Hasil Pencarian  ::  Simpan CSV :: Kembali

Abstrak :
Penelitian ini bertujuan untuk memperoleh isolat Actinobacteria termofilik potensial dari tanah di sekitar geiser Cisolok yang dapat mendegradasi xylan dan mengetahui hubungan kekerabatannya dengan taksa terdekat dari Actinobacteria penghasil xylanase. Tujuh belas isolat Actinobacteria termofilik diisolasi dari tanah di sekitar geiser Cisolok, Jawa Barat. Penapisan kemampuan 17 isolat Actinobacteria dan type strain Actinomadura keratinilytica NBRC 105837T mendegradasi xylan dilakukan menggunakan medium Minimal (Mm) padat dengan penambahan substrat xylan 0,5, inkubasi selama 7 hari. Pewarnaan dengan Congo red 0,2 (b/v) menunjukkan terbentuknya zona bening di sekitar koloni isolat Actinobacteria yang dapat mendegradasi xylan 0,5 pada suhu 45 C (15 isolat), 50 C (14 isolat), 55 C (4 isolat), dan 60 C (3 isolat). Type strain NBRC 105837T dapat mendegradasi xylan 0,5 pada suhu 45 C hingga 60 C. Tiga isolat (SL1- 2-R-2, SL1-2-R-3, dan SL1-2-R-4) yang mendegradasi xylan 0,5 hingga suhu 60 C dipilih sebagai isolat potensial. Tiga isolat potensial dan type strain NBRC 105837 dapat mendegradasi substrat Remazol Brilliant Blue R-xylan (RBB-xylan) 0,1 pada medium Mm padat setelah 3 hari inkubasi pada suhu 45 hingga 60 C. Tiga isolat potensial telah diidentifikasi pada penelitian sebelumnya sebagai Actinomadura keratinilytica berdasarkan karakter genotip dan fenotip. Crude enzyme dari tiga isolat potensial dan type strain NBRC 105837 dapat mendegradasi xylan 0,5 dan RBB-xylan 0,1 pada medium Mm padat setelah 24 jam inkubasi pada suhu 45 hingga 60 C. Berdasarkan analisis filogenetik sequence gen 16S rRNA menggunakan metode neighbor-joining, minimum evolution, dan maximum likelihood, 3 isolat potensial membentuk clade yang monofiletik dengan dua spesies Actinomadura termofilik yang dapat mendegradasi xylan (A. keratinilytica dan A. miaoliensis). Tiga isolat potensial membentuk clade yang monofiletik dengan empat spesies Actinomadura termofilik (A. keratinilytica, A. miaoliensis, A. rubrobrunea, dan A. viridilutea). Tiga isolat potensial menghasilkan miselium substrat yang bercabang dan tidak berfragmen, serta miselium aerial yang menghasilkan spora pada medium modified Bennetts padat setelah 14 hari inkubasi pada suhu 45 C. Penelitian ini memberikan informasi tambahan mengenai kemampuan typestrain A. keratinilytica NBRC 105837 mendegradasi xylan.

---

The aims of this study were to obtain the potential xylan-degrading thermophilic Actinobacteria isolates from soil of Cisolok geysers and to understand their relationship with the closely related taxa of xylanase-producing Actinobacteria. Seventeen thermophilic Actinobacteria isolates were isolated from soil collected around Cisolok geysers, West Java. Xylan-degrading ability of 17 Actinobacteria isolates and type strain Actinomadura keratinilytica NBRC 105837T were screened by using Minimal (Mm) agar medium with the addition of 0.5 xylan substrate, incubated for 7 days. Clear zone was formed around the colony of Actinobacteria isolates which showed xylan-degrading ability at 45 C (15 isolates), 50 C (14 isolates), 55 C (4 isolates), and 60 C (3 isolates) after staining by 0.2 (w/v) Congo red. Type strain NBRC 105837T was able to degrade 0,5 xylan at 45 to 60 C. Three isolates (SL1-2-R-2, SL1-2-R-3, dan SL1-2-R-4) that showed xylan-degrading ability at 45 to 60 C were choosen as potential isolates. Three potential isolates and type strain NBRC 105837T were able to degrade 0,1 Remazol Brilliant Blue R-xylan (RBB-xylan) substrate on Mm agar after 3 days incubation at 45 to 60 C. In the previous study, these potential isolates were identified as Actinomadura keratinilytica based on genotypic and phenotypic characters. Crude enzyme of 3 potential isolates and type strain NBRC 105837T were able to degrade both 0.5 xylan and 0.1 RBB-xylan on Mm agar after 24 hours at 45 to 60 C. Phylogenetic analyses based on 16S rRNA gene using neighbor-joining, minimum evolution, and maximum likelihood methods showed the 3 potential isolates formed monophyletic clade with two thermophilic xylan-degrading Actinobacteria species (A. keratinilytica and A. miaoliensis). Three potential isolates formed monophyletic clade with four thermophilic Actinobacteria species (A. keratinilytica, A. miaoliensis, A. rubrobrunea, and A. viridilutea). These isolates produced non-fragmented branched substrate mycelia and spores produced from aerial mycelia after 14 days incubation at 45 C. This study reports a new information regarding the xylan-degrading ability of A. keratinilytica NBRC 105837.

Abstrak :
Tujuan dari penelitian ini adalah untuk memperoleh isolat 'Actinobacteria' termofilik dari tanah di sekitar geiser Cisolok, Jawa Barat yang memiliki aktivitas selulolitik pada suhu tinggi serta mengetahui posisi filogenetik isolat terpilih terhadap spesies-spesies terdekatnya berdasarkan gen 16S rRNA. Penapisan kemampuan degradasi selulosa 17 isolat dilakukan secara kualitatif pada 'Minimal medium' (Mm) padat yang ditambahkan substrat yaitu 'carboxymethyl cellulose' (CMC) 1% (b/v) atau  'microcrystalline cellulose' (MCC) 1% (b/v) kemudian diinkubasi selama 7 hari. Pengamatan dilakukan dengan pewarnaan 'Congo red' 0,2% (b/v) dan zona bening pada sekitar koloni mengindikasikan degradasi substrat. Hasil penapisan menunjukkan bahwa 15 isolat mendegradasi CMC 1% dan 12 isolat mendegradasi MCC 1% pada suhu 45 ^oC, 14 isolat mendegradasi CMC 1% dan MCC 1% pada suhu 50 ^oC, 4 isolat mendegradasi CMC 1% dan MCC 1% pada suhu 55 ^oC, dan 3 isolat mendegradasi CMC 1% dan MCC 1% pada suhu 60 ^oC. Tiga isolat (SL1-2-R-2, SL1-2-R-3, dan SL1-2-R-4) yang mendegradasi CMC 1% dan MCC 1% hingga 60 ^oC merupakan isolat terpilih. Identifikasi dan karakterisasi telah dilakukan pada penelitian sebelumnya dan melaporkan tiga isolat terpilih memiliki kekerabatan terdekat dengan 'Actinomadura keratinilytica' WCC-2665^T(=NBRC 105837^T). Hasil pengujian menunjukkan 'type strain' NBRC 105837^T mendegradasi CMC 1% dan MCC 1% pada medium Mm padat dengan suhu 45, 50, 55, dan 60 ^oC setelah inkubasi 7 hari. 'Crude enzyme' dari tiga isolat potensial dan 'type strain' NBRC 105837^T menunjukkan aktivitas selulolitik pada medium Mm padat yang ditambahkan CMC 1% atau MCC 1% pada suhu 45, 50, 55, dan 60 ^oC. Analisis filogenetik tiga isolat terpilih berdasarkan gen 16S rRNA menggunakan metode 'Neighbor-Joining' (NJ), 'Minimum Evolution' (ME), dan 'Maximum Likelihood' (ML) menunjukkan bahwa tiga isolat terpilih berada pada satu 'clade' monofiletik dengan 'Actinomadura' 'keratinilytica' WCC-2665^T. Analisis filogenetik juga menunjukkan dua kelompok yang terpisah berdasarkan kemampuan menghasilkan selulase pada anggota famili 'Thermomonosporaceae'. ...... The aims of this study were to obtained thermophilic 'Actinobacteria' isolates from soil around Cisolok geyser, West Java with the ability to degrade cellulose at high temperatures and to analyze the phylogenetic position based on 16S rRNA gene of the selected isolates compared to closely related species. Cellulose degradation screening was performed on Minimal (Mm) medium with the addition of 1% (w/v) carboxymethyl cellulose (CMC) or 1% (w/v) microcrystalline cellulose (MCC) as substrate then incubated for 7 days. Cellulose degradations were observed by staining the plates with  0,2% (w/v) Congo red and clear zone formation around the bacterial colony would indicate the cellulose degradation. The results showed that 15 isolates were able to degrade 1% CMC and 12 isolates were able to degrade 1% MCC at 45 ^oC, 14 isolates were able to degrade 1% CMC and 1% MCC at 50 ^oC, 4 isolates were able to degrade 1% CMC and 1% MCC at 55 ^oC, and 3 isolates were able to degrade 1% CMC and 1% MCC at 60 ^oC. Three isolates (SL1-2-R-2, SL1-2-R-3, and SL1-2-R-4) were selected due to their CMC and MCC degrading ability at 60 ^oC. Molecular identification based on 16S rRNA gene and characterization in previous study showed that the three selected isolates are closely related to 'Actinomadura keratinilytica' WCC-2665^T(=NBRC 105837^T). The assay showed that type strain NBRC 105837^T was able to degrade 1% CMC and 1% MCC at 45, 50, 55, and 60 ^oC after 7 days of incubation. Cellulolytic activity show that the crude enzymes of the three selected isolates and type strain were able to degrade 1% CMC and 1% MCC at 45, 50, 55, and 60 ^oC. Phylogenetic analysis using Neighbour-Joining (NJ), Minimum Evolution (ME), and Maximum Likelihood (ML) methods showed that the  three selected isolates  were  clustered  together in monophyletic clade with 'Actinomadura keratinilytica' WCC-2265^T with 100% bootstrap value. Phylogenetic analysis also showed that cellulase  producers  and  non-cellulase  producers  in 'Thermomonosporaceae' were grouped into different clades.

Abstrak :
Penelitian ini bertujuan untuk memperoleh informasi mengenai pengaruh variasi medium pertumbuhan terhadap pembentukan miselium aerial dan aktivitas antimikroba delapan isolat rare Actinobacteria termofilik dari tanah di sekitar geiser Cisolok, Jawa Barat. Pengujian pertumbuhan, pembentukan miselium aerial, dan aktivitas antimikroba dilakukan dengan menumbuhkan isolat pada medium ISP 1 agar, ISP 1 gellan gum, ISP 2 agar, ISP 2 gellan gum, ISP 3 agar, ISP 3 gellan gum, Bennett’s agar, Bennett’s gellan gum, Minimal (Mm) 3 agar, Mm 3 gellan gum, 2% agar, dan 2% gellan gum. Isolat kemudian diinkubasi pada suhu 45 °C selama 7 dan 14 hari. Konfirmasi suhu pertumbuhan menunjukkan 2 isolat dapat tumbuh hingga suhu 45 °C dan 6 isolat dapat tumbuh hingga 50 °C. Hasil pengujian variasi medium pertumbuhan menunjukkan semua isolat rare Actinobacteria dapat menghasilkan miselium substrat pada semua medium. Hasil pengamatan setelah inkubasi selama 7 hari pada suhu inkubasi 45 °C menunjukkan isolat-isolat tersebut dapat menghasilkan miselium aerial pada medium ISP 1 agar (2 isolat), Mm 3 agar (3 isolat), 2% agar (5 isolat), dan 2% gellan gum (5 isolat). Hasil pengamatan setelah inkubasi selama 14 hari menunjukkan isolat-isolat tersebut dapat menghasilkan miselium aerial pada medium ISP 1 gellan gum (2 isolat), ISP 2 agar (1 isolat), ISP 2 gellan gum (3 isolat), ISP 3 agar dan gellan gum (2 isolat), Mm 3 agar 3 isolat, dan Mm 3 gellan gum (3 isolat). Hasil pengujian aktivitas antibakteri menunjukkan isolat SL3-2-R-11 yang ditumbuhkan pada medium ISP 3 gellan gum dan SL3-1-R-7 yang ditumbuhkan pada Bennett’s agar selama 7 hari dapat menghambat pertumbuhan Staphylococcus aureus. Hasil pengujian aktivitas antikhamir menunjukkan isolat SL3-2- R-11 yang ditumbuhkan pada medium ISP 3 gellan gum dan SL3-1-R-7 pada medium Bennett’s agar selama 14 hari dapat menghambat pertumbuhan Candida albicans. Hasil pengujian aktivitas antifungi menunjukkan tidak ada isolat yang dapat menghambat pertumbuhan Aspergillus flavus.

---

This study aims to obtain information about the effect of growth medium variations on the formation of aerial mycelium and antimicrobial activity of eight thermophilic rare Actinobacteria isolates from the soil around Cisolok geyser, West Java. The ability to grow at various media, aerial mycelium formation, and antimicrobial activity were carried out by growing isolates on medium ISP 1 agar, ISP 1 gellan gum, ISP 2 agar, ISP 2 gellan gum, ISP 3 agar, ISP 3 gellan gum, Bennett’s agar, Bennett’s gellan gum, Minimum (Mm) 3 agar, Mm 3 gellan gum, 2% agar, and 2% gellan gum. The isolates were then incubated at 45 oC for 7 and 14 days. Growth test at various temperatures showed that two isolates could grow at a temperature of 45 oC and six isolates could grow up to 50 oC. The results of the growth medium variation test showed that all rare Actinobacteria isolates could produce substrate mycelium in all mediums. Observations after incubation for 7 days at 45 °C showed that these isolates could produce aerial mycelium on ISP 1 agar medium (2 isolates), Mm 3 agar (3 isolates), 2% agar (5 isolates), and 2% gellan gum (5 isolates). Observations after incubation for 14 days showed that these isolates could produce aerial mycelium on the medium ISP 1 gellan gum (2 isolates), ISP 2 agar (1 isolate), ISP 2 gellan gum (3 isolates), ISP 3 agar and gellan gum (2 isolates), Mm 3 agar 3 isolates, and Mm 3 gellan gum (3 isolates). The results of antibacterial activity test showed that isolates SL3-2-R-11 grown on ISP 3 gellan gum and SL3-1-R-7 grown on Bennett’s agar for 7 days could inhibit the growth of Staphylococcus aureus. The antifungal activity test of isolates SL3-2-R-11 grown on ISP 3 gellan gum medium and SL3-1-R-7 on Bennett’s agar for 14 days showed inhibition towards Candida albicans. Meanwhile, all isolates did not show antifungal activity against Aspergillus flavus

Abstrak :
Enzim merupakan biokatalisator yang banyak digunakan di bidang industri, terutama deterjen, farmasi, makanan bahkan pemurnian minyak. Salah satu enzim yang banyak digunakan untuk pemurnian minyak ialah lysophospholipase. Sebanyak 50 kebutuhan enzim industri diperoleh dari mikroorganisme. Akan tetapi umumnya produk aktivitas enzim oleh mikroba galur liar kurang memadai untuk aplikasi di industri, sehingga perlu dilakukan rekayasa genetik. Pengklonaan gen penyandi lysophospholipase pernah dilakukan di Aspergillus niger dan Cryptococcus neoformans, tetapi belum pernah dilakukan dari bakteri alkalotermofilik. Bacillus halodurans CM1 merupakan bakteri alkalotrmofilik isolat BPPT. Penelitian terdahulu menujukkan bahwa bakteri tersebut memiliki enzim lipase, tetapi belum diteliti lebih lanjut mengenai jenis dan lipase rekombinannya. Penelitian ini bertujuan untuk mengklona gen penyandi lysophospholipase dari Bacillus halodurans CM1 ke Escherichia coli DH5? menggunakan vektor pGEM-T easy. Plasmid rekombinan tersebut disekuensing. Hasil penelitian diperoleh fragmen gen penyandi lysophospholipase yang berukuran 783 pasang basa serta tingkat homologi 100 dengan genom Bacillus halodurans C-125 yang menyandi gen lysophospholipase No akses GenBank: BA000004.3. ......Enzyme is a biocatalyst widely used in industry, for example detergent, pharmaceutical, food or oil purification. One of the most widely used enzymes for oil purification is lysophospholipase. As much as 50 of industrial enzyme needs are obtained from microorganisms. However, enzyme productivty from wild type microbial strain is usually limited and not applicable in industry, so that genetic engineering is necessary. Cloning gene encoding for lysophospholipase was once performed in Aspergillus niger and Cryptococcus neoformans, but has never been done from alkalothermophilic bacteria, such as Bacillus halodurans. Bacillus halodurans CM1 is an isolate of BPPT. Previous research has shown that this bacteria have lipase enzymes, but the study about their propertieshave not been conducted. This study aims to clone the gene t lysophospholipase from Bacillus halodurans CM1 to Escherichia coli DH5 using the pGEM T easy vector. The recombinant plasmid is sequenced. The results is gene fragment encoding lysophospholipase obtained with size 783 base pairs and 100 similiraty with gene encoding lysophospholipase from Bacillus halodurans C 125 No access GenBank BA000004.3.

Abstrak :
Penelitian ini berfokus pada keanekaragaman taksonomi Class Ktedonobacteria, kemampuannya sebagai penghasil enzim, deskripsi takson baru, dan analisis whole genome. Tujuh belas isolat diperoleh dari sampel tanah di hutan dekat geyser, kawasan geotermal Cisolok, Jawa Barat. Sequence gen 16S rRNA dari semua isolat dibandingkan dengan spesies terdekat pada database EzBioCloud. Seluruh isolat memiliki nilai homologi yang rendah terhadap Dictyobacter aurantiacus S-27T (97,82-98,18%). Penapisan kemampuan enzimatik menunjukkan bahwa sebagian besar isolat (88,23%) menghasilkan amilase dan selulase. Komposisi bakteri dari enam sampel dianalisis dengan metode metabarcoding gen 16S rRNA pada daerah V1-V3 menggunakan Illumina Mi-Seq Next Generation Sequencing. Ktedonobacteria merupakan kelas yang paling mendominasi dalam Phylum Chloroflexota (17,74-89,49%) pada lima sampel; Namun, kelas tersebut tidak terdeteksi pada satu sampel (tanah di bawah batu besar). Empat puluh tujuh amplikon gen 16S rRNA dari taksa terdekat Ktedonobacteria berhasil diperoleh dari enam sampel yang mewakili garis keturunan baru pada tingkat takson yang tinggi. Strain S3.2.2.5 diisolasi dari tanah di dalam serasah batang bambu. Karakter fenotipik, genotipik, dan filogenetik menunjukkan bahwa strain tersebut mewakili spesies berbeda dari Genus Dictyobacter; sehingga diusulkan spesies baru Dictyobacter halimunensis sp. nov. ......This study focuses on the taxonomic diversity of the class Ktedonobacteria, their ability as enzyme producers, description of novel taxon, and whole genome analysis. Seventeen isolates were obtained from soil samples in the forest near geyser, Cisolok geothermal area, West Java. The 16S rRNA gene sequence of all isolates was compared with all related species in the EzBioCloud database. All isolates had low similarity values to Dictyobacter aurantiacus S-27T (97.82-98.18%). Primary screening of enzymatic abilities showed that most isolates (88.23%) were amylase- and cellulase-producing Ktedonobacteria. Bacterial composition analyses from six samples were performed based on the V1-V3 of 16S rRNA gene metabarcoding using Illumina Mi-Seq Next Generation Sequencing. Ktedonobacteria was the most dominating class within the phylum Chloroflexota (17.74-89.49%) in five samples; however, it was not detected in one sample (the soil under a big rock). Forty-seven 16S rRNA gene amplicons of Ktedonobacteria-related taxa were generated from six samples and represented the putative new lineages in high taxonomic rank. A strain S3.2.2.5 was isolated from soil inside a decayed bamboo stem. The phenotypic, genotypic, and phylogenetic data suggest this strain represents a distinct species of the Dictyobacter genera; hence, a new species, Dictyobacter halimunensis sp. nov. is proposed.

Abstrak :
The aims of this study are to provide data regarding the taxonomic study of thermophilic Actinobacteria based on 16S rRNA gene sequences, description, and assessment for secondary metabolite biosynthetic gene clusters (BGCs) in the genome of novel taxa, and its antibacterial activity. Thirty-one isolates of thermophilic Actinobacteria were isolated from soil samples in Cisolok geothermal area, West Java. The 16S rRNA gene sequence-similarity search against all related species was performed using EzTaxon-e database. The sequences of 31 isolates showed similarity to member of family Micromonosporaceae, Nocardiaceae, Pseudonocardiaceae, Streptomycetaceae, Streptosporangiaceae, and Thermomonosporaceae. Six isolates displayed high similarity to genera in the family Pseudonocardiaceae, and most closely related to the genus Thermotunica, T. guangxiensis AG2-7T with similarity values from 94.6 to 95.2%. Phenotypic features and phylogenetic data differentiated strain SL3-2-4T from members of the family Pseudonocardiaceae. Therefore, the strain SL3-2-4T is proposed as a representative of a novel species in a novel genus, Gandjariella thermophila gen. nov., sp. nov. The genome of SL3-2-4T contained 21 antiSMASH-identified secondary metabolite regions harboring BGCs. These BGCs were for polyketide synthase, non-ribosomal peptide synthase, and ribosomally synthesized and post-translationally modified peptide family clusters. Thirteen and five regions displayed low (4–35%) and no similarity with known BGCs for secondary metabolites, respectively. Screening for antibacterial activity showed that strains SL3-2-4T and SL3-2-7 on MM 2 medium solidified with gellan gum at 45°C for 14 days demonstrated inhibitory activity against all Gram-positive, but not Gram-negative bacteria. Strain SL3-2-10 on ISP 3 gellan gum medium incubated for seven-days only active against K. rhizophila NBRC 12078. The results indicated that novel taxa have the potential for the discovery of active secondary metabolites.