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All Journal Jurnal Ilmu Tanah dan Lingkungan (Journal of Soil Science and Environment) International Journal of Biosciences and Biotechnology Jurnal Ilmu Lingkungan Journal of Tropical Soils Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Indonesian Journal of Biotechnology Jurnal Perlindungan Tanaman Indonesia Jurnal Ecolab Jurnal Rekayasa Proses
Irfan Dwidya Prijambada
Staf Pengajar Fakultas Pertanian UGM
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Environmental Science Immunology & microbiology Materials Science & Nanotechnology

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Cloning of Thermostable DNA Polymerase Gene from a Thermophilic Brevibacillus sp. Isolated from Sikidang Crater, Dieng Plateu, Central Java Lucia Dhiantika Witasari; Irfan Dwidya Prijambada; Jaka Widada; Dionysius Andang Arif Wibawa
Indonesian Journal of Biotechnology Vol 15, No 2 (2010)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (239.792 KB) | DOI: 10.22146/ijbiotech.7825

Abstract

Thermostable DNA polymerase has an important role for amplifying small amount of DNA through polymerase chain reaction (PCR). Thermophillic bacteria Brevibacillus sp. was isolated from Sikidang Crater, Dieng Plateu, Central Java. Previous study showed that crude protein of the isolate could be used in PCR. Unfortunately, like most native thermostable enzymes, the thermostable DNA polymerase of the isolate is synthesized in a very low level and therefore is cumbersome to purify. The purpose of this research is to clone thermostable DNA polymerase gene of the isolate. The DNA polymerase gene was amplified by means of PCR using spesific primers. The amplified fragment was then isolated, purified, and ligated into the pGEM-T cloning vector. The recombinant plasmid was then transformed to competent E. coli JM109 cells using heat shock method. The cloned thermostable DNA polymerase gene from the thermophilic isolate was then characterized for its nucleotide base sequence. The result showed that the DNA Pol I gene was successfully be amplified from the isolate DNA genom, resulting in ± 2,7 kb DNA fragment in length. Sequence analysis of segment of targeted gene showed high similarity to that of thermostable DNA polymerase genes from other Bacillus.Key words : Thermostable DNA Pol I, Brevibacillus sp., PCR, cloning
Diversity of Dibenzofuran-Utilizing Bacteria Isolated by Direct-Plating and Enrichment Methods Irfan Dwidya Prijambada; Jaka Widada; Pintaka Kusumaningtyas; Dhani Suryawan
Indonesian Journal of Biotechnology Vol 17, No 1 (2012)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (160.616 KB) | DOI: 10.22146/ijbiotech.7849

Abstract

The effect of enrichment bias on the diversity of Dibenzofuran (DBF)-degrading bacteria recovered from soil was evaluated by direct plating, plating after in-soil adaptation, and plating after batch culture enrichment. Among colonies appeared on Bushnell Haas agar with DBF as the sole carbon source, 119 colonies (49, 38, and 32 from direct plating, plating after in-soil adaptation, and plating after batch culture enrichment, respectively) were arbitrarily selected based on the appearance of the colonies. Total DNA were then extracted from the rest of the colonies and analyzed for their diversity using Ribosomal Intergenic Spacer Analysis (RISA). Number of DNA bands obtained from direct plating was higher than the ones obtained after in-soil enrichment and batch culture enrichment. The RISA bands obtained from direct plating were also found to be distributed more evenly than the ones obtained after in-soil enrichment and batch culture enrichment. Dominant bands were observed on RISA from samples obtained after in-soil enrichment and batch culture enrichment. Out of 119, only 9 isolates were consistently able to grow on Bushnell-Haas broth with DBF as the sole carbon source as indicated by broth turbidity. All of the isolates were obtained from soil samples which were enriched in a batch culture. Some of the isolates were able to degrade more then 80 % DBF in the minimal medium.
Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia Sri Wedhastri; Dinar Mindrati Fardhani; Siti Kabirun; Jaka Widada; Donny Widianto; Rusdi Evizal; Irfan Dwidya Prijambada
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (183.716 KB) | DOI: 10.22146/ijbiotech.7879

Abstract

Legume nodulating bacteria (LNB), known also as rhizobia, are soil bacteria, which are able to form rootnodules and fi x nitrogen in the leguminous plants. The LNB availability in the soil depends on the type ofagroecosystem, where plant grows. In this study, we isolated LNB from the shrub agroecosystem in Sumatera,Indonesia, and obtained four selected bacterial strains. Among them, the isolate UGM48a formed root nodulein Macroptilium atropurpureum and showed highest number of nitrogenase activity. UGM48a also contains nifHand nodA genes. An analysis of the PCR-amplifi ed 16S rDNA and BLASTn analysis showed that UGM48adisplayed 96% similarity with Achromobacter xylosoxidans. In addition, UGM48a were successfully nodulatedGlycine max (L.) merr var. wilis. This is the fi rst report detecting A. xylosoxidans as nodule-forming species forGlycine max possesing the positive copy of nodA gene. Keywords : Legume Nodulating Bacteria, shrub agroecosystem, Achromobacter xylosoxidans, nodA, Glycine max
Ethanol Fermentation on Mixed Sugars Using Mixed Culture of Two Yeast Strains J. Jasman; Irfan Dwidya Prijambada; Chusnul Hidayat; Donny Widianto
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (162.484 KB) | DOI: 10.22146/ijbiotech.7880

Abstract

The objective of this study was to evaluate the use of mixed cultures of the recommended yeast strainsfrom a previous study on ethanol fermentation using a substrate mixture consisting of sucrose, glucose, andfructose. There were three mixed (combination) cultures namely OUT7096/OUT7913, OUT7096/OUT7921,and OUT7913/OUT7921. The fermentation medium contained sugar mixture consisting of glucose, fructose,and sucrose with a composition generally close to the composition of sugars in sweet sorghum juice. Overall,fermentation is carried out in two stages. First fermentation was performed using the three mixed culturesto determine the best combination based on the concentration of ethanol produced and the concentration ofresidual sugar. Second fermentation was conducted using the best mixed culture obtained from the fi rst stage.This second stage was intended to describe the pattern of the changes in the concentration of ethanol, sugarsand biomass during the fermentation progresses and to determine some kinetic parameters namely ethanolyield (Yp/s), growth yield (Yx/s) and specifi c growth rate (μ). The results of the fi rst fermentation showed thatthe best mixed culture was OUT7913/OUT7921 and the subsequent fermentation using this culture providethe highest ethanol yield (Yp/s) = 0.47 g.g-1 that was reached at 53rd hour, growth yield (Yx/s) = 0.425 g.g-1, andμ = 0.12 hour-1.Keywords : fermentation, ethanol, mixed culture, mixed sugar
MERCURY ACCUMULATION IN GOLD MINE TAILING BY SWEET SORGHUM INOCULATED WITH CHROMIUM UPTAKE ENHANCING RHIZOBACTERIA Desi Utami; Sachiko Takahi; Irfan Dwidya Prijambada
International Journal of Biosciences and Biotechnology Vol 1 No 2 (2013)
Publisher : Central Laboratory for Genetic Resource and Molecular Biology, Faculty of Agriculture, Udayana University in cooperation with Asia-Oceania Bioscience and Biotechnology Consortium (AOBBC)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (226.91 KB)

Abstract

Small scale gold mining provides an important source of income for miners in rural communities whereeconomic alternatives are extremely limited. However, it releases mercury which damages the environmentand poses risks to those in the nearby community. Phytoremediation is considered as a simple and costeffective method for the cleanup of heavy metal from contaminated soil. Phytoremediation is a technologythat uses plants to degrade, extract, contain, or immobilize contaminants from soil and water. In particular,phytoextraction is the uptake of contaminants by plant roots and translocation within the plants to shootsor leaves. Contaminants are then removed by harvesting the plants. The objective of this research is toexamine the ability of sweet sorghum and its inoculation using chromium uptake enhancing rhizobacteriafor phytoremediation of gold mine tailing. Two varieties of sweet sorghum were used in this experiment, i.e.FS501, and KCS105. The seed of the sweet sorghum was sown in mercury containing tailing or a mixture ofit with uncontaminated soil. Plant biomass and its mercury content were determined 35 days after sowing.Only FS501 was able to grow on tailing containing 26.94ppm of mercury. Inoculation of the sweet sorghumwith the rhizobacteria does not aff ect its biomass but increase its mercury uptake signifi cantly. Mixing thetailing material with uncontaminated soil causes an increase in biomass but reduce the mercury content inplant signifi cantly. As a result, the amounts of removable mercury decrease signifi cantly. Inoculation withthe rhizobacteria has no eff ect on mixed material
Konstruksi Open Reding Frames (ORF) Artifisial Berukuran 798-bp yang Menyandi Protein dengan Urutan Asam Amino Acak Irfan Dwidya Prijambada; Khotibul Umam Al-Awally; Muhammad Saifur Rohman; Wayan Artama
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 9, No 1 (2004): February 2004
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v9i1.2828

Abstract

Penyusunan pustaka dari open reading frames (ORF) buatan yang tersusun atas 798 bp (pasangan basa), 576  di antaranya tersusun secara acak, yang mampu menyandi 266 asam amino telah berhasil dilakukan. Dalam upaya penyusunan tersebut diperoleh 32 transforman,  lima di antaranya membawa ORF buatan. Dari kelima transforman yang membawa ORF buatan tersebut, hanya satu transforman yang mampu berekspresi dan menyandi suatu protein. Protein yang dihasilkan memiliki ukuran 17 kDa, berukuran lebih kecil daripada ukuran yang diharapkan yaitu 29 kDa.
PERAN RHIZOBAKTERI DALAM FITOEKSTRAKSI LOGAM BERAT KROMIUM PADA TANAMAN JAGUNG MMA Retno Rosariastuti; Ali Pramono; Ngadiman Ngadiman; Irfan D Prijambada
Jurnal Ecolab Vol 6, No 1 (2012): Jurnal Ecolab
Publisher : Pusat Standardisasi Instrumen Kualitas Lingkungan Hidup Laboratorium Lingkungan (P3KLL)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20886/jklh.2012.6.1.38-50

Abstract

Logam berat bersifat persisten dalam lingkungan dan diketahui mengubah biodiversitas, struktur dan fungsi ekosistem tanah. Remediasi tanah terkontaminasi logam menjadi penting, karena tanah sebagai media penghasil bahan pangan. Pendekatan konvensional untuk remediasi tempat yang terkontaminasi logam meliputi fisika dan kimia, namun aplikasi proses-proses ini terbatas karena kendala teknologi dan ekonomi. Oleh karena itu diperlukan metode remediasi yang murah, aman dan ramah lingkungan seperti bioremediasi. Penelitian ini bertujuan untuk mengetahui kemampuan rhizobakteri dalam membantu fitoekstraksi logam berat kromium pada tanaman jagung. Tahapan penelitian meliputi 1) uji toleransi bakteri terhadap Cr(VI), 2) uji reduksi Cr(VI), dan 3) uji serapan Cr(VI) pada tanaman jagung. Hasil penelitian menunjukkan bahwa Isolat 27 toleran terhadap toksisitas Cr(VI) pada konsentrasi 15 ppm. Isolat 27 mereduksi Cr(VI) secara sempurna dalam waktu 18 jam. Isolat 27 membantu fitoekstraksi logam kromium pada tanaman jagung sebesar 241 kali dibandingkan kontrol. Perlu penelitian lebih lanjut untuk mengetahui jenis asam yang berperan dalam mekanisme fitoekstraksi pada tanaman jagung. Isolat 27 dapat digunakan sebagai inokulan dalam fitoremediasi dan pemacu pertumbuhan tanaman.
Peruraian anaerobik termofilik palm oil mill effluent dengan variasi konsentrasi substrat Kartika, Roberty Wisnu Alvania; Desman, Nadiya Salsabila; Prijambada, Irfan D.
Jurnal Rekayasa Proses Vol 16 No 1 (2022): Volume 16, Number 1, 2022
Publisher : Jurnal Rekayasa Proses

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jrekpros.69574

Abstract

Tingginya tingkat pengolahan kelapa sawit di Indonesia menghasilkan limbah palm oil mill effluent (POME). Limbah POME memiliki kandungan \textit{chemical oxygen demand} (COD) mencapai 100.000 mg/L yang dapat mencemari ekosistem jika dibuang ke lingkungan tanpa perlakuan yang tepat. Salah satu perlakuan yang digunakan dalam menangani limbah POME adalah peruraian anaerobik termofilik. Keuntungan dari proses ini adalah menghasilkan gas metana yang dapat digunakan sebagai energi alternatif. Konsentrasi substrat memengaruhi proses peruraian anaerobik. Penelitian pendahuluan ini bertujuan untuk mengetahui performa proses peruraian anaerobik termofilik pada berbagai konsentrasi POME sebagai substrat dengan suhu 55oC. Proses peruraian anaerobik menggunakan konsentrasi substrat 16.000, 11.000, dan 5.000 mg sCOD/L. Inokulum yang digunakan adalah digested cow manure (DCM). Proses peruraian dilakukan menggunakan sistem kontinyu dengan didahului proses aklimatisasi secara batch. Hasil penelitian menunjukkan konsentrasi 16.000 dan 11.000 mg sCOD/L menghasilkan lebih banyak gas metana. Namun, yield metana pada konsentrasi 16.000 dan 11.000 mg sCOD /L tidak berbeda signifikan berdasarkan uji Tukey (p=0,05). Konsentrasi POME 5.000 mg sCOD/L menghasilkan gas metana yang lebih rendah dan terjadi penurunan drastis setelah hari ke-85. Hal ini disebabkan penurunan konsumsi sCOD yang diiringi dengan peningkatan kadar volatile fatty acid (VFA) menunjukkan akumulasi asam yang menghambat proses pembentukan gas metana.
Perbandingan jenis media imobilisasi terhadap kinerja proses peruraian anaerob termofilik palm oil mill effluent Sakka, Deni Frans; Millenia, Salsabilla Fitri; Prijambada, Irfan Dwidya
Jurnal Rekayasa Proses Vol 16 No 1 (2022): Volume 16, Number 1, 2022
Publisher : Jurnal Rekayasa Proses

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jrekpros.69582

Abstract

Palm oil mill effluent (POME) merupakan limbah cair dengan kandungan organik yang tinggi sebagai bahan baku produksi biogas melalui peruraian anaerob. Dalam peruraian anaerob, efek washout selalu menjadi masalah seiring dengan meningkatnya organic loading rate (OLR) pada sistem kontinu. Oleh karena itu, dilakukan penambahan media imobilisasi untuk mengurangi risiko tersebut. Penelitian ini bertujuan untuk mengevaluasi pengaruh jenis dan pengaturan media imobilisasi terhadap kinerja peruraian anaerob termofilik POME. Dua media imobilisasi yang diuji yaitu media jenis carbon fiber textile (CFT) dan media berupa partikel zeolit alam. Kinerja proses anaerob ditentukan dengan mengukur konsentrasi asam lemak volatil (VFA), soluble chemical oxygen demand (sCOD) dan yield metana (CH4). Hasil penelitian ini menunjukkan bahwa reaktor dengan media imobilisasi menghasilkan yield CH4 yang lebih tinggi dibandingkan dengan reaktor tanpa media imobilisasi. Yield CH4 reaktor dengan zeolit alam sebesar 0,3487 L/g sCOD, 0,3050 L/g sCOD pada reaktor dengan media CFT dan 0,2873 L/g sCOD pada reaktor tanpa media imobilisasi. Selain itu, hanya zeolit alam yang dapat mempertahankan performa reaktor saat mengalami gangguan peningkatan suhu secara tiba-tiba dengan masa recovery selama 14 hari.
Secretion of Organic Acids by Phosphate Solubilizing Bacteria Prijambada, Irfan Dwidya; Widada, Jaka; Kabirun, Siti; Widianto, Donny
JOURNAL OF TROPICAL SOILS Vol. 14 No. 3: September 2009
Publisher : UNIVERSITY OF LAMPUNG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5400/jts.2009.v14i3.245-251

Abstract

Phosphorus availability is a major limiting for crop production.  Bacterial solubilization of insoluble inorganic phosphate has been studied as a means of providing available phosphorus for crop production.  Bacterial abilities to solubilize calcium phosphate and rock phosphate have been identified to be related with their abilities to produce gluconic acid and ketogluconic acid.  However, there is no information regarding the relationship between bacterial ability to solubilize aluminum phosphate and their ability to produce organic acids.  This study was conducted to investigate the relationship between bacterial ability to solubilize calcium and aluminum phosphates with their ability to produce organic acids.  Bacterial ability to solubilize calcium and aluminum phosphates were determined as the concentration of soluble phosphate in the filtrate of bacterial cultivation media, while bacterial ability to produce organic acids were assessed from the accumulated organic acids in its.  The results showed that bacterial abilities to solubilize calcium and aluminum phosphates well related to their abilities to produce organic acids.  Organic acids related with the solubilization of calcium phosphate differ from the ones relatedAlam, S., S. Khalil, N. Ayub,  and M. Rashid. 2002. In vitro solubilization of inorganic phosphate by phosphate solubilizing microorganisms (PSM) from maize rhizosphere. Int. J. Agri. Biol. 4: 454-458.Beauchemin, S., D. Hesterberg, J. Chou, M. Beauchemin, R.R. Simard, and D.E. Sayers. 2003. Speciation of phosphorus in phosphorus-enriched agricultural soils using X-ray absorption near-edge structure spectroscopy and chemical fractionation. J. Environ. Qual. 32:1809–1819.Bolan, N.S., R. Naidu, S. Mahimairaja, dan S. Baskaran. 1994. Influence of low-molecular-weight organic acids on the solubilization of phosphates. Biol. Fertil. Soils 18: 311-319.Cline, G.R., P.E. Powell, P.J. Szaniszlo, dan C.P. Reid. 1983. Comparison of the abilities of hydroxamic and other natural organic acids to chelate iron and other ions in soil. Soil Sci. 136: 145-157.Curtin, D., and J.K. Syers, 2001. Lime-induced changes in indices of soil phosphate availability. Soil Sci. Soc. Am. J. 65:147–152.Fox, T.R., N.B. Comerford, dan W.W. McFee. 1990. Phosphorus and aluminium release from a spodic Horizon mediated by organic acids. Soil Sci. Soc. Am. J. 54: 1763-1767.Hue, N.V., G.R. Craddock, dan F. Adams. 1986. Effect of organic acids on aluminium toxicity in subsoils. Soil Sci. Soc. Am. J. 50: 28-34.Johnson, S.E., and R.H. Loeppert. 2006. Role of organic acids in phosphate mobilization from iron oxide. Soil Sci. Soc. Am. J. 70:222–234.Kumari, A., K.K. Kapoor, B.S. Kundu, and R.K. Mehta. 2008. Identification of organic acids produced during rice straw decomposition and their role in rock phosphate solubilization. Plant Soil Environ. 54: 72–77Lopez-Hernandez, D., D. Flores, G. Siegert, dan J.V. Rodriguez. 1979. The effect of some organic anions on phosphate removal from acid and calcareous soils. Soil Sci. 128: 321-326.Lopez-Pineiro, A., dan A. Garcia-Navarro. 2001. Phosphate fractions and availability in Vertisols of South-Western Spain. Soil Sci. 166: 548-556.Olsen, S.R. dan Sommers, L.E. 1982. 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Aluminium and iron fractions affecting phosphorus solubility and reactions in selected sandy soils. Soil Sci. 166: 940-948.with the solubilization of aluminum phosphate.  Moreover, there is similarity in the production of organic acids related to the solubilization of aluminum phosphates and iron phosphate.
Co-Authors Abd. Rasyid Syamsuri Akbar Arofatullah Al-Awally, Khotibul Umam Ali Pramono Ali Pramono Arofatullah, Nur Akbar Artama, Wayan Chusnul Hidayat Desi Utami Desman, Nadiya Salsabila Dhani Suryawan Dhani Suryawan, Dhani Dinar Mindrati Fardhani Dionysius Andang Arif Wibawa Dionysius Andang Arif Wibawa, Dionysius Andang Donny Widianto Donny Widianto JAKA WIDADA Jasman . Jasman Jasman Kartika, Roberty Wisnu Alvania Khotibul Umam Al-Awally Kurniasari, Irianti Lucia Dhiantika Witasari Lucia Dhiantika Witasari, Lucia Dhiantika Maharani, Rina Millenia, Salsabilla Fitri Muhammad Saifur Rohman Muhammad Saifur Rohman N Ngadiman Ngadiman Ngadiman Pintaka Kusumaningtyas Retno Rosariastuti Rinda Fajrin Aldina, Rinda Fajrin Rusdi Evizal Sachiko Takahi Sakka, Deni Frans SITI KABIRUN Siti Kabirun Siwi Indarti Sri Wedhastri Triwibowo Yuwono Waele, Dirk De Wayan Artama Yudi Sastro Yudi Sastro