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All Journal HAYATI Journal of Biosciences Microbiology Indonesia Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Indonesian Journal of Biotechnology Proceeding Biology Education Conference Prosiding SNPBS (Seminar Nasional Pendidikan Biologi dan Saintek)

Langkah Sembiring

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Author-ID : 435209

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Environmental Science Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Public Health

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Molecular Phylogenetic Classification of Streptomycetes Isolated from the Rhizosphere of Tropical Legume (Paraserianthes falcataria) (L.) Nielsen LANGKAH SEMBIRING
HAYATI Journal of Biosciences Vol. 16 No. 3 (2009): September 2009
Publisher : Bogor Agricultural University, Indonesia

Intrageneric diversity of 556 streptomycetes isolated from the rhizosphere of tropical legume was determined by using molecular taxonomic method based on 16S rDNA. A total of 46 isolates were taken to represent 37 colour groups of the isolates. 16S rDNA were amplified and subsequently sequenced and the sequences data were aligned with streptomycete sequences retrieved from the ribosomal data base project (RDP) data. Phylogenetic trees were generated by using the PHYLIP software package and the matrix of nucleotide similarity and nucleotide difference were generated by using PHYDIT software. The results confirmed and extended the value of 16S rDNA sequencing in streptomycete systematic. The 16S rDNA sequence data showed that most of the tested colour group representatives formed new centers of taxonomic variation within the genus Streptomyces. The generic assignment of these organisms was underpinned by 16S rDNA sequence data which also suggested that most of the strains represented new centers of taxonomic variation. The taxonomic data indicate that diverse populations of streptomycetes are associated with the roots of tropical legume (P. falcataria). Therefore, the combination of selective isolation and molecular taxonomic procedures used in this study provide a powerful way of uncovering new centers of taxonomic variation within the genus Streptomyces. Key words: molecular phylogenetic, classification, streptomycetes, rhizosphere, Paraserianthes falcatharia

Production of Poly-α-hydroxybutyrate (PHB) from Sago Starch by The Native Isolate Bacillus megaterium PSA10 Nur Arfa Yanti; Langkah Sembiring; Sebastian Margino
Indonesian Journal of Biotechnology Vol 14, No 1 (2009)
Publisher : Universitas Gadjah Mada

A new bacterial strain that produces amylase and poly-a-hidroxybutyrate (PHB) using sago starch as carbon source was characterized and identified to be member of the Bacillus megaterium group based on phenotypic characteristics and 16S rDNA gene sequences. Amylase activity was determined spectrophotometrically on the basis of substrate concentration reduction. PHB production was quantified with UV spectrophotometer. The polymer produced by B. megaterium PSA10 was identified by Fourier Transform Infrared spectroscopy (FTIR). The result of the study showed that the amylase specific activity B. megaterium PSA10 was 593,61 DUN/mg protein and PHB production from sago starch was 52,28 % of cell dry weight (CDW). FTIR analysis of the polymer indicated that the strain B.megaterium PSA10 was a potent PHB producer.

Characterization of Streptomyces spp. Producing Indole-3-acetic acid as Biostimulant Agent Charlie Ester de Fretes; Langkah Sembiring; Yekti Asih Purwestri
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Twenty six isolates of Streptomyces spp. obtained from Cyperus rotundus L. rhizosphere were tested forability to produce indole-3-acetic acid (IAA) in yeast malt extract (YM) medium containing 2 mg/mL tryptophan.Screening of the isolates for ability to produce IAA was carried out by adding Salkowski reagent in bacteriaculture and was measured quantitatively by spectrophotometer at λ 530 nm. Thin Layer Chromatography (TLC)method was used to determine IAA. To ensure the IAA production in Streptomyces isolates, gene involved inIAA biosynthesis was detected by amplifying Tryptophan Monooxigenase (iaaM) gene. The study of the effectof tryptophan on the production of IAA was measured at different concentrations of tryptophan (0, 1, 2, 3,4, 5 mg/mL) in the bacterial culture. The result showed that there were two Streptomyces spp. isolates whichcould produce IAA, namely the isolates of Streptomyces sp. MS1 (125.48 μg/mL) and Streptomyces sp. BR27(104.13 μg/mL). The TLC result showed that the compound in both isolates was identifi ed to be IAA. Theamplifi cation results showed that iaaM gene was detected in both isolates. This results indicated that the IAMpathway is predicted involved in the biosynthesis of IAA in the selected isolates. Both of the isolates were ableto produce IAA after 24 h incubation and the highest production was at 120 h incubation with the concentrationof tryptophan was 2 mg/mL dan 1 mg/mL, respectively. Therefore, it is concluded that Streptomyces spp.isolates are able to produce IAA and potentially to be utilized as biostimulat agent. Keywords: Streptomyces spp., indole-3-acetic acid (IAA), indole-3-acetamide (IAM), Tryptophan Monooxigenasegene (iaaM)

A Study on Production of Poly-β-Hydroxybutyrate Bioplastic from Sago Starch by Indigenous Amylolytic Bacteria Nur Arfa Yanti; Langkah Sembiring; Sebastian Margino; Nurhayani H. Muhiddin
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Bacillus sp. PSA10 and Bacillus sp. PPK5 were two indigenous strain amylolytic bacteria from SoutheastSulawesi that have ability to produce bioplastic poly-β-hydroxybutyrate (PHB) from sago starch. The study wasattempted to determine the mechanism of PHB production by bacteria amylolytic was grown on sago starchcontainingmedia. Two amylolytic bacteria i.e. Bacillus sp. PSA10 and Bacillus sp. PPK5 was grown for 168 hin a mineral salts medium with sago starch as carbon source. Growth of amylolytic bacteria was monitoredby cell dry weight. Extraction of PHB was done by N-hexane acetone-diethyl ether method and PHB contentwas quantifi ed with UV spectrophotometer at 235 nm. Glucose level was determined by using kit of glucoseGOD 10” and was quantifi ed with spectrophotometer at 500 nm. Sago starch concentration was determinedby phenol method using specthrophotometer at 490 nm. The result of the study showed that Bacillus sp.PSA10 was produced PHB up to 66,81 % (g PHB/g cell dry weight) at 48 h and Bacillus sp. PPK5 up to 24,83% (g PHB/g cell dry weight) at 84 h. Bacillus sp. PSA10 has ability to converse sago starch to be PHB directlywithout glucose accumulation in the media, whereas Bacillus sp. PPK5 have to accumulate glucose as productof sago starch hydrolysis to produce of PHB. PHB synthesis by Bacillus sp. PHB production on sago starchof the Bacillus sp. PSA10 was found to be growth-associated whereas Bacillus sp. PPK5 was found to be nongrowth-associated. Therefore, two indigenous amylolytic bacteria were having of difference in biosynthesismechanism of PHB in sago starch medium and their characteristics of PHB synthesis should be consideredin developing cultivation methods for the effi cient production of PHB. Keywords : Production, PHB, Amylolytic bacteria, Sago starch.

Phylogenetic relationship of Gram Negative Bacteria of Enterobacteriaceae Family in the Positive Widal Blood Cultures based on 16S rRNA Gene Sequences Sri Darmawati; Langkah Sembiring; Widya Asmara; Wayan T. Artama; Masashi Kawaichi
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

The purpose of this study was to analyze the phylogenetic relationship of Gram negative bacteria (3strains of Salmonella typhi, 1 strain of Escherichia coli, 1 strain of Serratia marcescens, and 3 strains of Enterobactercloacae) of Enterobacteriaceae family in positive Widal blood cultures based on 16S rRNA gene sequences. Theresults respectively showed that each two 16S rRNA gene clones of Serratia marcescens KD 08.4 had a closerelationship with 16S rRNA gene of Serrratia marcescens ATCC 13880 (similarity: 99.53-99.8%), Eschericia coliBA 30.1 with Eschericia coli ATCC 11775T (similarity: 99.38-99.67%), Salmonella typhi BA 07.4, Salmonella typhiKD 30.4, and Salmonella typhi SA 02.2 with Salmonella typhi ATCC 19430T (similarity: 99.4-100%) as well as theisolates of Enterobacter cloacae SA 02.1, Enterobacter cloacae BA 45.4.1, one 16S rRNA gene clone of Enterobactercloacae TG 03.5 with Enterobacter cloacae ATCC 23373 (similarity: 99.0-99.87%).

Klasifikasi Numerik-fenetik Salmonella typhi Asal Jawa Tengah dan Daerah Istimewa Yogyakarta Berdasarkan Hasil Karakterisasi Fenotipik Sri Darmawati; Langkah Sembiring; Widya Asmara; Wayan T. Artama
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 16, No 1 (2011): February 2011
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v16i1.67

Demam tifoid adalah penyakit endemis yang disebabkan oleh strain bakteri S. typhi, bakteri tersebut dapat dikelompokkan berdasarkan perbedaan mikromorfologi, morfologi koloni, penggunaan sumber karbon, produksi enzim, kemampuan mendegradasi makromolekul. Oleh karena itu penelitian ini bertujuan melakukan klasifikasi numerik-fenetik 4 starin S. typhi asal Jawa Tengah dan 2 strain asal DIY dengan 2 strain acuan S. typhi NCTC 786 dan BLKS berdasarkan karakterisasi fenotipik dengan analisis hubungan similaritas yang didasarkan atas analisis Simple Mattching Coefficient (SSM) serta algoritme UPGMA (unweighted pair group methode with averages) yang kemudian dipresentasikan dalam bentuk dendogram. Hasilnya dapat dikelompokkan menjadi empat klaster, klaster pertama beranggotakan 3 strain berasal dari Jawa Tengah dan 1 strain acuan BLK Semarang (similaritas 100%). Klaster kedua beranggotakan satu strain acuan S. typhi NCTC 786 (similaritas 98,6%) dengan klaster pertama. Klaster ketiga beranggotakan 1 strain MDA dari Jawa Tengah (similaritas 96,8%) dengan klaster pertama dan kedua. Klaster keempat beranggotakan 2 strain S. typhi asal DIY yang memiliki (similaritas 96,4%) dengan ketiga klaster lainnya.

Aplikasi Metode Sidikjari Protein (SDS-PAGE) untuk Identifikasi Isolat Bakteri Endogenik Indonesia (Bacillus thuringiensis Berliner) yang Patogenik terhadap Hama Kubis (Crocidolomia binotalis Zell) Christina L. Salaki; Langkah Sembiring; Jesmandt Situmorang; Niken Satut Nur Handayani
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 17, No 2 (2012): June 2012
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v17i2.135

Isolat bakteri Bacillus thuringiensis endogenik Indonesia yang patogenik terhadap hama kubis (Crocidolomia binotalis Zell.) dikarakterisasi dan diidentifikasi secara kimiawi dengan metode sidikjari protein. Total protein selular terlarut 10 isolat terpilih (SLK2.3, SRNG4.2, TKO1, TK9, YPPA1, UG1A,BLPPN8.2, YWKA1, BAU3.2, LPST1) dan 2 strain acuan (B. thuringiensis serovar kurstaki ATCC 10792 dan B. thuringiensis serovar israelensis H14) diperoleh melalui pemecahan sel dengan sonikasi. Ekstrak sel disentrifugasi dengan kecepatan 13000 rpm selama 5 menit untuk memperoleh supernatant. Protein dipisahkan dengan metode elektroforesis (SDS-PAGE) untuk menghasilkan profil sidikjari protein yang didokumentasikan dalam bentuk file elektronik. Selanjutnya, sidikjari protein dianalisis secara kualitatif maupun secara kuantitatif menggunakan software MVSP (Multivariate Statistical Package) untuk menghasilkan dendrogram. Hasil penelitian menunjukkan bahwa profil protein yang dihasilkan oleh tiap-tiap isolat dan strain acuan memberikan pola yang bermakna sehingga dapat digunakan untuk mengkarakterisasi dan mengidentifikasi isolat secara tegas. Analisis terhadap dendrogram menunjukkan bahwa strain acuan B. thuringiensis serovar kurstaki HD1 dapat dibedakan secara tegas dan jelas dengan strain acuan B. thuringiensis serovar israelensis H14. Dengan demikian, dapat disimpulkan bahwa aplikasi profil sidikjari protein merupakan instrumen yang sangat ampuh untuk menyingkap keanekaragaman strain anggota B. thuringiensis yang disolasi dari habitat alami. Isolat yang diteliti diidentifikasi sebagai strain baru anggota B. thuringiensis serovar kurstaki karena menunjukkan kemiripan yang tinggi dengan strain acuan B. thuringiensis serovar kurstaki ATCC 10792 meskipun ke-10 isolat ini juga menunjukkan keanekaragaman genetik yang cukup tinggi.

Sistematik Numerik Strain-Strain Anggota Genus Pseudomonas Pendegradasi Alkilbenzen Sulfonat Liniar Berdasarkan Sifat Fenotip dan Protein Fingerprinting Suharjono Suharjono; Langkah Sembiring; Jusup Subagja; Tri Ardyati; Lisa Lisdiana
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 12, No 1 (2007): February 2007
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v12i1.2536

Bacteria strains consisting of Pseudomonas sp. strain J and R isolated from river ecosystem polluted and Pseudomonas sp. strain A and B isolated from river ecosystem unpolluted by detergent were capable to degrade of LAS. The objective of this research was to determine similarity value by numerically of LAS-degrading Pseudomonas strains based on phenotype character and protein fingerprinting using three reference strains consist of Pseudomonas putida FNCC071, P. fluorescens FNCC070, and P. aeruginosa FNCC063. Phenotype characteristics examined are cellular and colony morphology, biochemical nature, capability to degrade polysaccharide, tolerance to various environmental factors and antibiotics, and ability to ferment sugar. Cellular protein fingerprinting was analyzed using SDS–PAGE discontinuous. Strains classification was determined based on Simple Matching Method similarity index by UPGMA (Unweight Pair Group Method with Average) algorithm. Based on phenotype nature, all strains have similarity value 0.61; however, based on cellular protein fingerprinting, those strains have similarity value 0.52. All strains of LAS-degraded were including in the genus of Pseudomonas.

Seleksi, Karakterisasi dan Identifikasi Bakteri Pendegradasi 2-(thiocyanomethylthio) benzothiazole (TCMTB) Langkah Sembiring; Lela Susilawati; Dwi Suhartanti
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 13, No 3 (2008): October 2008
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v13i3.2565

The objective of this research was to investigate the capabilities of bacteria isolated from industrial tanning waste to degrade TCMTB. The bacteria was initialy screened, based on their tolerance to various concentration of TCMTB using paper disk method. Then, those strains were further analyzed in terms of their ability to produce ammonia (NH4+) and sulphate (SO42-). Degradation activity was measured based on remaining residue of TCMTB analyzed using HPLC. The superior strain that showed the highest activity in degradation of TCMTB then were characterized and identified based on phenotypic and 16S rDNA sequence analysis. The result of the experiments showed that four selected strains among seven were choosen based on their high tolerance to various concentration of TCMTB, namely PK1, PK2, PK4 and PK6. All four strains showed the ability to produce ammonia and sulphate but three of which, namely PK2, PK4 and PK6 showed the high capability to degrade TCMTB. One particular strain (PK2) was observed to degrade TCMTB 40.8% within 7 days, but the others were less than 30%. Based on the phenotypic characteristics and 16S rDNA sequence analysis, the best strains (PK2) was identified to be member of genus Pseudomonas.

Kondisi Optimum untuk Produksi Kitinase dari Streptomyces Rkt5 dan Karakterisasi pH dan Suhu Enzim Yurnaliza Yurnaliza; Sebastian Margino; Langkah Sembiring
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 13, No 3 (2008): October 2008
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v13i3.2571

Chitinase is chitin degrading enzyme which is produced by Streptomyces Rkt 5 is isolated microorganism from peanut rhizosfer. This enzyme and its microorganism can be used in many agricultural, medicine and industrial purposes. The aim of the research was to find out the optimum condition for production of chitinase and to characterize of pH and temperature to chitinase activity. Optimalizing production the research had 4 treatments. The optimum conditions were achieved at mineral liquid medium containing with chitin 0,2% (w/v) as inducer, 10% (v/v) inoculum, pH 7 and 48 hours incubation. The crude enzyme was partially purified by salting out with 70% ammonium sulfate resulted in 3.31 time more purity enzyme than the crude one. This enzyme had maximum activity at 50oC and pH 5.5.

Co-Authors Bambang Setiaji C. J. Soegihardjo Charlie Ester de Fretes Christina L. Salaki Dwi Suhartanti Elisa Nurnawati ENDANG S. SOETARTO I Wayan Tunas Artama Jamhari Jamhari Jesmandt Situmorang Jusup Subagja Laksono Trisnantoro Lela Susilawati Lisa Lisdiana Masashi Kawaichi Michael Goodfellow Niken Handayani Niken Satut Nur Handayani Nur Arfa Yanti Nurhayani H. Muhiddin Sarkono Sarkono SATRIYAS ILYAS Sebastian Margino Sri Darmawati Subagus Wahyuono Sukarti Moeljopawiro Tanti Azizah S Tjut S. Djohan Tri Ardyati Wayan T. Artama Widya Asmara Wiwik E. Widayati Yekti Asih Purwestri Yuliana Retnowati Yurnaliza, Yurnaliza Yusup Subagja

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