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PHYTOREMEDIATION OF MERCURY CONTAMINATED SOILS IN A SMALL SCALE ARTISANAL GOLD MINING REGION OF INDONESIA Oh, Kokyo; Takahi, Sachiko; Wedhastri, Sri; Sudarmawan, Hardita Librasanti; Rosariastuti, Retno; Prijambada, Irfan Dwidya
International Journal of Biosciences and Biotechnology Vol 3 No 1 (2015)
Publisher : Faculty of Agriculture, Udayana University in cooperation with Asia-Oceania Bioscience and Biotechnology Consortium (AOBBC)

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Abstract

In the small gold mining regions of Indonesia, the tailings or waste water containing mercury commonly may be released into agricultural lands resultimg soil contamination. Phytoremediation is a low-cost and environmental friendly alternative to traditional techniques such as soil heating, soil removal, and soil washing. In this study, a sweet sorghum combined with the inoculation of a rhizobacteria, Agrobacterium tumefaciens, was tested in a field experiment with mercury contaminated soil from a small scale gold mining. Plant growth, uptake and accumulation of mercury by the sweet sorghum, and effects of the Agrobacterium tumefaciens inoculation on mercury accumulation were investigated. The average of mercury content in the soil was 3.76 mg/kg. The results showed that the sorghum grew well, and the inoculation of Agrobacterium tumefaciens promoted the plant growth, but did not increased the mercury concentration in both root and stem parts of the sorghum. The accumulation of mercury was 6.2?/plant for sorghum without Agrobacterium tumefaciens, and 14.0?/plant for sorghum with Agrobacterium tumefaciens. It was estimated that the phytoremediation efficiency of mercury was 414 and 934 mg/ha for sweet sorghum without Agrobacterium tumefaciens inoculation and with Agrobacterium tumefaciens inoculation, respectively.
SELEKSI ISOLAT BAKTERI AMILOLITIK DARI RHIZOSFER CANNA EDULIS, KERR. UNTUK PRODUKSI POLI HIDROKSI ALKANOAT DARI LIMBAH CAIR TAPIOKA Nurhayati, Nurhayati; Radjasa, Ocky Karna; Prijambada, Irfan Dwidya
Jurnal Rekayasa Proses Vol 11, No 2 (2017)
Publisher : Departemen Teknik Kimia Fakultas Teknik Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (250.8 KB) | DOI: 10.22146/jrekpros.33194

Abstract

Petrochemical-based plastic waste accumulated in landfills have been posing serious threat to the environment as this kind of plastics are non-biodegradable. Replacing petrochemical-based plastics with biodegradable plastics constitutes a challenging solution both in terms of mechanical design of the process and most importantly the availability of powerful local microorganism for the process. Therefore, the current study was searching for appropriate local microorganisms for poly hydroxyl alkanoate (PHA) production from starch waste, which was considered as one of cheap carbon sources. Waste water of cassava industry is a good resource of such starch waste water. The microbes were isolated from Canna edulis, Kerr. rhizosphere from Cangkringan.  The expected isolates were the bacteria enable the coupling of carbon catabolic pathways with PHA anabolic pathways. It was found that ten isolates were able to use waste water of cassava flour industry as carbon source. The PHA quantitative analysis by spectrophotometer showed that the isolate of Bacillus sp. C8 produced the highest PHA of 2,095 g/L. Further FTIR analysis showed specific bands near 1363,67 cm-1, 1641,42 cm-1, 2929,87 cm-1, 3408,22 cm-1 wavelengths which revealed the presence of CH3, ester carbonyl group (C=O), C-H and terminal OH group of PHA. ABSTRAKAkumulasi sampah plastik berbasis petrokimia di tempat pembuangan sampah mengganggu lingkungan karena plastik sifatnya tidak mudah didegradasi secara biologi dan sangat tahan di lingkungan. Penggantian plastik yang berasal dari bahan petrokimia dengan bahan plastik yang mudah terdegradasi secara biologi merupakan tantangan tersendiri, baik dari sisi perancangan proses maupun ketersediaan mikrobia lokal yang sesuai untuk proses tersebut. Oleh karena itu, penelitian ini dilakukan sebagai upaya untuk mendapatkan bakteri lokal penghasil PHA yang mampu mengkonsumsi substrat berupa pati. Substrat pati dipilih karena ketersediaan limbat industri tapioka sebagai bahan baku potensial dan murah untuk produksi PHA. Bakteri amilolitik untuk produksi PHA telah berhasil diisolasi dari rhizosfer Canna edulis, Kerr. di Cangkringan, Sleman, Yogyakarta, Indonesia. Bakteri yang diisolasi merupakan bakteri dengan kemampuan memproduksi PHA dan memiliki kemampuan melakukan rangkaian reaksi pada limbah cair industri tapioka dan rangkaian reaksi pembentukan PHA. Telah berhasil didapatkan 10 bakteri yang memiliki aktivitas amilolitik dan dapat menghasilkan PHA  menggunakan limbah cair industri tapioka. Analisis kuantitatif PHA menggunakan spektrofotometer menunjukkan bahwa isolat Bacillus sp. C8 menghasilkan PHA paling tinggi sebesar 2,095 mg/mL. Analisis hasil metabolism isolat C8 menggunakan FTIR memperlihatkan puncak spesifik 1363,67 cm-1, 1641,42 cm-1, 2929,87 cm-1, 3408,22 cm-1 adalah verifikasi adanya CH3, C=O, C-H dan OH dari PHA.
Ethanol Production by Fermentation of Various Sweet-Stalk Sorghum Juices Using Various Yeast Strains Widianto, Donny; Arofatullah, Akbar; Yuwono, Triwibowo; Prijambada, Irfan Dwidya
Indonesian Journal of Biotechnology Vol 15, No 2 (2010)
Publisher : Universitas Gadjah Mada

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Abstract

The ethanol production by fermentation of sweet-stalk sorghum juice is affected by the juice composition and the capability of the yeast strain to ferment it. Eight yeast strains were tested on their growth and ethanol fermentation abilities in sweet-stalk sorghum juices extracted from three cultivars of sweet sorghum. The best specific growth rate of the yeast strains grown aerobically in the yeast extract peptone dextrose (YEPD) broth and the sweet-stalk sorghum juices of KCS105, FS501, and FS902 cultivars, were achieved by OUT7903, OUT7913, OUT7903, and OUT7027 yeast strains, respectively. However, the best specific CO2 evolution rate of the yeast strain during fermentation of the juices was achieved by OUT7027 yeast strains. The highest ethanol concentration, ethanol yield, and sugar conversion efficiency (SCE) were obtained by strain OUT7921 when it was employed to ferment sweet-stem sorghum juice of FS902 cultivar. It was also observed that the juice extracted from sweet-stalk sorghum of FS902 cultivar is the most suitable medium for all yeast strains to achieve their best fermentation abilities. Thus, it is likely that the growth and ethanol production ability of a yeast strain in sweet-stalk sorghum juice depend on the physiological responses of the yeasts to nutrientcomposition of the sorghum juice and the sorghum cultivar from which the juice was extracted.Key words : Sweet-stalk sorghum juice, ethanol, fermentation, yeast
Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia Wedhastri, Sri; Fardhani, Dinar Mindrati; Kabirun, Siti; Widada, Jaka; Widianto, Donny; Evizal, Rusdi; Prijambada, Irfan Dwidya
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

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

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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
Ethanol Fermentation on Mixed Sugars Using Mixed Culture of Two Yeast Strains ., Jasman; Prijambada, Irfan Dwidya; Hidayat, Chusnul; Widianto, Donny
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

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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
Diversity of Dibenzofuran-Utilizing Bacteria Isolated by Direct-Plating and Enrichment Methods Prijambada, Irfan Dwidya; Widada, Jaka; Kusumaningtyas, Pintaka; Suryawan, Dhani
Indonesian Journal of Biotechnology Vol 17, No 1 (2012)
Publisher : Universitas Gadjah Mada

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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.
Identification of Protease Producing Halophilic Bacteria from Bledug KuwuMud Volcano Rohman, Muhammad Saifur; Prijambada, Irfan Dwidya; Indriyani, Yohanna Anisa; Hendrosatriyo, Heri
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 (221.147 KB) | DOI: 10.22146/ijbiotech.15995

Abstract

The objective of this research was to isolate and identify the halophilic bacteria from Bledug Kuwu-mudvolacano having an ability to produce proteolytic enzyme. From this work, 6 bacterial isolates were obtainedfrom mud and water samples using artificial sea water media after incubation at room temperature. Threeout of the 6 isolates (BKL-3, BKL-5, and BKA-1) were selected for further analysis. BKL-3, BKL-5 and BKA-1exhibited an ability to grow at salt concentration greater than 10%. BKL-3 could grow on media supplementedwith 15% of salt, meanwhile BKL-5 and BKA-1 could grow at 20% of salt, respectively. Furthermore, thoseisolates also exhibited proteolytic activity when they were grown on casein media. The phylogenetic analysisbased on the 16SrRNA gene sequences showed that the BKL-3 belong to the group of Bacillaceae, whilst BKL-5and BKA-1 isolates were relatively distance from the group of Halomonadaceae. Therefore, BKL-5 and BKA-1could be considered as the allegedly new species that were separated from Halomonadaceae
Selection of Yeast Strains for Ethanol Fermentation of Glucose-FructoseSucrose Mixture Jasman, J.; Prijambada, Irfan Dwidya; Hidayat, Chusnul; Widianto, Donny
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.16001

Abstract

This study was aimed to compare the ability of some yeast strains to consume sugars (sucrose, glucoseand fructose) and to convert them into ethanol during fermentation. The results of this comparison will be thebasis of considerations in choosing the right strain to be used as a mixed culture to increase the productionof ethanol from substrate containing a mixture of sucrose, glucose and fructose, such as juice of cane andsweet sorghum. The study was conducted using fermentation in substrate consisting of glucose, fructose,and sucrose separately, glucose-fructose mixture, and glucose-fructose-sucrose mixture using some yeaststrains: FNCC3012, OUT7009, OUT7027, OUT7055, OUT7080, OUT7096, OUT7903, OUT7913, and OUT7921.Following the fermentation, analysis of the produced ethanol and the remaining sugar was conducted. Theresults of study indicated that the strains with the highest substrate consumption were OUT7921, OUT7096,OUT7055, OUT7027, and OUT7913 for glucose, fructose, glucose-fructose mixture, sucrose, and glucosefructose-sucrose mixture, respectively. Strains that produced highest concentration ethanol were OUT7096 inglucose and sucrose substrates, OUT7921 in substrate of glucose-fructose mixture and sucrose, OUT7913 insubstrate of glucose-fructose-sucrose mixture. Upon consideration of each strain capacity, both in consumingsugar and producing ethanol, the recommended strains for use in mixed culture in bioethanol fermentationusing mixed substrate of glucose, fructose and sucrose are OUT7096, OUT7913, and OUT7921.
Ethanol Fermentation on Mixed Sugars Using Mixed Culture of Two Yeast Strains Jasman, J.; Prijambada, Irfan Dwidya; Hidayat, Chusnul; Widianto, Donny
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