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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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1377.267 KB) | DOI: 10.4308/hjb.22.3.113

Abstract

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

Abstract

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

Abstract

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.
Characteristics of Lactic Acid Bacteria Isolated from Gastrointestinal Tract of Cemani Chicken and Their Potential Use as Probiotics Siti Nur Jannah; Achmad Dinoto; Komang Gede Wiryawan; Iman Rusmana
Media Peternakan Vol. 37 No. 3 (2014): Media Peternakan
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (5594.722 KB) | DOI: 10.5398/medpet.2014.37.3.182

Abstract

The aims of this study were to screen and characterize lactic acid bacteria (LAB) isolated from gastrointestinal (GI) tract of Cemani chicken, one of Indonesian local chicken and to investigate their potential use as probiotics. LAB were isolated from GI tract using MRSA and GYPA media and incubated anaerobically. Selected LAB were determined their probiotic properties with several assays. Identification of selected LAB was based on 16S rDNA sequences, morphological and biochemical characteristics. Ninety five bacteria  were isolated and characterized as lactic acid bacteria (Gram positive, catalase negative, non sporeforming and acid producing). Twenty four isolates of LAB demonstrated antimicrobial activity against Escherichia coli JCM 1649 and Salmonella enteritidis B2586, and three selected isolates, i.e. CCM011, CSP004, and CVM002 showed the highest inhibition activity. The isolates had characters of high cell surface hydrophobicity and inter-isolate coaggregation ability of LAB, high survival at low pH, high  phytase and protease activity (but no amylase and lipase activity), weak coaggregation with pathogen and no resistance to the examined antibiotics. The isolates were identified based on sequence analysis of 16S rRNA gene as Lactobacillus salivarius, however, each isolate had different profiles of sugar fermentation. Therefore the three LAB isolates had potential application as probiotics for chicken.Key words: Cemani chicken, gastrointestinal tract, lactic acid bacteria, probiotic
Produksi Serasah Musiman pada Berbagai Spesies Mangrove di Pesisir Kabupaten Muna Barat, Sulawesi Tenggara Rahman Rahman; Yusli Wardiatno; Fredinan Yulianda; Iman Rusmana
Jurnal Ilmu Pertanian Indonesia Vol. 25 No. 3 (2020): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.25.3.323

Abstract

Mangrove litter production is important in the displacement of organic matter from mangrove vegetation to water such as in the coast of West Muna Regency. However, one factor influencing it is the frequency of rainfall. This research, therefore, aims to determine the influence of the frequency of rainfall in mangrove ecosystem by obtaining data through the fractional wet weight. The results showed that the biomass fraction with the largest amount were Rhizophora mucronata, Rhizophora apiculata, and Sonneratia alba with of 31.59; 31.07; and 30.96%, respectively, while the lowest was Rhizophora stylosa, Bruguiera cylindrica, and Bruguiera gymnorrhiza with of 30.07; 30.10; and 31.95%, respectively. The species with the largest leaf litter production was Bruguiera cylindrica, with of 1.72 g.m-2.day-1 which occurred in April and the lowest was Rhizophora apiculata, 0.24 g.m-2.day-1 in August. The species with the largest leaf litter production was Bruguiera cylindrica, 1.96 g.m-2.day-1 which occurred in May and the lowest was Sonneratia alba, 0.29 g.m-2.day-1 in August. In addition, the species with the largest fruit litter production was Rhizophora apiculata, 1.76 g.m-2.day-1 in April and the lowest was Sonneratia alba, 0.32 g.m-2.day-1 in September. The total litter production was 18,75 g.m-2.day-1 consisted of 6,69 g.m2.day-1 leaf litter, 6,54 g.m-2.day-1 branch litter, and 5,52 g.m-2.day-1 fruit litter. The higher the frequency of the rain, the greater the litter production. Keywords: biomass fraction, seasonal litter production, West Muna Regency
PENAPISAN BAKTERIOSIN DARI BAKTERI ASAM LAKTAT ASAL BEKASAM Desniar .; Iman Rusmana; Antonius Suwanto; Nisa Rachmania Mubarik
Jurnal Pengolahan Hasil Perikanan Indonesia Vol 14 No 2 (2011): Jurnal Pengolahan Hasil Perikanan Indonesia
Publisher : Department of Aquatic Product Technology IPB University in collaboration with Masyarakat Pengolahan Hasil Perikanan Indonesia (MPHPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (839.067 KB) | DOI: 10.17844/jphpi.v14i2.5321

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
Soil Chitinolytic Bacteria from Jambi Province to Produce Antifungal of Plant Pathogens Risky Hadi Wibowo; Sipriyadi Sipriyadi; Nisa Rachmania Mubarik; Iman Rusmana
Mangifera Edu Vol 5 No 1 (2020): Jurnal Mangifera Edu
Publisher : Universitas Wiralodra

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31943/mangiferaedu.v5i1.95

Abstract

Chitinolytic bacteria are bacteria that have chitinolytic activity, which is able to hydrolysis the composition of chitin which composes many fungal cell walls. Chitinolytic bacteria are currently more widely used because of their ability as a biological control agent to the pathogenic fungi especially in horticultural and plantation crops. This research was conducted with the aim of obtaining isolates of chitinolytic bacteria that were able to inhibit the growth of plant pathogenic fungi in Vitro on chitin agar media. Fusarium oxysporum, Sclerotium rolfsii, and Rhizoctonia solanii are used in the inhibition test of chitinolytic bacteria. Bacteria were isolated and screened from the soil of Bukit Dua Belas National Park and Oil Palm Plantations in Jambi using 0.3% chitin agar media. The results showed that two of 10 bacterial isolates were able to produce inhibition zones to the growth of hyphae of pathogenic fungi on potato dextrose agar (PDA) media. TB04-13 isolate was able to produce the largest inhibition in F. oxysporum and R. solanii about 42% and 42.05% respectively, while TB04-15 isolate produced the biggest inhibition in S. Rolfsii ranged to 25.50%. Based on the chitinolytic index (CI) values, isolates TB04-13 and TB04-15 produced CI values ​​of 1.60 and 0.63, respectively. The morphological characteristics and Gram staining of both TB04-13 and TB04-15 chitinolytic isolates are included in rod-shaped and Gram-positive bacteria. Both of these isolates can be used as antifungal-producing candidates for plant pathogenic fungi in Indonesia.
Application of Biological Nitrogen Fixation Cyanobacteria To Paddy Plant Cultivated Under Deep-Water Culture System Dian Hendrayanti; Iman Rusmana; Dwi Andreas Santosa; Hamim Hamim
Jurnal Biodjati Vol 5, No 2 (2020): November
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v5i2.8510

Abstract

 The Biological Nitrogen Fixing (BNF) cyanobacteria can reduce atmospheric nitrogen into ammonium. This ability makes BNF cyanobacteria a potential eco-friendly N-source for soil-planted pad-dy. Apart from a few success stories of BNF cyanobacteria applica-tion in the rice field, its role as an ammonium producer is still an open question. There is also a possibility that indeed cyanobacteria biomass which provides nitrogen through the biological decomposing process. This study aimed to analyze the influence of three strains BNF cyanobacteria on paddy grown in the Deep-Water Culture (DWC) hydroponic system. Yoshida Nutrient Solution was used as a growth medium with the application of 0, 45.7, and 91.4 gL-1 of ammonium nitrate (NH4NO3) with five replications. The result showed that inter-action between cyanobacteria and nitrogen significantly influenced the total nitrogen of paddy plant, but not the paddy plant height, the num-ber of tillers, and biomass. Cyanobacterial filaments were found most-ly attached to the paddy root rather than floated in the DWC system. Paddy treated with cyanobacteria had more lateral root than control. The result suggested that cyanobacteria support paddy growth indi-rectly through nitrogen deposition in plant tissue and root development. 
Identifikasi Entomopatogen Bakteri Merah pada Wereng Batang Coklat (Nilaparvata lugens Stål.) Tri Puji Priyatno; Yohana A Dahliani; Yadi Suryadi; I Made Samudra; Dwi Ningsih Susilowati; Iman Rusmana; Baskoro S Wibowo; Cahyadi Irwan
Jurnal AgroBiogen Vol 7, No 2 (2011): Oktober
Publisher : Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/jbio.v7n2.2011.p85-95

Abstract

Indentification of Entomopathogenic Red Bacterial fromBrown Planthopper (Nilaparvata lugens Stål.). Tri P.Priyatno, Yohana A. Dahliani, Yadi Suryadi, I MadeSamudra, Dwi N. Susilowati, Iman Rusmana, Baskoro S.Wibowo, and Cahyadi Irwan. Red bacteria isolated frombrown planthopper (BPH) has been proven pathogenicagainst BPH and others insects. Application of 106 to 107cells/ml of red bacteria caused 65.6-78.2% mortality of BPH.The 50% effective concentration (EC50) and lethal time of redbacteria against BPH is 2.8 x 105 cells/ml and 6.8 days,respectively. Based on phenotypic characters tested on GNMicroPlateTM Biolog kit and 16S rRNA sequneces analysis,red bacteria was identified as Serratia marcescens with 99%similarity. Red pigmen produced by S. marcescens strainBPH is secondary metabolite determined as prodigiosinshowing bactericidal activities against Xanthomonas oryzaepv. oryzae. We concluded that S. marcescens did not onlypotent as biocontrol agent to BPH, but also it can be used tocontrol plant pathogenic bacteria.
Pengaruh Media terhadap Produksi Prodigiosin Isolat Bakteri Entomopatogen Serratia marcescens Asal Wereng Batang Cokelat Ifa Manzila; Tri P. Priyatno; Rahminovita Herlis; Iman Rusmana; I Made Samudra; Yadi Suryadi
Jurnal AgroBiogen Vol 10, No 2 (2014): Agustus
Publisher : Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/jbio.v10n2.2014.p77-84

Abstract

Prodigiosin, the red pigment producedby the bacterium Serratia marcescens, is a secondarymetabolite of the family tripyrrole that has been widely usedas an antibiotic in the multifunction treatment ofantibacterial as well as antifungal. This study was aimed tostudy the effect of Luria-Bertani (LB) broth and nutrientbroth (NB) media suplemented with several concentrationsof FeSO4 and CaCO3 on the production and characteristic ofprodigiosin derived from S. marcescens. The study wasarranged in a completely randomized factorial design withfour replications. The LB and NB media were supplementedwith 0, 2.5, 5, and 10 mM CaCO3 and 0, 0.25, 0.5, and 1 mMFeSO4. Results showed a red pigment produced by S.marcescens when cultured on both LB and NB media. Redlikepigmentation was varied when supplemented withdifferent concentration of Fe2+ and Ca2+. The higher theconcentration of Fe2+, the more intense the red color,conversely, the higher the concentration of Ca2+, the lighterthe red color. The interaction was found between the mediaand concentrations of CaCO3 and FeSO4 on the productionof prodigiosin. The highest prodigiosin production wasobtained on NB media supplemented with FeSO4.Meanwhile, the addition of CaCO3 did not affect theprodigiosin production. An addition of 1 mM FeSO4 to LBand NB media produced crude prodigiosin of 486.0 mg/mland 489.0 mg/ml, respectively. Based on purification bycolumn chromatography using silica gel, the prodigiosinproduction on LB and NB media was 378 mg/ml and 450mg/ml, with the purity level of 77.8% and 92%, respectively.Detection of prodigiosin by thin-layer chromatography usingsilica gel showed the red pigment had Rf value of 0.83 andbioautography assay showed there was an antibacterialactivity against Xanthomanas oryzae pv. oryzae.
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 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 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 Nurfahmi, Riziq Ilham 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 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,