63 research outputs found

    Pemodelan protein dan analisis molecular docking enzim β-glukanase solat Bacillus subtilis W3.15

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    The β-glucanase enzyme is an enzyme protein that can hydrolyze β-glucan, one of the main components of the fungal cell wall. This enzyme protein is produced by several bacteria, one of which is B. subtilis. The three-dimensional (3D) structure of proteins is necessary to understand their properties and functions of proteins. Enzyme proteins can be analyzed for their structure and function using in silico method. This study aims to detect the β-glucanase gene from B. subtilis W3.15 and analyze it using the in silico method. The methods in this research are homology modeling and molecular docking analyses. Modeling was carried out using the SWISS-MODEL server and docking analysis using the PLANTS 1.1 program. Modeling the β-glucanase enzyme is based on the template of the β-glucanase enzyme protein model with PDB code 3o5s. The results of sequence alignment and model visualization were quite good as indicated by the model having a Ramachandran Plot value in the favored area of 91.10 %, a MolProbity score of 0.95, and a QMEAN value of 0.90 ± 0.06. The β-glucanase enzyme model was then docked using the PLANTS1.1 program with native ligand B3P, 1,4-β-D-Glucan, D-glucose, β-D-Glucan from oats, and N-Acetyl glucosamine. The results of docking analysis showed that the β-glucan ligand (β-D-glucan from oats) used as a substrate in the cultivation of isolate B. subtilis W3.15 had a better binding energy prediction value compared to the B3P ligand, which is a natural ligand in the template proteins

    Peranan Pseudomonas aeruginosa ATCC 15442 terhadap Pertumbuhan Tanaman Cabai Rawit (Capsicum frutescens L.) Varietas Bonita pada Kondisi Salin: The Role of Pseudomonas aeruginosa ATCC 15442 on the Growth of Bonita Hot Pepper (Capsicum frutescens L.) Variety in Saline Conditions

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    Hot pepper (Capsicum frutescens L.) is one of the food crop commodities that is widely cultivated in Indonesia. Salinity stress can reduce the bioavailability of potassium and its uptake by plants, which will ultimately reduce plant growth and production. One way to reduce the effect of salinity and increase potassium uptake by plants is to use potassium-solubilizing bacteria. One of the bacteria that can solubilize potassium is Pseudomonas aeruginosa. This research aims to study the role of Pseudomonas aeruginosa ATCC 15442 on the growth of the Bonita variety of hot pepper under saline conditions. This study used a completely randomized factorial design with four concentration levels of NaCl treatment: 0, 4, 8, and 12 g/L, as well as two levels of bacteria administration: without bacteria and with bacteria. The results showed that the application of bacteria, salt concentration, and the interaction of the two had no effect (p-value> 0.05) on the growth of hot pepper plants with the observed parameters namely plant height, number of leaves, shoot fresh weight, root fresh weight, shoot dry weight, root dry weight, and chlorophyll content

    Seleksi dan Karakterisasi Bakteri Halotoleran Penghasil Enzim Amilase Dari Produk Fermentasi Ikan-Inasua: Selection and Characterization of Halotolerant Bacteria that produce Amylase Enzyme from Fish-Inasua Fermented Food

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    Fish-inasua fermented food is a potential source to obtain halotolerant bacteria-producing amylase. Previously, four bacterial isolates such as IG12, IG6, IG66, and IG31, isolated from this food, have been reported to be able to produce protease and lipase enzyme, but their potential as amylase enzyme producers have not been studied. This study aims to characterize and test the potential of halotolerant bacteria isolated from this food in producing amylase enzymes. Based on Gram staining, four bacterial isolates were Gram-positive. The qualitative test of amylase on NA medium with the addition of 1% starch showed four bacteria were able to produce amylase in NaCl (0 to 5%)-containing medium. IG66 isolate was the most potential isolate because it had the highest enzyme activity in a medium with 5% NaCl concentration, which was 0.095 U/ml. The amylase activity was produced maximum at the 8th hour, which is the early stationary phase. Its maximum activity in the 5% NaCl-containing medium was at the 10th hour. In addition, amylase produced by IG66 isolate reached optimum activity at a temperature of 50°C and pH 7. This study concluded that IG66 isolate was the most potential halotolerant isolate that could be developed as an amylase-producing agent

    Antifungal Substances Produced by B. subtilis Strain W3.15 Inhibit the Fusarium oxysporum and Trigger Cellular Damage

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    Soybean Fusarium wilt and root rot disease caused by a necrotrophic ascomycete pathogen, F. oxysporum, triggered severe damage to the plant tissues and organs and impacted heavy losses. Biocontrol agents, Bacillus subtilis, were commonly used to produce a broad spectrum of antifungal substances and were gradually used in biocontrol studies for plant disease management. Investigation and determination of the inhibiting mechanism of antifungal substance produced by B. subtilis on F. oxysporum should be done to protect the soybean plant. This study revealed that basal nutrient broth (NB) gives the best antifungal activity. The stationary phase of the bacterial growth curve was obtained on two days of cultivation and showed the maximum antifungal activity against F. oxysporum. Ethyl acetate (EA) extraction of bacterial supernatant generated crude EA extract, which showed half inhibition (IC50) at 306.42 µg/ml obtained from the dose-response regression curve. Post-treatment mycelia of F. oxysporum with bacterial extract were demonstrated as hyphal deformation followed by malondialdehyde (MDA) accumulation. Furthermore, cellular leakage on fungal cells that may be triggered by antifungal compounds from strain W3.15 occurred. Last, the related antifungal compounds were predicted to be epicatechin and benzophenone from the LC-MS/MS analysis of crude EA extract. Accordingly, the biocontrol agent B. subtilis strain W3.15 promises a strong potency for biofungicide development

    Penapisan dan Karakterisasi Enzim Amilase dari Bakteri Asal Ekoenzim

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    Ekoenzim merupakan salah satu sumber potensial untuk mendapatkan isolat bakteri amilolitik. Penelitian ini bertujuan untuk menapis isolat bakteri amilolitik dari ekoenzim, melakukan karakterisasi enzim amilase hasil semipemurnian, serta mengidentifikasi bakteri amilolitik secara molekuler menggunakan marka 16S rRNA. Penapisan bakteri amilolitik dilakukan dengan mengukur indeks amilolitik pada media Nutrient agar yang mengandung 1% tepung tapioka. Isolat amilolitik yang memiliki indeks tertinggi dan tidak patogen dipilih untuk proses karakterisasi amilase. Pengujian aktivitas amilase dilakukan menggunakan metode Bernfeld, protein diukur menggunakan metode Bradford. Ekstrak ekstraseluler dipekatkan menggunakan presipitasi amonium sulfat. PKL2 adalah bakteri gram positif yang berasal dari ekoenzim dengan indeks amilolitik tertinggi 1,77, yang tidak patogen pada agar-agar darah yang diuji. Amilase optimum dihasilkan oleh PKL2 pada fase diam pada 21 jam. pH dan suhu optimum untuk pengujian aktivitas amilase diamati masing-masing 7,0 dan 50ºC. Enzim amilase dari PKL2 meningkat kemurniannya 1,82 kali lipat dengan pengendapan amonium sulfat pada konsentrasi 60%. Isolat bakteri amilolitik dengan aktivitas tertinggi diidentifikasi lebih lanjut menggunakan penanda 16S rRNA. Hasil identifikasi menunjukkan bahwa PKL2 yang diperoleh memiliki kemiripan dengan spesies Bacillus amyloliquefaciens.   Kata kunci : Aktivitas milase, Bacillus amyloliquefaciens, ekoenzim, pH optimum

    Analysis of Soil Bacterial Diversity from Tropical Rainforest and Oil Palm Plantation In Jambi, Indonesia by 16S rRNA-DGGE Profiles

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    Oil palm plantations are the most invasive land use changes in Southeast Asia. It must have affected unique natural biodiversity. This study aimed to investigate the diversity of soil bacteria based on 16S rRNA gene profiles from tropical forest and oil palm plantation in Jambi Province, Indonesia. Soil sample was taken from tropical forest and oil palm plantation from Jambi province, Indonesia. The forest site is in Bukit Duabelas National Park, and the nearby oil palm plantation is in Sarolangun District, Jambi Province, Indonesia. The diversity of bacterial communities from topsoil was studied using Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene and common biodiversity indices. PCR amplification of 16S rRNA gene was successfully conducted primers-using 33F/ 518R primers. Phylogenetic approach was used for revealing the community shift of bacterial phyla and genera in both areas. Phylogenetic analysis showed there were 4 phyla of bacteria i.e., Firmicutes, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, respectively. Actinobacteria was the most dominant group in both areas. The composition of soil bacterial community in the oil palm plantation, based on total number of bands 16S rRNA generated from DGGE was richer than that in the Bukit Dua Belas National Park. It was probably caused by plantation year circle more than 10 years and routine activities during the plantation management, such as applications of agricultural lime, herbicide and fertilizer.

    Antioxidant Activity of Endophytic Bacteria Derived from Hoya multiflora Blume Plant and Their Cellular Activities on Schizosaccharomyces pombe

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    Endophytic bacteria isolated from plant tissues can produce the same secondary metabolites as their host plants. One of the metabolites that the bacteria can produce is antioxidants. This research aimed to analyze and measure the antioxidant activities of two endophytic bacteria, i.e. Bacillus siamensis HMB1 and Bacillus aryabhattai HMD4 cultures, derived from Hoya multiflora Blume plant, a tropical epiphytic plant species that grows in Indonesia, and to identify their cellular effects on Schizosaccharomyces pombe. The active compounds went through extraction process, and the antioxidant activities were measured, the extracts went under phytochemical analysis, and their phenol and flavonoid contents were measured. In vitro analysis was carried out using S. pombe. The results of this research indicated that both cultures had antioxidant activities, where HMB1 showed the highest IC50 value (51.18 mg/ml) among all. In vitro analysis indicated that HMD4 bacterial crude extract in 250 ppm concentration showed the highest resistance effect and significantly enhanced S. pombe growth. In addition, the results of the LC-MS analysis suggested that a total of 14 compounds potentially had antioxidant activity

    EFEKTIVITAS PENGHAMBATAN BAKTERI KITINOLITIK TERHADAP Fusarium proliferatum

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    Fusarium spp. merupakan penyebab penyakit pada beberapa jenis tanaman salah satunya bawang merah sehingga dapat menurunkan produktivitas tanaman bawang merah (Allium cepa L.). Bakteri kitinolitik diketahui memiliki sifat antagonis terhadap Fusarium spp.  Penelitian bertujuan mengetahui kemampuan isolat  bakteri ABP5.1, ABP5.2.2, ABS4.1.2, BBP5.2.2 yang berasal dari pertanian bawang merah dalam menghambat pertumbuhan F. proliferatum. Sebanyak empat isolat bakteri terpilih hasil isolasi dari penelitian sebelumnya diuji kemampuannya dalam menghambat pertumbuhan Fusarium proliferatum.  Tahapan penelitian terdiri atas karakterisasi isolat, uji aktivitas kitinolitik, uji antagonis antar isolat bakteri, dan uji antagonis isolat bakteri terhadap cendawan Fusarium proliferatum. Keempat isolat bakteri ABP5.1, ABP5.2.2, ABS4.1.2, dan BBP5.2.1 merupakan bakteri gram negatif. Uji kualitatif kitinolitik menunjukkan keempat isolat menghasilkan zona bening dengan indeks kitinolitik antara 0,04-1,0.   Isolat bakteri ABS4.1.2 memiliki nilai indeks kitinolitik terbesar yaitu 1,09. Uji antagonis antar isolat bakteri menunjukkan hasil keempat isolat bakteri tidak bersifat saling antagonis. Uji antagonis bakteri terhadap cendawan Fusarium proliferatum dengan metode dual culture menunjukkan bahwa sebanyak dua dari empat  isolat mampu menghambat pertumbuhan cendawan F.proliferatum. Isolat ABP5.2.2 memiliki daya hambat terbesar yaitu 41%, sedangkan isolat ABS4.1.2 memiliki daya hambat sebesar 40%

    Aplikasi Bakteri Asam Laktat dari Inasua sebagai Biopreservatif Ikan Patin (Pangasius sp.) : Lactic Acid Bacteria Aplication from Inasua As Biopreservative for Catfish (Pangasius sp.)

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    Lactic Acid Bacteria or LAB are bacteria that are categorized as generally recognized as safe (GRAS) because they are safe for human health and are non-pathogenic, so they have the potential to be biopreservative. Several metabolic products produced by LAB have antibacterial properties, including bacteriocin, diacetyl, hydrogen peroxide and organic acids. Isolates of L. plantarum IN05 and L. rhamnosus IN13 isolated from fermented inasua food were studied for their potential as biopreservatives because of their antibacterial properties. The content of animal protein in fish is in great demand by the public, one of which is catfish which is in great demand by the public, but catfish is easy to damage and decrease in quality. This is due to the presence of the pathogenic bacterium Listeria monocytogenes which has the ability to grow at cold storage temperatures (refrigeration) to freezing. This study aimed to apply a neutral cell-free supernatant, cell-free supernatant, and bacterial cell biomass from L. rhamnosus IN13 and L. plantarum IN05 isolates and formalin in storage of catfish fillets contaminated with Listeria monocytogenes bacteria. The methods used include the production of antibacterial compounds, determination of the sensitivity of antibacterial compounds to test bacteria, confirmation test of antibacterial compounds with the addition of proteinase K, application of antibacterial compounds to catfish fillets, calculation of total bacterial colonies, bacterial colonies of L. monocytogenes, and lactic acid bacteria, as well as measurement of the pH value of catfish fillet. The SBSN antibacterial compound from L. rhamnosus IN13 has the ability to maintain catfish fillets for up to 14 days of storage in accordance with the requirements for fresh fish that are suitable for consumption according to the 2017 SNI standard on general requirements and guidelines for microbiological testing. The total microbial value was 5.65 log CFU/g, the pH value of catfish fillet meat was 6.37, and the total value of L. monocytogenes bacteria decreased during storage time.Bakteri Asam Laktat atau BAL merupakan bakteri yang dikategorikan sebagai generally recognized as safe (GRAS) karena bersifat aman bagi kesehatan manusia dan non patogen sehingga berpotensi sebagai biopreservatif. Beberapa produk metabolisme yang dihasilkan oleh BAL memiliki kemampuan sebagai antibakteri, diantaranya ialah bakteriosin, diasetil, hidrogen peroksida dann asam organik. Isolat L. plantarum IN05 dan L. rhamnosus IN13 yang diisolasi dari makanan fermentasi inasua dikaji potensinya sebagai biopreservatif karena kemampuannya memiliki sebagai antibakteri. Kandungan protein hewani dalam ikan sangat diminati oleh masyarakat, salah satunya adalah ikan patin yang banyak diminati masyarakat, namun ikan patin mudah mengalami kerusakan dan penurunan mutu. Hal ini disebabkan oleh hadirnya bakteri patogen Listeria monocytogenes yang memiliki kemampuan tumbuh pada suhu penyimpanan dingin (refrigerasi) hingga beku. Penelitian ini bertujuan untuk mengaplikasikan supernatan bebas sel netral, supernatan bebas sel, dan biomassa sel bakteri dari isolat L. rhamnosus IN13 dan L. plantarum IN05 serta formalin dalam penyimpanan ikan patin fillet yang terkontaminasi bakteri Listeria monocytogenes. Metode yang digunakan mencakup produksi senyawa antibakteri, penentuan sensitivitas senyawa antibakteri terhadap bakteri uji, uji konfirmasi senyawa antibakteri dengan penambahan proteinase K, aplikasi senyawa antibakteri pada ikan patin fillet, perhitungan total koloni bakteri, koloni bakteri L. monocytogenes, dan bakteri asam laktat, serta pengukuran nilai pH ikan patin fillet. Senyawa antibakteri SBSN dari L. rhamnosus IN13 memiliki kemampuan mempertahankan ikan patin fillet sampai lama penyimpanan 14 hari sesuai dengan syarat ikan segar yang layak untuk dikonsumsi sesuai standar SNI tahun 2017 tentang Persyaratan umum dan pedoman untuk pengujian mikrobiologi. Nilai total mikrob 5,65 log CFU/g, nilai pH daging ikan patin fillet 6,37, dan nilai total bakteri L. monocytogenes yang menurun selama waktu penyimpanan

    Kontribusi Sifat Biokimia Tanah sebagai Determinan Produktivitas Lahan Perkebunan Nanas (Ananas comosus [L.] Merr.) di Kabupaten Lampung Tengah

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    One of the management challenges in pineapple cultivation at plantation scale is the still occurrence of disparity in land productivity across the cultivated area although the cropping practices have been implemented for many years. In the case of a pineapple plantation in Central Lampung Regency, contribution of soil biochemical properties in terms of various soil enzyme activities as a determinant factor of land productivity has never been elaborated. This research was aimed to study the relationships among biochemical and other soil properties with land productivity or pineapple yield at plantation scale. Rhizosphere soil-composite samples were taken purposively from 4 stations at the largest Indonesian pineapple plantation representing blocks with high and low yield and growth at vegetative and generative phase. Relationships amongst the studied parameters were evaluated using PCA and linear multiple regression analysis. The results showed significant contributions of the rhizosphere soil properties on the pineapple yield according to equation: Yield = 64.895 – 6.546 PCA1 +13.057 PCA2 – 7.722 PCA4 (R2= 0.612), where PCA1 consisted of soil available-P, available-K, and CEC; PCA2 was of soil base saturation, total microbe population, enzyme activities of cellulase and invertase, while PCA4 was of soil organic C, silt fraction, and phosphatase activities.Salah satu tantangan manajemen dalam budidaya nanas skala perkebunan adalah masih adanya disparitas atau heterogenitas dalam hal produktivitas lahan pertanaman meskipun praktik budidaya telah dilakukan puluhan tahun. Pada perkebunan nanas di Kabupaten Lampung Tengah, kontribusi sifat biokimia tanah terkait aktivitas beragam enzim tanah rizosfer sebagai faktor penentu produktivitas lahan belum pernah dielaborasi. Penelitian ini bertujuan memelajari hubungan antar sifat biokimia dan sifat tanah rizosfer lainnya dengan produktivitas lahan atau tingkat produksi nanas pada skala perkebunan. Contoh komposit tanah rizosfer diambil secara purposif dari 4 stasiun di perkebunan nanas terbesar di Indonesia yang mewakili blok dengan tingkat produksi tinggi dan rendah serta pertumbuhan nanas pada fase vegetatif dan generatif. Hubungan antar parameter yang dipelajari dievaluasi menggunakan PCA dan analisis regresi linier berganda. Hasil penelitian menunjukkan kontribusi signifikan dari sifat-sifat tanah rizosfer terhadap tingkat produksi nanas menurut persamaan: Produksi = 64.895 – 6.546 PCA1 +13.057 PCA2 – 7.722 PCA4 (R2= 0.612), dimana PCA1 terdiri atas P-tersedia, K-tersedia, dan KTK tanah; PCA2 terdiri atas kejenuhan basa, total populasi mikrob, aktivitas enzim tanah selulase dan invertase, sedangkan PCA4 terdiri atas C-organik, fraksi debu, dan aktivitas fosfatas
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