwarnai dengan larutan Rose Bengal. Pengamatan dan identifikasi specimen dilakukan dengan menggunakan mikroskop. Data yang didapat dianalisis dengan pendekatan statistik. Beberapa hasil dari penelitian ini adalah: 1) secara umum, diantara spesies endopsammon terjadi tumpang tindih relung dan asosiasi, dan 2) tingkat tumpang tindih relung dan tingkat asosiasi spesies dipengaruhi oleh tingkat kekerabatan diantara spesies endopsammon.Kata kunci: endopsammon, tumpang tindih relung, asosiasi spesies.
PERENCANAAN LANSKAP WISATA PESISIR BERKELANJUTAN DI TELUK KONGA, FLORES TIMUR, NUSA TENGGARA TIMUR Yusiana, Lury Sevita; Nurisjah, Siti; Soedharma, Dedi
Jurnal Lanskap Indonesia Vol 3, No 2 (2011): Jurnal Lanskap Indonesia (JLI)
Publisher : http://web.ipb.ac.id/~landscapearch/

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Abstract

Konga Bay is a beautiful natural coastal landscape enriched with local culture and vernacular architecture which is still preserved. There are two objectives of this study, firstly is to propose alternative plan of coastal tourism interpretation trail for KongaBay to support its landscape conservation. Second objective is to plan Konga Bay landscape –in lines with sustainable tourism development, to be a beautiful, pleasant, and long-lasting tourism landscape; as well as giving better living opportunity forlocal community. The study applied descriptive-quantitative method to assess coastal environmental quality, potency of coastal tourism development, acceptability level and local community development in tourism. Those three assessments were integrated to obtained land suitability zone for tourism which was subsequently developed to spatial and circulation programs of coastal tourism in order to plan coastal tourisminterpretation trail and sustainable coastal tourism landscape as well. Tourism zone consisted of (1) main zone for aquatic and terrestrial tourism areas and (2) supporting zone contains welcome and transition areas. Circulation of coastal tourism comprises primary, secondary, tertiary, and tsunami evacuation circulations. Coastal tourism interpretation plan provides three alternatives of interpretative trail. Development plan of Konga Bay coastal tourism landscape includes aquatic and terrestrial tourism landscape.
KETERKA1TAN STRUKTUR KOMUNITAS MEIOFAUNA DENGAN KERAPATAN LAMUN DAN PARAMETER LINGKUNGAN DI SELAT DOMPAK, KEPULALIAN RIAU Soedharma, Dedi; Wardiatno, Yusli; Sanusi, Harpasis S.
Jurnal Perikanan Dan kelautan Vol 12, No 01 (2007)
Publisher : Jurnal Perikanan Dan kelautan

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Abstract

A study on the relationship between meiofauna community structure with seagrassdensity and environmental parameters has been carried out in the Dompak Straitwaters, Riau Archipelago. This study were investigated on four different seasonsthroughout a year, from May 2005 to April 2006. Three sampling site, i.e.., Al, A2and A3 were chosen to represent research sites. The sediment samples were tekenby PVC cores, in which six layers were separated (i.e. 0-5 cm, 5-10 cm, 10-15 cm,15-20 cm, 20-25 cm and 25-30 cm). The environmental parameters, such ascurrent velocity, the sediment composition, total organic carbon (TOO, totalorganic matter (TOM), pH and redox potential (Eh), were also observed. The dataon meiofauna, seagrass density and environmental parameters were analyzedstatistically by a regression analyisis. This analysis was run using a SPSS softwareversion 11.5 for Windows. The meiofauna was dominated by Nematodes,Copepods, Polychaetes, Foraniiniferans and Turbellarians. The results areshowing that the meiofaunal community structure would depend on severalconditions such as seagrass density, environmental factors and hydrologicalcharacteristics. The regression results are showing that the meiofaunal communitystructure patterns was significantly correlated with seagrass density and to theenvironmental parameters. Vertically, the meiofaunal community structurepatterns seems to be more affected by TOC and TOM. While the horizontally, itseems to he more affected by current velocity, TOM and pH.
THE COMPOSITION AND DISTRIBUTION OF BENTHIC FORAMINIFERA AT CORAL REEF ECOSYSTEM IN THOUSANDS ISLAND Toruan, Lumban Nauli Lumban; Soedharma, Dedi; Dewi, Kresna Tri
Jurnal Ilmu dan Teknologi Kelautan Tropis Vol 5, No 1 (2013): Elektronik Jurnal Ilmu dan Teknologi Kelautan Tropis
Publisher : Jurnal Ilmu dan Teknologi Kelautan Tropis

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Abstract

Composition and distribution of foraminifers are affected by human activities and have close association with coral reef ecosystem. The aims of this research were to investigate the benthic foraminifers’ composition and distribution in sediment of coral reef ecosystem. Eleven stations of Karang Bongkok, Pramuka, and Onrust Island were observed in this study. The sediments were taken from surface substrate up to 2 cm under the substrate. Samples were washed on sieve with mesh size 0,063 mm, and then dried in oven with 50°C of temperature  for two hours. After separating from the sediment, the foraminifers were laid on foraminiferal slide and indentified using binocular microscope. The highest composition of symbiont-bearing foraminiferal assemblages which associated with reef ecosystem was in East Pramuka (78.17%) and the lowest was in South Onrust (21,83%). The opportunistic type had the highest composition in South Onrust (38.67%) and the lowest was in South Karang Bongkok. In west Pramuka had the highest composition of heterotrophic type (57.17%) and the lowest was in North Onrust (11.33%). Onrust Island was dominated by opportunistic type, indicating high nutrient. The highest amount of foraminifers’ taxa was found in Karang Bongkok with good coral reef coverage, while the lowest in Onrust facing with Jakarta Bay. Keywords: composition, distribution, benthic foraminifers, coral reef.
MORPHOLOGY AND CELL BIOMASS OF SPONGE Aaptos aaptos AND Ismet, Meutia Samira; Soedharma, Dedi; Effendi, Hefni
Jurnal Ilmu dan Teknologi Kelautan Tropis Vol 3, No 2 (2011): Elektronik Jurnal Ilmu dan Teknologi Kelautan Tropis
Publisher : Jurnal Ilmu dan Teknologi Kelautan Tropis

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Abstract

Aaptos aaptos and Petrosia sp. sponges are known for their ability to produce potential marine bioactive compound. As a metazoan animal with simple body structure, the morphology and it association with symbiont-bacteria could influence their bioactive compound both type and activity, as much as their habitat adaptation. In order to determine morphology and its cell biomass of Aaptos aaptos dan Petrosia sp., samples were taken from the West Pari Island, at 7 m depth. Preserved samples (in 4% formaldehyde) were examined using a histological mounting and centrifugation method to separate the cells fraction of sponge’s tissues. A. aaptos sponge has a soft body structure with 55.9% skeleton-forming fraction, 14.2% sponge cell fraction and 29.9% bacteria fraction. Meanwhile, Petrosia sp. sponge has a rigid body with dominant skeleton-forming fraction (68.6%), and lesser sponge cell and bacteria associated (19.7% and 11.7%, respectively).Keywords: A. aaptos, Petrosia sp, morphology, cell biomass
Co-Authors ', Rachmaniar ', Zulfikar , Suharsono A. Zaenal Mustopa Abdul Haris Achmad Nasir Biasane, Achmad Nasir Adi Winarto Adi, Nyoman Darma Aditya Bramandito Agus Nuryanto Agus Saptono, Agus Ahmad Taufik Ghozali Aileen Tan Shau Hwai, Aileen Akhmad Fauzi Akhmad Solihin Andin H Taryoto, Andin Andry Indrawan ANI MARDIASTUTI Ario Damar Ayhuan, Hendrik Victor Ayu Ervinia Bambang Sulistiyarto Bambang Widigdo Beginer Subhan Chair Rani Chairul Muluk Citra S.U. Dewi D Djokosetiyanto, D Daniel R. Monintja DEDY DURYADI Denny Khaerudi DIETMAR BLOHM Dietriech G Bengen, Dietriech Dondy Arafat Edi Rudi Edison Harteman Edy Supriyono Ekowati Chasanah Elvi Yetti, Elvi Enan M. Adiwilaga Fadillah Rahmawati Fifi Widjaja Fredinan Yulianda Haeruddin . Harpasis S . Sanusi, Harpasis Harpasis S Sanusi Harpasis S. Sanusi Hawis H Madduppa, Hawis H Hawis Madduppa HEDI INDRA JANUAR Hefni Effendi Ida Ayu Lochana, Ida Ayu Ida Bagus Jelantik Swasta John I Pariwono, John John I. Pariwono Kardiyo Praptokardiyo KholiPdan, KholiPdan Kresna Tri Dewi Kurdi Gunawan, Kurdi Lilik B Prasetyo Luky Adrianto Lumban Nauli Lumban Toruan LURY SEVITA YUSIANA M. F. Rahardjo, M. F. MAULINIA MAULINIA Maya F Tamimi, Maya Melki . Mennofatria Boer Meutia Samira Ismet Moh Muhaemin MUJIZAT KAWAROE Muliari Muliari Nasir Haya, Nasir Neviaty P Zamani Neviaty P. Zamani Neviaty P. Zamani NEVIATY PUTRI ZAMANI Niken T.M. Pratiwi Nurlisa A Butet, Nurlisa Nurul Khakhim Parwinia ., Parwinia Paulus Boli R Widodo Rachmaniar Rachmat Ratna Siahaan Richardus F Kaswadji Ridwan Affandi Rilus Kinseng SIGID HARIYADI Siti Nurisjah Soehartini Sekartjakrarini Sumardjo, nFN Suparno Suparno Supriadi Supriadi Tatag Budiardi Tjahjo Winanto, Tjahjo Vincentius P. Siregar Walukow, Auldry F Yudi Herdiana Yusli Wardiatno Zulfigar Yasin, Zulfigar Zulfikar Zulfikar