NISA RACHMANIA MUBARIK
Department of Biology, Faculty of Mathematics and Natural Sciences, Jl. Raya Darmaga, Bogor 16680, West Java. Indonesia

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Screening and Characterization of Protease Inhibitors from Marine Bacteria Associated with Sponge Jaspis sp. WAHYUDI, ARIS TRI; QATRUNNADA, .; MUBARIK, NISA RACHMANIA
HAYATI Journal of Biosciences Vol 17, No 4 (2010): December 2010
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (172.867 KB) | DOI: 10.4308/hjb.17.4.173

Abstract

Three isolates among 138 sponge-associated bacteria were isolated from Waigeo Island, Raja Ampat West Papua Province, Indonesia, have been shown protease inhibitory activity against subtilisin (serine protease), thermolysin (metalloprotease), and crude extract from pathogenic bacteria (Eschericia coli enteropathogenic/EPEC K.1.1, Staphylococcus aureus, and Pseudomonas aeruginosa). Those three isolates were designated as sponge associated bacteria SAB S-12, SAB S-21, and SAB S-17. A simple casein and Sea Water Complete (SWC) double layer agar method was used to screen the bacteria against pathogenic bacteria producing protease, i.e. EPEC K.1.1, S. aureus, and P. aeruginosa. Among them, SAB S-12 isolate showed no inhibitory zone indicated. The isolate had the highest inhibitory activity against subtilisin and crude extract enzyme of pathogenic bacteria, the inhibitory activity was 91.6 and 98.9%, respectively. In addition, the SAB S-21 isolate had the highest inhibitory activity against thermolysin, it was 70.4%. The optimum pH and temperature for protease inhibition of the three isolates was at pH 7.0-8.0 and 40-50 oC respectively. Based on 16S rRNA gene sequence, the closest related with SAB S-12, SAB-17, and SAB-21 isolates was Providencia sp. (92% identity), Paracoccus sp. (86% identity), and Bacillus sp. (% identity), respectively.
Extracellular Protease Activity of Enteropathogenic Escherechia coli on Mucin Substrate BUDIARTI, SRI; MUBARIK, NISA RACHMANIA
HAYATI Journal of Biosciences Vol 14, No 1 (2007): March 2007
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (32.236 KB) | DOI: 10.4308/hjb.14.1.36

Abstract

Enteropathogenic Escherichia coli (EPEC) causes gastrointestinal infections in human. EPEC invasion was initiated by attachment and aggressive colonization on intestinal surface. Attachment of EPEC alter the intestine mucosal cells. Despite this, the pathogenic mechanism of EPEC infectior has not been fully understood. This research hypothesizes that extracellular proteolytic enzymes is necessary for EPEC colonization. The enzyme is secreted into gastrointestinal milieu and presumably destroy mucus layer cover the gastrointestinal tract. The objective of this study was to assay EPEC extracellular protease enzyme by using mucin substrate. The activity of EPEC extracellular proteolytic enzyme on 1% mucin substrate was investigated. Non-pathogenic E. coli was used as a negative control. Positive and tentative controls were Yersinia enterocolitica and Salmonella. Ten EPEC strains were assayed, seven of them were able to degrade mucin, and the highest activity was produced by K1.1 strain. Both positive and tentative controls also showed the ability to digest 0.20% mucin. Key words: EPEC, protease, mucin, diarrhea
The Use of Acid-Aluminium Tolerant Bradyrhizobium japonicum Inoculant for Soybean Grown on Acid Soils SITUMORANG, ANGELIA REZTY FITRIANI; MUBARIK, NISA RACHMANIA; TRIADIATI, TRIADIATI
HAYATI Journal of Biosciences Vol 16, No 4 (2009): December 2009
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (54.714 KB) | DOI: 10.4308/hjb.16.4.157

Abstract

Land with low pH soil spread widely in Indonesia can be used for soybean (Glycine max) cultivation, although the production is low. The use of acid tolerant soybean and acid-Al tolerant nitrogen-fixing bacteria was an alternative way to increase soybean productivity on acid soils. This research was conducted to study the influence of acid-Al tolerant Bradyrhizobium  japonicum  on growth of Slamet cultivar soybean planted on acid soils in greenhouse. Three strains of acid-Al tolerant B. japonicum, i.e. BJ 11 (19), BJ 11 (5), and BJ 11 (wt), were used in this experiment. The result showed that inoculation of all acid-Al tolerant B. japonicum strains could increase plant height, shoot and root weight, number of flowers, pods, seeds, seeds dry weight, and shoot and seed nitrogen content.                   Key words: Bradyhizobium japonicum, acid-aluminium tolerant, soybean, Slamet cultivar
Respon Pertumbunan Tanaman Kedelai terhadap Bradyrhizobium japonicum Toleran Masam dan Pemberian Pupuk di Tanah Masam Triadiati, ,; Mubarik, Nisa Rachmania; Ramasita, Yoan
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol 41, No 1 (2013): Jurnal Agronomi Indonesia
Publisher : Bogor Agricultural University

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Abstract

The use of acid tolerant rhizobacteria such as Bradyrhizobium japonicum is one effort for increasing soybeanproductivity in acid soil. B. japonicum is a N-fixing bacteria that can promote soybean growth through symbiosis with thehost plants. The objective of this study was to investigate the growth and production of soybean var. Wilis inoculated by B.japonicum and NPK inorganic fertilizer application in acid soil. Two isolates of B. japonicum that were BJ 11(19) and BJ11(wt) were used as inoculant for soybean. BJ 11(19) was resulted by transposons mutagenesis, whereas BJ 11(wt) is a wild type of bacteria. Both isolates of B. japonicum were acid tolerant. Soybean was inoculated with BJ 11(19) and BJ 11(wt)combined with compost and nitrogen fertilizer (with two rates). The field experiment was conducted at Cikabayan, Darmaga,in a randomized complete block design with 12 treatments and 3 replicates. The results showed that application of the acidtolerant B. japonicum BJ 11(wt), compost, and nitrogen fertilizer (10 g m-2) increased the plant height, dry weight of shootsand roots, nodule number, dry weight of nodules, nitrogenase activity, number of pod and seed, seed weight, and nitrogencontent of seeds in acid soil.Keywords: acid soil, acid tolerant rhizobia, Bradyrhizobium japonicum, compost, nitrogen fertilizer
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.
ENERGI LISTRIK DARI SEDIMEN LAUT TELUK JAKARTA MELALUI TEKNOLOGI MICROBIAL FUEL CELL Riyanto, Bambang; Mubarik, Nisa Rachmania; Idham, Fitriani
Jurnal Pengolahan Hasil Perikanan Indonesia Vol 14, No 1 (2011): Jurnal Pengolahan Hasil Perikanan Indonesia
Publisher : Departement of Aquatic Product Technology

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Abstract

Sediment microbial fuel cell (SMFC) is one form of the microbial fuel cell (MFC) that can convert organic complex material in the sediment to generate electrons. This research was conducted to determine the characteristicsof marine sediments from the Bay of Jakarta, to know the amount of electric current can be generated through SMFC, and to identify bacteria at the anode SMFC. This research was conducted in several stages which include the characterization of marine sediment samples, making SMFC circuit, electric current measurement, characterization SMFC substrate, and the isolation, characterization, and identi cation of bacteria. The study shows that marine sediments of Jakarta Bay have characteristics which include silty clay loam texture, organic carbon 2.19%, total nitrogen 0.19%, and phosphorus 128 ppm. The electric current generated by the SMFC using  xed value resistors 820 Ω ± 5% reach peak production of electric currents on day 21, that is 139.51 mA/m2 with SMFC substrate having organic carbon 1.88%, total nitrogen 0.15%, and phosphorus 88 ppm. Isolation of bacteria at the anode was found three types of isolates, that suspected are Aeromonas hydrophila, Acinetobacter sp., and Bacillus marinus.Keywords: electrical energy, Jakarta bay, marine sediment, sediment microbial fuel cell
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
Screening of Proteolytic Enzymes of Streptomyces sp. Local Strain and Their Characterization YURATMOKO, DERI; MUBARIK, NISA RACHMANIA; MERYANDINI, ANJA
Microbiology Indonesia Vol 1, No 2 (2007): August 2007
Publisher : Indonesian Society for microbiology

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Abstract

Protease of two Streptomyces sp. strain were chosen for characterization because of the large clear zone surrounding the colony in nutrient agar media containing 1% (w/v) skim milk. Extracellular protease from the two isolates SLW 8-1 and 45I-3 were characterized following incubation of the isolate in Nutrient Broth media containing skim milk or chicken feather (1%). The optimum activity of the protease SLW 8-1 was at pH 9 and 80 ºC, whereas that of the keratinase was at pH 6.5 and 70 +C. Protease of strain 45I-3 showed its optimum activity at pH 7.5 and 50 ºC whereas the keratinase was at pH 8.5 and 80 ºC.
Genetic Diversity of Plant Growth Promoting Rhizobacteria of Bacillus sp. Based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis SYAMSUL BAHRI, SYAMSUL BAHRI; WAHYUDI, ARIS TRI; MUBARIK, NISA RACHMANIA
Microbiology Indonesia Vol 3, No 1 (2009): April 2009
Publisher : Indonesian Society for microbiology

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Abstract

Plant-growth promoting rhizobacteria (PGPR) are rhizosphere associated soil-borne bacteria that can enhance plant growth and inhibit the development of root pathogens. Many soil bacteria have been used as PGPR, and one of them is Bacillus sp. The implementation of PGPR is constrained by genotype fluctuation that makes it inactive on the rhizosphere. Our previous study had characterized and revealed that 11 Bacillus sp. isolated from the soybean plant rhizosphere were PGPR. To asses and compare the genetic diversity of these isolates, Amplified Ribosomal DNA Restriction Analysis (ARDRA) and DNA sequence analysis of 16S rRNA were conducted. The construction of Neighbor-joining trees and bootstrap analysis of 100 resamples of ARDRA and 16S rRNA gene sequences were performed using Treecon software for windows ver. 1.3b. ARDRA analysis was done by using four restriction enzymes (RsaI, HaeIII, CfrI and HinfI), resulting in four phylotypes, respectively phylotype I (Bacillus sp. Cr24, Cr33, Cr64 and Cr68), phylotype II (Bacillus sp. Cr 31 and Cr66), phylotype III (Bacillus sp. Cr44 and Cr71) and phylotype IV (Bacillus sp. Cr67, Cr28 and Cr69). Results of BLASTN from 16S rRNA gene sequences showed that these isolates are genetically diversed. The evolution relationship of Bacillus sp. could be shown by the 16S rRNA gene sequences analysis, while ARDRA based on the digestion sites showed their variability.
Effect of pH, Temperature and Medium Composition on Xylanase Production by Bacillus sp. AQ-1 and Partial Characterization of the Crude Enzyme WAHYUNTARI, BUDIASIH; MUBARIK, NISA RACHMANIA; SETYAHADI, SISWA
Microbiology Indonesia Vol 3, No 1 (2009): April 2009
Publisher : Indonesian Society for microbiology

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Abstract

Bacillus sp. AQ-1 was isolated from household aquarium sediment. The isolate produced extracellular xylanolytic enzymes on xylan containing agar medium. Based on morphological, and physiological analysis, the isolate was identified as Bacillus sp. AQ1. The effect of temperature and pH on isolate growth and xylanase production were observed. The best condition observed for the enzyme production in Luria Broth supplemented with 0.5% oat spelt xylan medium was at 40 °C pH 7. The maximum enzyme production was 0.23 U mL-1 after 20 h of fermentation. Two different medium compositions (A and B) were examined for xylanase production. The maximum growth of the isolate and the xylanase production was better in A medium. Replacing oat spelt xylan in medium A with fruitless oil palm bunch in the medium caused the growth slightly slower than that of in the original formula. However, the xylanase production was 3 times higher in fruitless oil palm bunch medium. Optimum activity of the crude enzyme was observed at 60 °C and pH 7. Each ml of the crude enzyme contained 55.21 U xylanase, 8.12 U amylase and 0.50 U carboxymethylcellulase