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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 Ilmu Pertanian Indonesia Jurnal Fitopatologi Indonesia Jurnal Akuakultur Indonesia Jurnal Pengolahan Hasil Perikanan Indonesia Jurnal Ilmu dan Teknologi Kelautan Tropis Jurnal Akuatika Microbiology Indonesia BIOTROPIA - The Southeast Asian Journal of Tropical Biology Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Biogenesis: Jurnal Ilmiah Biologi Jurnal AgroBiogen Current Biochemistry Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) Jurnal Sumberdaya Hayati Elkawnie Journal of Tropical Biodiversity and Biotechnology JURNAL BIOLOGI INDONESIA Jurnal Biodjati Omni-Akuatika Jurnal Penelitian Pendidikan IPA (JPPIPA) Jurnal Biologi Tropis ANNALES BOGORIENSES LIMNOTEK - Perairan Darat Tropis di Indonesia Biosaintifika: Journal of Biology & Biology Education Jurnal Teknik Pertanian Lampung (Journal of Agricultural Engineering) Jurnal Riset Akuakultur Menara Perkebunan Jurnal Mangifera Edu Grouper: Jurnal Ilmiah Perikanan Konservasi Hayati Journal of Multidisciplinary Applied Natural Science Makara Journal of Science Jurnal Ilmu Kehutanan Jurnal Ilmu Kehutanan Annales Bogorienses

Iman Rusmana

Departmen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Kampus IPB Darmaga, Bogor 16680, Indonesia

Author-ID : 286105

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Energy Engineering Environmental Science Immunology & microbiology Library & Information Science Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics Veterinary

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

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.

Characterization of Bacteriophage Specific to Bacillus pumilus from Ciapus River in Bogor, West Java, Indonesia ANIK KUSMIATUN; IMAN RUSMANA; SRI BUDIARTI
HAYATI Journal of Biosciences Vol. 22 No. 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Bacillus pumilus is a spore-forming bacteria that is rod-shaped, gram positive, and aerobic. B. pumilus produced pumilacidins, known to have toxic effects on epithelial cells. Antibiotics were usually used to treat the disease caused by bacteria. Antibiotic typing test of B. pumilus indigenous from sewage water showed that this isolate was resistant to ampicillin and clindamycin. An alternative way was by application of bacteriophages as biocontrol agents to reduce B. pumilus in environment. The aim of this study were to isolate and characterize B. pumilus bacteriophage isolated from Ciapus River in Bogor, West Java. Bacteriophages infecting B. pumilus were isolated from river water using the double agar overlay method. Phages were defined by plaque morphology, structure, host range, and characteristic of molecular weight protein phage. Phage FBa1, FBa2, and FBa3 had narrow host range and they were specific for infecting B. pumilus. Electron microscope observation showed that phage FBa1 had icosahedral head without tail (166.67 nm in diameter), so it is called phage-like particles. Characterization of phage FBa1 by SDS-PAGE showed five proteins band. Molecular weight of FBa1 proteins was 70.9, 54.9, 33.8, 28.3, and 21.4 kDa.

Analysis of Intestinal Mucosal Immunoglobulin A in Sprague Dawley Rats Supplemented with Tempeh SUSAN SOKA; ANTONIUS SUWANTO; IMAN RUSMANA; DONDIN SAJUTHI; DIAH ISKANDRIATI; KATHARINA JESSICA
HAYATI Journal of Biosciences Vol. 22 No. 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Tempeh is a well-known Indonesian fermented food made from soybean. During the fermentation process, microorganisms play an important role in the flavor, texture, and nutritional quality of tempeh. Tempeh has been show to have immuno-modulatory and immune-stimulating properties that may also be caused by the microorganisms in tempeh as they interact between the microbial population in the intestinal tract. The objective of this study was to quantify IgA gene expression at both the transcription and translation levels in Sprague Dawley (SD) rats supplemented with tempeh. A total of 6 female SD rats were divided into 3 groups of 2 rats. The first group was the control and was fed a standard diet without tempeh. The second- and third group were fed with a standard diet supplemented with raw and cooked tempeh, respectively. Ileum tissue samples were collected after tempeh supplementation for 28 days. RNA was extracted from ileum samples, and measurement of IgA gene expression was further analyzed using semi quantitative real-time PCR. The concentration of IgA protein was quantified from ileum lysate using the half sandwich ELISA method. IgA gene expressions in rats supplemented with raw, and with cooked tempeh, were 1.18 and 1.17 fold higher, respectively, compared to the control group. Moreover, IgA protein secretion levels also increased 2.46 and 2.08 fold, respectively, compared to the control group. The result of this study indicates that both raw and cooked tempeh may stimulate IgA secretion, and also that both viable and non-viable microorganisms might stimulate IgA gene expression.

Metagenomic of Actinomycetes Based on 16S rRNA and nifH Genes in Soil and Roots of Four Indonesian Rice Cultivars Using PCR-DGGE . Mahyarudin; Iman Rusmana; Yulin Lestari
HAYATI Journal of Biosciences Vol. 22 No. 3 (2015): July 2015
Publisher : Bogor Agricultural University, Indonesia

The research was conducted to study the metagenomic of actinomycetes based on 16S ribosomal RNA (rRNA) and bacterial nifH genes in soil and roots of four rice cultivars. The denaturing gradient gel electrophoresis profile based on 16S rRNA gene showed that the diversity of actinomycetes in roots was higher than soil samples. The profile also showed that the diversity of actinomycetes was similar in four varieties of rice plant and three types of agroecosystem. The profile was partially sequenced and compared to GenBank database indicating their identity with closely related microbes. The blast results showed that 17 bands were closely related ranging from 93% to 100% of maximum identity with five genera of actinomycetes, which is Geodermatophilus, Actinokineospora, Actinoplanes, Streptomyces and Kocuria. Our study found that Streptomyces species in soil and roots of rice plants were more varied than other genera, with a dominance of Streptomyces alboniger and Streptomyces acidiscabies in almost all the samples. Bacterial community analyses based on nifH gene denaturing gradient gel electrophoresis showed that diversity of bacteria in soils which have nifH gene was higher than that in rice plant roots. The profile also showed that the diversity of those bacteria was similar in four varieties of rice plant and three types of agroecosystem. Five bands were closely related with nifH gene from uncultured bacterium clone J50, uncultured bacterium clone clod-38, and uncultured bacterium clone BG2.37 with maximum identity 99%, 98%, and 92%, respectively. The diversity analysis based on 16S rRNA gene differed from nifH gene and may not correlate with each other. The findings indicated the diversity of actinomycetes and several bacterial genomes analyzed here have an ability to fix nitrogen in soil and roots of rice plant.

Impact of Methanotrophic and N2O-reducing Bacterial Inoculation on CH4 and N2O Emissions, Paddy Growth and Bacterial Community Structure in Paddy Field Yuli Siti Fatma; Iman Rusmana; Aris Tri Wahyudi; Hamim Hamim
HAYATI Journal of Biosciences Vol. 27 No. 3 (2020): July 2020
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.27.3.197

Paddy field is one of the anthropogenic sources that produce greenhouse gases emission. This study aimed to investigate the impact of methanotrophic and N2O-reducing bacterial inoculation on CH4 and N2O emissions, paddy growth and bacterial community structure in paddy field. Two treatments of 100% synthetic fertilizer (250 kg urea/ha) without biofertilizer and 50% synthetic fertilizer (125 kg urea/ha) with biofertilizer consisted of methanotrophic and N2O-reducing bacteria were applied in the paddy field. Inoculation of methanotrophic and N2O-reducing bacteria was able to reduce CH4 and N2O emission up to 4.19 mg CH4/m2/day and 351.29 µg N2O/m2/day, respectively. Those bacterial applications were also able to increase paddy growth and yield productivity. According to DGGE profile, inoculation of the biofertilizer seemed to have a transient impact on bacterial communities in paddy soil at 36 days after transplanting (DAT) which showed the lowest similarity with all samples (a similarity index of 0.68). DGGE bands successfully excised have closest relative to uncultured bacteria which comprised 5 phyla, i.e. Proteobacteria (Alphaproteobacteria and Deltaproteobacteria), Nitrospirae, Actinobacteria, Firmicutes, and Acidobacteria. In this study, Alphaproteobacteria was the most dominant phylum. We provide basic information for developing the biofertilizer which supports sustainable agriculture.

Characteristics and Activity of Anti Qourum Sensing Bacillus spp. Isolated from Penaeus vannamei Shrimp Ponds Iman Rusmana; Yuni Puji Hastuti; Rizal Khoirun Alfisah; Alina Akhdiya
HAYATI Journal of Biosciences Vol. 29 No. 1 (2022): January 2022
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.29.1.97-106

Certain strains of V. parahaemolyticus carry a gene that encodes a toxin that causes Acute hepatopancreatic necrosis disease (AHPND) in P. vannamei. AHPND attacks shrimp post larvae within 20-30 days after stocking causing up to 100% mortality. The expression of these virulent genes is controlled by the quorum sensing system. This system is inhibited by an anti-quorum sensing (AQS) mechanism. Several Bacillus strains have AQS mechanism by producing AHL-Lactonase enzyme. Therefore, this study aimed to obtain Bacillus spp. having AQS activity for controlling AHPND. The study was conducted from isolation and selection of Bacillus isolates, as well as determination of AQS activity. From 22 samples consisting of shrimp intestines, water and pond sediment samples, a total of 151 isolates of Bacillus spp. were isolated. The screening test for AQS activity obtained 11 isolates that showed AQS activity on Cromobacterium violaceum. Determination of violacein pigment in liquid cultures of C. violaceum showed the index value of the pigment formation was between 0.025-0.166 and 0.026-0.567 at 24-hour and between 48-hour incubations, respectively. The quantitative analysis of violacein production showed that there were six isolates of Bacillus could inhibit the pigment production more than 75%. The isolates were identified as Bacillus cereus (four isolates), Bacillus thuringiensis (one isolate), and Bacillus velezensis (one isolate), respectively. The molecular analysis had confirmed that the isolates have aiiA genes encoding AHL-lactonase enzyme. These Bacillus isolates have potential application for controlling AHNPD disease.

Bacterial and Fungal Communities in Tempeh as Reveal by Amplified Ribosomal Intergenic Sequence Analysis SEUMAHU, CECILIA ANNA; SUWANTO, ANTONIUS; RUSMANA, IMAN; SOLIHIN, DEDY DURYADI
HAYATI Journal of Biosciences Vol. 20 No. 2 (2013): June 2013
Publisher : Bogor Agricultural University, Indonesia

Tempeh is an Indonesian traditional fermented food produced using Rhizopus as a starter culture. In practice, however, the starter culture as well as fermentation processes would yield a polymicrobial fermentation, which generated a unique tempeh flavor and texture. This condition makes Indonesian tempeh as one of the most complex fermented food, while at the same time would make it difficult to scale up tempeh production with uniform quality and consistency. The aim of this study was to compare a number of tempeh microbial communities employing Amplified Ribosomal Intergenic Sequence Analysis (ARISA). Fresh tempeh samples were obtained from tempeh producers in Java and Moluccas. 16S rRNA gene libraries and DNA sequencing were employed to analyze further the nature of bacterial diversity in two selected tempeh samples. The results of our study showed that different tempeh producer possessed different Bacterial ARISA (BARISA) or fungi ARISA (FARISA) profiles. However, BARISA profiles were found to be more discriminative than FARISA, and therefore BARISA would be more useful for tempeh genetic fingerprint or barcoding.

The Potential of Clove Rhizospheric Bacteria to Produce Vanillin from Eugenol Nurfahmi, Riziq Ilham; Mubarik, Nisa Rachmania; Rusmana, Iman; Tambunan, Ika Roostika; Akhdiya, Alina
HAYATI Journal of Biosciences Vol. 31 No. 4 (2024): July 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.4.702-711

Vanillin is one of the most important flavoring agents worldwide. Currently, consumers' awareness and concern for biovanillin production has been increasing. This study aimed to screen the potential of clove rhizospheric bacteria isolates producing vanillin through a biotransformation process of eugenol and to conduct the preliminary optimization of the biotransformation condition. Twenty-eight bacteria isolates were screened for their capability to transform eugenol into vanillin. BKL 15 isolate, which was identified as Lysinibacillus xylanilyticus, was selected as the highest vanillin producer among the isolates. The optimum molar yield of vanillin produced by the selected isolate was 4.99% (1.11 g/L) after 168 hours of biotransformation process in the medium consisting of TSB (30 g/L), eugenol (24 g/L), yeast extract (20 g/L), and concentration of casamino acid (20 g/L). Throughout the publications we have read, this is the first report of L. xylanolyticus that produces vanillin.

Denitrifier Still Has the Important Role in Nitrate Reduction to N2 Although It is Not the Predominant Population in the Estuarine Bacterial Community of Nitrate Reducing Bacteria Rusmana, Iman; Nedwell, David B.
HAYATI Journal of Biosciences Vol. 31 No. 4 (2024): July 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.4.630-640

Denitrification and nitrate-ammonification are the responsible processes for nitrate removal in the estuaries. Temperature, nitrate and organic carbon availability are key factors controlling a rate of the nitrate reduction processes. This mixed cultures chemostat study investigates the competition ability and their nitrate reduction end-products of the bacteria isolated from an estuary at different temperatures. This study will help us to understand the seasonal nitrate reduction processes in an estuary. The experiments showed that a nitrate-ammonifier was the predominant process in the steady-state chemostat at high temperature. While a facultative denitrifier-nitrate ammonifier was the predominant process at low temperature. However, the main end products of nitrate reduction at high temperature were up to 61% N2 indicating a denitrifier still had an important role in the end products of nitrate reduction in the estuary. The data also showed that a nitrite respiring bacterium reduced nitrite to N2, that responsible for approximately 6-9% of total N2 produced in the culture. This study confirmed that nitrate ammonifiers out-compete denitrifiers at high temperature, however, denitrifiers still had an important role in end products of nitrate reduction.

Diversity of Indigenous Bacteria from Mangrove Sediments in the Waters of Ambon Bay, Maluku Tuasalamony, Mutia Musdalifah; Widiyanto, Tri; Rusmana, Iman
HAYATI Journal of Biosciences Vol. 32 No. 2 (2025): March 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.2.395-404

This study aimed to analyze the diversity of indigenous bacteria by comparing culture and non-culture methods and to analyze the physicochemical effects on bacterial diversity in polluted and natural mangrove sediments. The environmental parameter values of mangrove sediments for bacterial growth can change owing to differences in adaptation and tolerance to fluctuations in physicochemical conditions. The number of colonies in natural and polluted areas using the culture method was 6.2 × 104 CFU/g and 5.5 × 104 CFU/g, respectively. A total of 33 isolates were identified, with 17 and 16 isolates from the natural and polluted areas, respectively. The most common isolates found in both areas were Acinetobacter haemolyticus strain FBC636 and Exiguobacterium acetylicum strain IAE17. Using the nanopore sequencing method, the total number of colonies in the natural and polluted areas was 69,761 and 58,412 colonies, respectively. A total of 12,954 bacterial species were identified, with 6,837 species in the natural area and 6,117 in the polluted area. The most common isolate found was Sulfurovum aggregans. Physicochemical conditions influenced the differences in bacterial diversity between the natural and polluted areas in the mangrove areas of Ambon Bay.

Co-Authors Abdjad Asih Nawangsih ACENG RUYANI Achmad Dinoto Aderiana Masthura AKHADIYA, ALINA Alfan Cahyadi Alfisah, Rizal Khoirun Aliati Iswantari ALINA AKHDIYA Alina Akhdiya Alina Akhdiya Amanda, Nisa Widya Andi Ernawati Angela Mariana Lusiastuti Angela Mariana Lusiastuti Ani Suryani Ani Suryani Ani Widiyati ANIK KUSMIATUN Anja Meryandini Anja Meryandini Antonius Suwanto Apon Zaenal Mustopa Ari Fina Bintarti Ari Fina Bintarti, Ari Fina Aris Tri Wahyudi Armanisa, Khafifah Baskoro S Wibowo Cahyadi, Alfan Cecep Kusmana CECILIA ANNA SEUMAHU CECILIA ANNA SEUMAHU Ciptadi Achmad YUSUP Daniel Djokosetiyanto Darmono Taniwiryono Desniar - - Dewi Puspaningsih DIAH ISKANDRIATI Dian Hendrayanti Dinamella Wahjuningrum Dondin Sajuthi DWI ANDREAS SANTOSA Dwi Ningsih Susilowati Eddy Supriyono Emei Widiyastuti Fachriyan Hasmi Pasaribu Fachriyan Hasmi Pasaribu Fahmi, Riziq Ilham Nur Faturrahman Faturrahman Ferbiyanto, Andri Fredinan Yulianda Frijona Fabiola Lokollo GALUH WENING PERMATASARI Gunawan Djajakirana Hamim Hamim Happy Widiastuti Hefni Effendi Hessy Novita Hessy Novita I Komang Gede Wiryawan I MADE ARTIKA I Made Samudra Ifa Manzila Ika Roostika Tambunan, Ika Roostika Ika Setianingsih, Ika Indriyani, Yohanna Anisa Irwan Cahyadi It Jamilah KATHARINA JESSICA Khairul Syahputra Kukuh Nirmala Kuntari, Wahyu Budi Lena Novita Lingga, Rahmad Lizawati . Maggy Thenawidjaya Suhartono Maggy Thenawidjaya Suhartono Mahdani, Wilda Mahyarudin, Mahyarudin Manguntungi, Baso Masrukhin Masrukhin Masthura, Aderiana Miftahudin . Mukti Ali MUNTI YUHANA MUTTAQIN, MAFRIKHUL Nedwell, David B. Niken T.M Pratiwi, Niken T.M NISA RACHMANIA MUBARIK Nisa Widya Amanda Novita, Lena Nurhakiki Nurjanah PRIHASTO SETYANTO Prihasto Setyanto Priyo Handoyo Wicaksono Rahman Rahman Rahman Rahman Rahminovita Herlis RATNA SETYANINGSIH RATNA SETYANINGSIH RATNANINGTYAS, SUSI RIDWAN AFFANDI Rika Indri Astuti RIKA RAFFIUDIN Rina Hesti Utami Risky Hadi Wibowo Risky Hadi wibowo Roedhy Poerwanto Rosadela, Fitri Sipriyadi Sipriyadi Sipriyadi Siti Nur Jannah Sobir Sobir Solly Aryza Sri Budiarti Poerwanto sri murtini . Suhartono Suhartono SUSAN SOKA Syaiful Anwar T. Widiyanto Taruna D. Satwika TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN Thenawidjaya, Maggy Tri Eko WAHYONO Tri Handayani Kurniati Tri Handayani Kurniati Tri Muji Ermayanti Tri P. Priyatno Tri Panji Tri Puji Priyatno Tri Widiyanto Tridesianti, Siska Tuasalamony, Mutia Musdalifah Utut Widyastuti Wahyuni, Reza Wibowo, Risky Hadi WIDANARNI WIDANARNI Widiyanto, Tri Wilda Mahdani Wildan Nurusallam Wiraswati, Sri Martina Yadi Suryadi Yani Aryati Yohana A Dahliani Yohanna Anisa Indriyani Yuli Siti Fatma Yuli Siti Fatma YULIN LESTARI Yuni Puji Hastuti Yusli Wardiatno Zaenal Arifin, Sukarya Zulfarina Zulfarina Zulfarina,

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