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"DEnaturing gradient get electrophoresis was used to identify the bacterial community at the Gedongsongo (WGS-2) hot spring....."

"Many microorganisms capable of degrading petroleum components have been isolated and few of the seem to be important for petroleum biodegradation in natural environments...."

"Eksplorasi bakteri termofilik di Indonesia sangat penting untuk berbagai aplikasi industri. Penelitian ini bertujuan untuk identifikasi Gen 16S-rRNA dari bakteri termofilik yang terdapat di Mata Air Panas Cisolong, Banten. Ekstraksi dilakukan dengan dua metode yaitu komersial GeneAll® Exgene™ dan LOC ChipGenie® Edition P. Hingga saat ini, belum ada yang melakukan identifikasi bakteri dari mata air panas dengan menggunakan LOC untuk purifikasi DNA. Oleh karena itu, dalam penelitian ini dilakukan pengujian identifikasi bakteri dengan membandingkan kedua metode. Harapan kedepannya LOC dapat membantu purifikasi DNA secara langsung sehingga mempermudah identifikasi tanpa perlu di laboratorium.Penelitian selanjutnya juga akan dilakukan reverse engineering sehingga dapat membuat LOC sendiri. Variabel yang diujikan adalah hasil kemurnian, konsentrasi template DNA, dan identifikasi jenis bakteri. Purifikasi dilakukan dengan variasi jumlah kultur bakteri berdasarkan absorbansi agar dapat mengetahui jumlah bakteri optimum untuk LOC. Didapatkan hasil bahwa bakteri berhasil dipurifikasi menggunakan LOC pada variasi waktu kultur 4 dan 28 jam. Konsentrasi template DNA bakteri yang dihasilkan LOC juga baik dan dapat bersaing dengan kit komersial. Hasil PCR didapatkan bakteri sumber berada pada 1518 bp dan bakteri kolam 1422 bp. Bakteri berhasil diidentifikasi dengan BLAST dan berdasarkan pohon filogenetik, hubungan terdekat bakteri sumber yaitu Geobacillus kaustophilus strain BGSC 90A1 dan bakteri kolam yaitu Geobacillus thermoleovorans strain V0 chromosome.

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Exploration of thermophilic bacteria in Indonesia is important for various industrial applications. This study aims to identify the 16S-rRNA gene from thermophilic bacteria found in Cisolong Hot Springs, Banten. Extraction was carried out by two methods, namely GeneAll® Exgene™ commercial kit and LOC ChipGenie® Edition P. To date, there has not yet been bacteria identification from hot springs using LOC for DNA purification. Therefore, in this study, a bacterial identification test carried out by comparing the two methods. The hope of this research is that in the future, LOC can be directly implemented in DNA purification, making it easier to identify without the need for laboratory procedures. In future research, reverse engineering will also be carried out so that we can make our own LOC. The variables tested were the results of DNA purity, templates concentration, and identification of the type of bacteria. Purification was also carried out by varying the number of bacterial cultures based on absorbance in order to determine the optimum number of bacteria for LOC. It was found that the bacteria were successfully purified using LOC at 4 and 28 hours of culture. The concentration yield of LOC is good and can compete with commercial kits. From the PCR results, it was found that the source bacteria were at 1518 bp and the pool bacteria at 1422 bp. Bacteria were identified by BLAST and based on the phylogenetic tree, the closest relationship to the source bacteria is Geobacillus kaustophilus strain BGSC 90A1 and the pool bacteria is Geobacillus thermolevorans strain V0 chromosome."

"Among twenty one isolates, obtained from "aren" (Aretga Rinnata) vinegar, 10 isolates were identified as acetic acid bacteria, belong to genus Acetobacter. Isolates no. 12 was used as inoculum for vinegar fermentation. Saccharomyces cerevisiae (Y-17) was provided by University of Indonesia Culture Collection.Two hundred fifty grams of pineapple (Ananas comosus) peel was boiled for 1.5 hours and then filtered to obtain the extract. Aquadest was added into substrate to obtain 1 litre of extract and then added with 15% or 20% castor sugar. Substrate was sterilised at 121°C for 10 minutes.Fermentation was carried out in syrup bottle containing 540 ml substrate. Approximately 60 ml of starter containing mix-culture with diffrent ratio of 1 day old S. cer visiae (106 cfu/ml) and 5 days old Acetobacter sp. no.12 {10 cfu/ml) was inoculated into the substrate. The ratio of yeast cells to bacteria were follow: (1:1); (2:1); (3:1} or (4:1). Fermentation was set up in room temperature (3O -- 32°C for 1 month. The concentration of acetic acid was titrated with standarised NaOH.Result of this study showed that substrate with 15% sugar yielded (1.1 - 1.4)% acetic acid. The average acetic acid concentration from substrate with 20% sugar were (0.44 - 0.89%). It was concluded that substrate with 15% sugar gave higher concentration and the best ratio of starter was (1 : 1)."

"Sugar is a very important carbon and energy source for human. Thelocal production of sugar in indonesia is not adequate and alternativesources should be found. Microorganisms (Bacillus amyfoiiquefaciens, B. Iicheniformis, B. cereus, B. circulans, B. megaterium, B. polymyxa, B. stearothermophilus, Pyrococcus woeseg P. furiosus, Clostndium thermosulfurogenes, C. thermohydrosulfuricum, Aspergillus awamorL A. nigen A. oryzae, A. saitoil Mucor rouxianus, Penicillium oxalicum, Rhizopus deleman Aerobacter aerogenes, and Streptomyces) are known as producer ot on-amylase, glucoamylase, and pullulanase enzymes through of starch fermentation which may be converted into a sugar compound. A preliminary study on endophytic bacteria proved their ability to grow on soluble starch, glutinous rice, and pullulan. Pullulanase convert pullulan to maltotriosa. This enzyme may work synergistically with on-amylase and with glucoamylase for a better conversion of starch to glucose. An endophytic bacteria lCMe3 obtained from the Research and Development Centre for Biotechnology LIP! at Cibinong, Bogor was examined on its ability to produce pullulanse _ For this purpose, soluble starch 1%, cassava starch 1%, and pullulan 1% (all wlv), were used as carbon and energy source in Bakshi medium (Bakshi etal., 1993). The concentration of the inoculum_was 1.25 x 10° cells/ml. Incubation was carried out at : 30°C (room temperature) and 37°C (Mapiliandari, 1999), at pH 7.0 (Bakshi et al., 1993) and pH 5.0 (Mapiliandari, 1999). The fermentation process was terminated after 24 - 26 hours. The growth of lCNle3 varied depending on carbon source, temperature, and pH. The best growth was found on pullulan at pH 7.0 and incubation temperature of of 30°C . However, when the pH of the medium was lowered to 5.0 (Mapiliandari, 1999) and the incubation temperature 30°C a higher cell number (79.5) x 108 cells/ml was obtained on pullclan as carbon source. The bacteri was grown on cassava starch medium and the pullulanase activity studied. The synergism of pullulanase with amylase and with glucoamylase to degrade cassava starch was also studied. To obtain the crude enzyme extract, the cell mass was centrifuged with a Sorval RC - 26 Plus centrifuge. The Hltrate was then concentrated with UHF, sedimented with (NH4)2SO4, and dialized with buffer Na-acetat (pH 4.8). Activity of the crude enzyme was examined on cassava starch and onpullulan. The unit activity of enzyme was 1.374 U/ml on cassava starch,1.290 U/ml on pullulan, and the protein content was 0.039 mglml. The activity of the crude enzyme, after treatment with UHF, was 2.225 U/ml for pullulan, 2.527 U/mt for cassava starch, and the protein content was 0.014 mg/ml. The activity of the crude enzyme obtained after sedimentation with 60% saturation of (NH4)2SO4, was 1.156 U/ml for pullulan, 1.162 U/mi for cassava starch, the protein content 0.579 mg/ml. After dialysed with buffer Na-acetate (pH 4.8) the activity was 6.25 U/ml for pullulan, 6.45 U/ml for cassava starch with the protein content of 2.997 mg/ml. To study the optimum pH and temperaturefor the enzyme production, the isolate iCMe3 was grown on Bakshi medium with various pHs, : 4.0, 4.5, 4.8, 5.0, 5.5, 6.0, 6.5, 7.0 and incubated at various temperatures 30°C, 40°C 50°C, 60°C, 70°C, 80°C, 90°C. The optimum pH for enzyme sinthesis on puliulan was 5.0 (4.81 U/ml) and on cassava starch 4.8 (13.27 U/ml). The optimum temperature for enzyme synthesis on pullulan was 40°C (26416 U/ml) and on cassava starch 50°C (22.34 U/ml). The best synergism of pullulanase with on-amylase for both C sources was 25% (dilution of enzyme), while the synergism with glucoamylase was 100% for pulluian and 50% for cassava starch to convere the starch (pullulanand cassava starch) glucose."

"ABSTRAKUndang-undang RI No. 19 tahun 2009, pengesahan konvensi Stockholm tentang bahan pencemar organik yang persisten, dan telah melarang penggunaan kategori insektisida yaitu aldrin, klordan, dieldrin, endrin, heptaklor, heksaklorobenzena, mirex, toxaphene dan poliklorinatbifenil (PCB), serta membatasi penggunaan insektisida diklorodifenildikloroetana (DDT). Faktanya, keberadaan insektisida organoklorin tersebut masih ditemukan di tanah sawah Kabupaten Karawang yaitu aldrin, DDT, endosulfan, endrin, heptaklor dan lindan dengan konsentrasi berkisar antara 1,5 ng/g sampai dengan 5,37 ng/g. Teknologi pengendalian residu pestisida dapat dilakukan melalui ameliorasi secara biologi dengan bioremediasi, secara fisika dengan adsorpsi arang aktif, sedangkan, secara kimia melalui penambahan alum dan lain-lain. Bioaugmentasi adalah introduksi mikroba tertentu pada daerah yang akan diremediasi. Bakteri tempatan potensial pendegradasi heptaklor hasil isolasi adalah Citrobacter sp. Setelah diidentifikasi dengan 16S rRNA, bakteri tersebut adalah Raoultella ornithinolytica B4, bakteri ini golongan Enterobacteriaceae, Gram negatif, dan menghasilkan enzim katalase. Biochar tempurung kelapa (BTK) memiliki sifat adsorben berdasarkan nilai daya serap iod sebesar 570,22 mg/g, luas permukaannya 371,943 m2/g, dan diameter pori 0,4-7,0 mm karena proses karbonasi 300 oC menghasilkan ukuran makropori. Hasil uji adsorpsi BTK 5% (b/b) terhadap heptaklor 2 mg/L secara adsorpsi fisik, terlihat dari persamaan Langmuir memiliki linearitas y=1,704x ? 0,002, kapasitas adsorpsinya 1,704 mg/g, dengan efisiensi adsorpsinya sebesar 75,01%. Proses bioaugmentasi tanah sawah tercemar heptaklor oleh bakteri tempatan Raoultella ornithinolytica B4 dengan bantuan BTK 5%, menghasilkan degradasi heptaklor (Rt 11,31 menit) menjadi 1-hidroksiklordene (Rt 12,38 menit), dengan nilai efisiensi remediasi sebesar 75,38%.

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ABSTRACTThe regulation of Republic of Indonesia No. 19 in 2009, about the ratification of the Stockholm Convention on Persistent Organic Pollutans (POPs), that bann the use of insecticides category, namely aldrin, chlordane, dieldrin, endrin, heptachlor, hexachlorobenzene, mirex, toxaphene and polychlorinated biphenyls (PCB), and as well as the restriction use of insecticide dichlorodiphenyldichloroethane (DDT). In fact, the presence of insecticides organochlorine are still found on paddy filed, from nine villages and sub-districts in Karawang contained seven types, they are aldrin, DDT, endosulfan, endrin, heptachlor and lindane concentrations in the district ranges from 0.3 ng/g in up to 5.37 ng/g. Bioaugmentation is the applications of indigenous or allochthonous wide type or genetically modified microorganisms to hazardous waste polluted sites in order to accelerate the removal of undesired compounds. Indigenous Bacteria that is potential to degrade heptachlor is obtained from the isolation of Citrobacter sp and finally identified by 16S rRNA identification technique, that this bacteria is Raoultella ornithinolytica B4 which is classified as a group of bacteria of Enterobacteriaceae, as a Gram-negative, and produce the enzyme catalase. Biochar coconut shell (BCS) as adsorbent was tested for its quality by SNI-06-3730-1995 method. It has a water content of 11.88% (w/w), ash content of 3.32%, an easily evaporated substance content of 13.61%, bounded carbon to 71.20%, and iod number of 570.22 mg/g. The adsorption result of BCS 5% (w/w) to heptachlor was 2 mg/L which was fit with physical adsorption of Langmuir equation with adsorption linearity y = 1,704x - 0,002, adsorption capacity of 1.704 mg / g, so BCS can adsorb heptachlor well. Bioaugmentation using single strain of R. ornithinolytica B4 successful for removal of heptachlor with efficiency was observed in 35 days incubation was 75.38%, and heptachlor (11,31 minute) degraded to 1-hydroxychlordene (12,38 minute). "

"ABSTRAKTujuan: Spons merupakan salah satu dari biodiversitas laut yang banyak menghasilkan senyawa antibiotik, salah satunya adalah Xestospongia testudinaria. Metabolit sekunder dapat dihasilkan dari simbiosis bakteri dengan spons Xestospongia testudinaria. Tujuan dari penelitian ini adalah untuk identifikasi potensi antibiotik dari bakteri yang bersimbiosis dengan X. testudinaria dan mekanisme kerja sebagai antibiotik untuk bidang kesehatan. Metode: Pengambilan spons dilakukan secara purposive menggunakan SCUBA Diving pada kedalam laut 20 m. Waktu penelitian dilakukan pada Maret 2015-September 2017. Isolasi dan skrining mikroba penghasil antibiotik dilakukan dengan mengambil sampel spons dari Perairan Sorong Papua dan Perairan Tanjung Pecaron Jawa Timur . Isolat terpilih digunakan dalam proses fermentasi untuk produksi senyawa metabolit sekunder. Isolat bakteri diekstraksi dengan menggunakan pelarut organik antara lain n-heksana, etilasetat dan etanol dari ketiga ekstrak diuji aktivitas antibakteri. Ekstrak etilasetat difraksinasi dengan kromatografi kolom dan hasil fraksinasi digabung berdasarkan persamaan bentuk dan jarak rambat dari spot. Hasil fraksinasi di lakukan uji antibakteri dan dipilih subfraksi yang paling kuat. Subfraksi yang terpilih dilakukan isolasi dengan menggunakan KLT preparatif dan diuji kemurniannya. Senyawa murni yang dihasilkan dikarakterisasi strukturnya dengan spektrofotometer UV-Vis, FT-IR dan KG-MS. Mekanisme aksi dari senyawa antibakteri dilakukan dengan mengukur kebocoran membran sel bakteri menggunakan Spektrofotometer AAS dan morfologi sel bakteri dengan menggunakan Transmisi Elektrom Mikroskop TEM .Uji aktivitas antibakteri dilakukan terhadap beberapa bakteri isolat rumah sakit yang resisten dan beberapa bakteri uji laboratorium baik bakteri Gram positif maupun bakteri Gram negatif. Hasil: Diperoleh mikroba penghasil antibakteri Micrococcus luteus MB 26 yang diisolasi dari spons X.testudinaria asal Perairan Sorong Papua dan Bacillus licheniformis yang diisolasi dari spons X. testudinaria asal Perairan Tanjung Pecaron Jawa Timur . Isolat bakteri simbion Xp 4.2 memiliki aktivitas antibakteri terhadap E. coli ATCC 25922 dengan diameter hambatan 2,4 2,5 cm, K. pneumoniae ATCC 13833 dengan diameter hambatan 2,2 0,5cm dan B. subtilis ATCC 6633 dengan diameter hambatan 1,2 0,64 cm. Ekstrak etilasetat dari isolat bakteri simbion Xp 4.2 memiliki aktivitas antibakteri terhadap K. pneumoniae ATCC 13833 dengan diameter hambatan 1,95 0,55 cm. Hasil fraksinasi ekstrak etilasetat dengan kromatografi kolom di dapatkan 109 fraksi dan digabung menjadi 13 subfraksi. Hasil uji antibakteri subfraksi V memiliki aktivitas antibakteri terhadap K. pneumoniae ATCC 13833 dengan diameter hambatan 1,35 0,65 cm. Hasil isolasi dengan KLT preparatif di dapat senyawa murni dan memiliki aktivitas antibakteri yang lemah pada konsentrasi 100, 50, 25, 10, 5 dan 0,5 g/disk dengan diameter hambatan berturut-turut sebesar 1,24 0,11, 1,18 0,13, 1,05 0,14, 1,03 0,10, 0,93 0,14 dan 0,67 0,14 karena diameter hambatan < 12 mm. Hasil karakterisasi senyawa metabolit sekunder yang diisolasi dari M. luteus MB 26 diperkirakan merupakan golongan asam lemak rantai panjang seperti asam octakosanoat, metil palmitat, asam heksadekanoat, 1-tetradekanol, asam benzenpropionat dan piridin 3-karboheksamit. Mekanisme kerja antibakteri berdasarkan integritas membran menyebabkan kebocoran membran sehingga terjadi pelepasan ion-ion Ca 2 , Mg2, K dan metabolit seluler pada membran sel bakteri. Isolat bakteri simbion Xp 2-10 memiliki aktivitas antibakteri terhadap P. aeruginosa ATCC 27853 dengan diameter hambatan 1,963 0,35 cm dan P. aeruginosa isolat RS dengan diameter hambatan 2,34 0,95cm. Ekstrak etilasetat dari isolat bakteri simbion X2-10memiliki aktivitas antibakteri terhadapP. aeruginosa ATCC 27853 dengan diameter hambatan 1,756 0,25 cm dan P. aeruginosa isolat RS dengan diameter hambatan 2,51 0,45cm. Hasil fraksinasi dengan kromatografi kolom di dapatkan 160 fraksi dan digabung menjadi 3 subfraksi. Hasil uji antibakteri subfraksi III memiliki aktivitas antibakteri terhadap P. aeruginosa ATCC 27853 dengan diameter hambatan 2,51 0,75 cm dan P. aeruginosa isolat RS dengan diameter hambatan 1,95 0,45cm. Kesimpulan: Senyawa metabolit sekunder yang dihasilkan dari M.luteus MB 26 tidak memiliki aktivitas antibakteri terhadap bakteri isolat rumah sakit yang resisten tetapi mampu menghambat bakteri Klebsiella pneumoniae ATCC 13833 secara in vitro. Senyawa metabolit sekunder yang dihasilkan dari B. licheniformis memiliki aktivitas antibakteri terhadap P. aeruginosaATCC 27853 serta P. aeruginosa isolat RS. Penelitian ini menunjukan potensi senyawa metabolit sekunder dari bakteri yang bersimbiosis dengan spons X. testudinaria sebagai antibakteri untuk aplikasi di bidang biomedik.

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ABSTRACTObjective Sponsge is one of marine biodiversities that produces many antibiotic compounds, one of which is Xestospongia testudinaria. Secondary metabolites can be produced from sponge association between Xestospongia testudinaria and bacteria. The research aims is to explore the richness of Indonesian marine biodiversity by isolating and screening bacteria producing antibiotics as well as their characterization and working mechanism produced as antibiotics for the health. Method Sponsge taking is done by purposive using SCUBA Diving 20 m into sea. The study was conducted in March 2015 to September 2017. Isolation and screening of antibiotic producing microbes was done by taking sponsge samples from Sorong Waters Papua and Tanjung Pecaron Waters East Java . Selected isolates were used in the fermentation process for the production of secondary metabolite compounds. Bacterial isolates were extracted by using organic solvents such as n hexane, ethylacetate and ethanol from all three extracts tested for antibacterial activity. Ethylacetate extracts were fractionated by column chromatography and the fractionation results were combined based on form equations and creepage distances from the spot. Fractionation results in the antibacterial test and selected the most powerful subfraction. The selected substraction is isolated by preparative and purified TLC. The resulting pure compounds were characterized by their structure with UV Vis, FT IR and GC MS spectrophotometers. The action mechanism of the antibacterial compound was performed through measuring the leakage of bacterial cell membranes by using AAS Spectrophotometer as well as measuring the morphology of bacterial cells by using the Transmission Electron Microscope. Result Micrococcus luteus MB 26 antibacterial bacteria isolated from X.testudinaria sponsge from Sorong waters Papua and Bacillus licheniformis isolated from sponsge X. testudinaria from Tanjung Pecaron East Java waters. Bacterial isolates symbiont Xp 4.2 had antibacterial activity against E. coli ATCC 25922 with diameter of inhibition as 2.4 2.5 cm, K. pneumoniae ATCC 13833 with a diameter of inhibition of 2.2 0.5 cm and B. subtilis ATCC 6633 with a diameter of inhibition as 1.2 0.64 cm. Ethylacetate extract from bacteria isolated symbiont Xp 4.2 has antibacterial activity against K. pneumoniae ATCC 13833 with a diameter of inhibition as 1.95 0.55 cm. The result of fractionation by column chromatography was obtained 109 fractions and merged into 13 subfractions. The result of antibacterial test of subfraction V has antibacterial activity against K. pneumoniae ATCC 13833 with a diameter of inhibition 1.35 0.65 cm. The results of isolation with preparative TLC in pure compound and have antibacterial activity at concentrations of 100, 50, 25 and 10 g disc with diameter of inhibiton respectively of 1.24 0.11, 1.18 0.13, 1.05 0.14 and 1.03 0.10 whereas concentrations of 5 and 0.5 g disc had no antibacterial activity due to a diameter of inhibition "