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All Journal HAYATI Journal of Biosciences MEDIA PETERNAKAN - Journal of Animal Science and Technology Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Fitopatologi Indonesia Jurnal Akuakultur Indonesia Jurnal Pengolahan Hasil Perikanan Indonesia Jurnal Ilmu Kehutanan Jurnal Akuatika Microbiology Indonesia BIOTROPIA Medical Journal of Indonesia Jurnal AgroBiogen Current Biochemistry Journal Jurnal Sumberdaya Hayati JURNAL BIOLOGI INDONESIA Omni-Akuatika E-Journal Menara Perkebunan Jurnal Biologi Tropis ANNALES BOGORIENSES Biosaintifika: Journal of Biology & Biology Education Jurnal Riset Akuakultur E-Journal Menara Perkebunan
Iman Rusmana
Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University. Jl. Raya Darmaga, Bogor 16680, West Java. Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Economics, Econometrics & Finance Education Environmental Science Immunology & microbiology Medicine & Pharmacology

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Comparison of DNA Extraction Methods for Microbial Community Analysis in Indonesian Tempe Employing Amplified Ribosomal Intergenic Spacer Analysis SEUMAHU, CECILIA ANNA; SUWANTO, ANTONIUS; RUSMANA, IMAN; SOLIHIN, DEDY DURYADI
HAYATI Journal of Biosciences Vol 19, No 2 (2012): June 2012
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (136.378 KB) | DOI: 10.4308/hjb.19.2.93

Abstract

Tempe fermentation involved complex microbial communities which are only revealed partially through culture dependent methods. Culture-independent methods would be potential to unravel this complex microbial fermentation. Appropriate DNA extraction is an essential tool to obtain reliable data from culture independent method. In this study, we employed two commercial DNA extraction methods to find the best one for microbial community characterization employing amplified ribosomal intergenic spacer analysis (ARISA). Our result showed that PowerFood Microbial DNA Isolation Kit-MOBIO (PFMDIK) is an excellent method for microbial DNA extraction from tempe. It gave high quantity and quality of DNA suitable for PCR amplification of 16S-23S rRNA intergenic spacer to yield a diverse and reproducible ARISA profile.
Pertumbuhan Bibit Tanaman Manggis (Garcinia mangostana L.) Setelah Inokulasi dengan Berbagai Galur Agrobacterium rhizogenes1 Lizawati, ,; Poerwanto, Roedhy; Sobir, ,; Rusmana, Iman; Ermayanti, Tri Muji
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol 35, No 2 (2007): Jurnal Agronomi Indonesia
Publisher : Bogor Agricultural University

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Abstract

Growth of mangosteen essentially depends on its root system.  Therefore, it needs technology to obtain stringer mangosteen root system.  The use of Agrobacterium rhizogenes bacterium is an alternative.  The objectives of this experiment were : 1) to find the effective strain of A. rhizogenes bacterium for inoculation of mangosteen seedling root, 2) to find the best inoculation method for inducing mangosteen seedling root.  The materials used in this experiment were ; mangosteen fruit and A. rhizogenes collection from Puslit Biotechnology LIPI Cibinong-Bogor.  The experiment was arranged in completely randomized design with two factorial treatments.  The first factor : 11 strains A. rhizogenes (ATCC-15834, ATCC-8196, R-1000, 07-20001, A4, A4-J, 509, 510, 511, MAFF 01-1724, and control), the second factor : 2 inoculation methods (cutting and dipping).  The results showed that A. rhizogenes  of ATCC-15834, 509, 07-20001, A4, and R-1000 increased stem diameter, plant height, leaf number, lateral and tertiary root number, better than ATCC-8196, MAFF 01-1724, 510, 511, A4-J, and control.  Cutting root method of inoculation resulted in higher live plant percentage compared to dipping root method.   Key words :  Agrobacterium rhizogenes, Garcinia mangostana, inoculation
SENYAWA ANTIMIKROBA YANG DIHASILKAN OLEH BAKTERI ASAM LAKTAT ASAL BEKASAM -, Desniar -; Rusmana, Iman -; Suwanto, Antonius -; Mubarik, Nisa Rachmania
Jurnal Akuatika Vol 3, No 2 (2012): Jurnal Akuatika
Publisher : Fakultas Perikanan dan Ilmu Kelautan

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Abstract

Bakteri asam laktat (BAL) adalah mikroba dominan yang ditemukan dalam fermentasi ikan. Tujuan penelitian ini adalah menentukan perkiraan kuantitatif awal dari substansi antimikroba yang dihasilkan oleh isolat BAL asal bekasam dan mengetahui aktivitas antimikrobnya terhadap lima bakteri patogen. Perkiraan kuantitatif asam laktat dan H2O2, menggunakan metode titrasi. Uji aktivitas antimikroba menggunakan metode difusi sumur agar. Karakterisasi (morfologi, fisologi dan pertumbuhan) dan identifikasi menggunakan API 50 CHL (Bio-Mereux, France). Produksi asam laktat dan H2O2 meningkat dengan waktu inkubasi untuk semua isolat kecuali pada isolat BP(3). Produksi asam laktat tertinggi adalah 21,765 g/L yang dihasilkan oleh isolat SK(5) (48 jam inkubasi). Konsentrasi H2O2 yang dihasilkan oleh semua isolat jauh lebih rendah dibandingkan dengan asam laktat. Konsentrasi H2O2 tertinggi ialah 0,079 g/L pada isolat BI(3) dan BP(20) dalam 72 jam inkubasi. Supernatan bebas sel yang dinetralkan tidak menghambat pertumbuhan bakteri uji, sedangkan yang tidak dinetralkan dapat mengambat bakteri uji yang digunakan dengan zona hambat 9 -15 mm. Zona penghambatan terbesar dihasilkan oleh isolat SK(5) (24 jam inkubasi) terhadap S. aureus. Isolat BI(3), BP(3) dan BP(20) adalah Pediococcus pentosaceus 1 dengan kemiripan sebesar 99,9%. Isolat SK(5) adalah Lactobacillus plantarum 1 dengan kemiripan sebesar 99,9%. Penelitian ini menunjukkan bahwa isolat BAL asal bekasam dapat dijadikan sebagai kandidat biopreservatif pangan terutama untuk pengolahan hasil perikanan. Kata kunci: antimikrobial, asam laktat, bakteri asam laktat, bekasam, dan hidrogen peroksida.
PENAPISAN BAKTERIOSIN DARI BAKTERI ASAM LAKTAT ASAL BEKASAM ., Desniar; Rusmana, Iman; Suwanto, Antonius; Mubarik, Nisa Rachmania
Jurnal Pengolahan Hasil Perikanan Indonesia Vol 14, No 2 (2011): Jurnal Pengolahan Hasil Perikanan Indonesia
Publisher : Departement of Aquatic Product Technology

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Abstract

Bacteriocin is proteinaceous compound that has bactericidal action against other microorganisms. Bacteriocin-producing lactic acid bacteria (LAB) is generally considered safe for human consumption and can be applied in food preservation. One source of indigenous LAB is from Indonesian fermented fish products, bekasam. This study aimed to obtain LAB isolates from bekasam that have high potential as  producer of bacteriocin. The steps were screening of bacteriocin compound and protein precipitation using ammonium sulfate with a concentration of 0-10% to 70-80%. Screening of bacteriocin compounds of 25 isolates LAB from bekasam showed that there were 11 isolates (44%) that have the potential as  producer of bacteriocin, in which the cell-free supernatant to pH 5 and or pH 6 produce inhibitory zones on the indicator bacteria Escherichia coli, Salmonella typhimurium ATCC 14028, Bacillus cereus, Staphylococcus aureus and Listeria monocytogenes. Then, the precipitation of proteins from the cell-free supernantant was done for the selected four isolates that have the potential as  producer of bacteriocin. The supernatant and  the precipitate from yield of protein precipitation in the selected four isolates showed that inhibition zone against the indicator bacteria E. coli, S. typhimurium ATCC 14 028, and L. monocytogenes with inhibition zone around 3.0 to 10.0 mm. Inhibition zones in the supernatant and the precipitate were indication that  active compound is organic acid and bacteriocin, respectively. The highest inhibition zone of the supernatant and the precipitate of the BP(3) and SK(5) isolates against L. monocytogenes and S. typhimurium, respectively.  The highest inhibition zone of the supernatant of the BP(20) and BI(3) isolates against S. typhimurium and  S. typhimurium and E. coli, respectively. While the highest inhibition zone of precipitate of the BP(20) and BI(3) isolates were same, that is against E. coli. Each with ammonium sulfate concentrations were different.Key words: Bacteriocin, lactic acid bacteria, bekasam
Profiles of traditional farms: soil texture, total inorganic N and bacteria-producing estate Hastuti, Yuni Puji; Rusmana, Iman; Widiyanto, T.
Jurnal Akuakultur Indonesia Vol 9, No 2 (2010): Jurnal Akuakultur Indonesia
Publisher : Jurnal Akuakultur Indonesia

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Abstract

Pond traditional system is the pond in still activity with a symple management system.  This activity indicated by low technology and relatively low production level.  Aquaculture activities in traditional pond not loss from nitrification and denitrification prosess, however this process is more low production rather than semiintensive and intensive system. This study aims to observe abundance of bacteria nitrification along with changes soil texture, and N-organic in the soil of traditional pond. Chemical and biological analyses were done using spectroscopy and Most Probable Number methods to determine the amount of nitrite and ammonium production of bacteria.  Based of the result, each stratum traditional ponds have relatively similar abundance in nitrite producing bacteria of 7.08-7.47 Log CFU/g.  Increasing abundance in ammonium producing bacteria was found in all stratum, range from 5.63 Log cfu/g to 8.12 Log cfu/g. From the first day of preparation, traditional ponds have a lot of nitrite and ammonium producing bacteria.Keywords: traditional, pond, nitrification, abundance of bacteri. ABSTRAKTambak sistem tradisional merupakan tambak yang dalam kegiatannya masih menggunakan sistem manajemen sederhana.  Hal ini ditandai dengan penerapan teknologi sederhana, dan tingkat produksi relatif rendah.  Kegiatan budidaya di tambak tradisional tidak akan terlepas dari proses nitrifikasi dan denitrifikasi, namun demikian proses ini relatif lebih rendah aktivitasnya daripada tambak sistem semiintensif dan intensif.  Tujuan dari penelitian ini adalah mempelajari kelimpahan bakteri penghasil senyawa nitrit, amonium seiring dengan perubahan tekstur tanah, dan N-organik pada tanah tambak tradisional. Media pertumbuhan bakteri dikondisikan bebas oksigen (oxygen free nitrogen/OFN method) , sedangkan kelimpahan bakteri dianalisis dengan rumus most porbable number (MPN). Berdasarkan hasil, setiap strata tanah tambak tradisional memiliki jumlah bakteri penghasil nitrit yang relatif sama, yaitu antara 7,08-7,47 Log cfu/g. Peningkatan kelimpahan bakteri penghasil amonium terjadi pada semua strata, yaitu berkisar antara 5,63 Log cfu/g sampai dengan 8,12 Log cfu/g.  Dari hari pertama persiapan, tambak tradisional telah memiliki kelimpahan bakteri penghasil nitrit dan amonium yang berlimpah.Kata kunci:  tradisional, tambak, nitritifikasi, kelimpahan bakteri.
Effects of Temperature on Denitrifying Growth and Nitrate Reduction End Products of Comamonas testosteroni Isolated from Estuarine Sediment RUSMANA, IMAN
Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

Predictions of seasonal changes in N2O emission that occur in natural estuaries are important to anticipate the future implications of global warming. This study showed the effect of temperature on denitrifying growth and nitrate reduction end product of Comamonas testoteroni isolated from estuarine sediment using both batch and continuous cultures. The μmax values of Comamonas testosteroni grown in anaerobic batch culture were increased with increasing temperature, and the highest μmax was found at 26 oC. Concentrations of nitrate reduced (mg-1 dried weight cells) were higher at low temperature. Concentrations of N2 produced were higher at low temperature and the production of N2 was higher than both NO2- and N2O productions
Activity of Proteolytic and Amylolytic Enzymes from Bacillus spp. Isolated from Shrimp Ponds JAMILAH, IT; MERYANDINI, ANJA; RUSMANA, IMAN; SUWANTO, ANTONIUS; MUBARIK, NISA RACHMANIA
Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

Accumulation of feed excess in commercial shrimp ponds due to overfeeding could decrease water quality. Protein and starch are the primary components of shrimp feed. This study was conducted to characterize extracellular proteases and amylases of Bacillus spp. isolated from shrimp ponds. 72 proteolytic and amylolytic Bacillus spp. isolates were screened from shrimp ponds in Karawang, West Java. Ten isolates were selected for further characterization for their growth and ability to reduce total suspended solid generated from commercial shrimp feed. Bacillus sp. DA 5.2.3 and L5 showed excellent activity in reducing total suspended solid, by 37 and 30% respectively. Protease and a-amylase activities of Bacillus sp. DA 5.2.3 isolate were consistently higher than that of L5. Maximum total and specific protease activity of DA 5.2.3 isolate was 2.0 U mL-1 and 40.9 U mg-1 respectively, while the activities of the L5 isolate were 2.1 U mL-1 and 23.0 U mg-1 respectively. Based on its 16S rRNA gene sequences, Bacillus sp. DA 5.2.3 showed 99% similarity to Bacillus cereus XHJ-2-6. Bacillus sp. DA 5.2.3 could potentially be applied to maintain water quality by reducing total suspended solid in water columns of shrimp ponds.
Physiological Characterization and Molecular Identification of Denitrifying Bacteria Possesing Nitrous Oxide High Reduction Activity Isolated from Rice Soils SETYANINGSIH, RATNA; RUSMANA, IMAN; SETYANTO, PRIHASTO; SUWANTO, ANTONIUS
Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

Rice  fields are one of the main sources of high nitrous oxide N2O emission.  Soil denitrifiers possessing high N2O reduction activity are important for controlling N2O emission.  Nitrous oxide reduction is the last step of denitrification process.  The aims of this study were to characterize and to identify denitrifying bacteria isolated from rice soils possessing high activity of N2O reduction.  Soil samples were taken from 6 locations of rice fields in Bogor (West Java) and Tangerang (Banten), Indonesia.  Physiological characterization was performed using API 20 NE, while molecular identification was conducted based on the 16S rRNA gene sequence.   It was found that ten isolates of denitrifying bacteria were able to grow using N2O as an electron acceptor as indicated by decreasing N2O concentration in the headspace of the cultures.  The bacterial  growth indicated by optical density,  increased up to 0.12-0.47  after 5 days incubation.  Isolate BL2 had the highest activity of  N2O reduction followed by BL1 and BLN1 at up to 5.41, 4.09, and 3.91 μmol mL-1 bacterial cultures, respectively.  The BL1, BL2, and BLN1 isolates had some different physiological characteristics.  Based on their 16S rRNA sequence, BL1 and BLN1 were closely related to Ochrobactrum anthropi ATCC 49188 with similarity of 99%.
Guide for Authors Rusmana, Iman
Microbiology Indonesia Vol 4, No 1 (2010): April 2010
Publisher : Indonesian Society for microbiology

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Abstract

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ISOLATION AND CHARACTERIZATION OF METHANOTROPHIC BACTERIA FROM RICE FIELDS Iman Rusmana; ALINA AKHADIYA
BIOTROPIA Vol 16, No 2 (2009)
Publisher : SEAMEO BIOTROP

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Abstract

Methane is a greenhouse gas and has potency to deplete ozone layer.  Rice fields are a significantly sources of atmospheric methane.  Chemical fertilizers application in rice fields can increase methane emission. Methanotrophic bacteria are unique in their ability to utilize methane as a sole carbon and energy source.  This research was successfully isolating and characterizing methanotrophic bacteria from rice fields in Bogor and Sukabumi, West Java, Indonesia.  Determination of methane oxidation activity using Gas Chromatography showed that all isolates performed methane oxidation activity.  The highest methane oxidation activity was performed by BGM 9 isolate. And DNA amplification of BGM 9 genome was performed single band of mmoX in the size of 500 bp and three bands of pmoA  in the size of 1000, 750 and 500 bp respectively
Co-Authors , Lizawati , Sobir -, Rahman . Mahyarudin, . Achmad Dinoto Aliati Iswantari ALINA AKHADIYA ALINA AKHDIYA Amanda, Nisa Widya Ani Suryani ANIK KUSMIATUN ANIK KUSMIATUN ANJA MERYANDINI Antonius - Suwanto ANTONIUS SUWANTO ANTONIUS SUWANTO Ari Fina Bintarti, Ari Fina ARIS TRI WAHYUDI Baskoro S Wibowo, Baskoro S Cahyadi Irwan, Cahyadi Cahyadi, Alfan CECEP KUSMANA CECILIA ANNA SEUMAHU Daniel Djokosetiyanto DEDY DURYADI SOLIHIN Desniar - - Desniar -, Desniar Desniar . DIAH ISKANDRIATI DIAH ISKANDRIATI DONDIN SAJUTHI DONDIN SAJUTHI DWI NINGSIH SUSILOWATI Eddy Supriyono Fachriyan Hasmi Pasaribu Ferbiyanto, Andri Fredinan Yulianda HAPPY WIDIASTUTI Hefni Effendi I MADE ARTIKA I Made Samudra It Jamilah KATHARINA JESSICA KATHARINA JESSICA Khairul Syahputra, Khairul Komang Gede Wiryawan Kukuh Nirmala Kuntari, Wahyu Budi Lena Novita MIFTAHUDIN ., MIFTAHUDIN Munti Yuhana MUTTAQIN, MAFRIKHUL Niken T.M Pratiwi, Niken T.M NISA RACHMANIA MUBARIK Novita, Hessy PANJI, TRI - PRIHASTO SETYANTO Puspaningsih, Dewi Rahman Rahman RATNA SETYANINGSIH RATNANINGTYAS, SUSI Ridwan Affandi RIKA RAFFIUDIN Rina Hesti Utami ROEDHY POERWANTO Siti Nur Jannah SRI BUDIARTI SRI BUDIARTI SUSAN SOKA SUSAN SOKA T. Widiyanto Thenawidjaya, Maggy TRI EKO WAHYONO, TRI EKO Tri Handayani Kurniati Tri Muji Ermayanti Tri Puji Priyatno Tri Widiyanto UTUT WIDYASTUTI Wibowo, Risky Hadi Widiyati, Ani Yadi Suryadi Yohana A Dahliani, Yohana A YULIN LESTARI Yuni Puji Hastuti Yuni Puji Hastuti Yusli Wardiatno Yusup, Ciptadi Achmad