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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Fitopatologi Indonesia Jurnal Pengolahan Hasil Perikanan Indonesia Jurnal Akuatika Jurnal Ilmu Dasar Microbiology Indonesia BIOTROPIA - The Southeast Asian Journal of Tropical Biology BERKALA SAINSTEK Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Indonesian Journal of Agricultural Science Indonesian Journal of Biotechnology Jurnal Perlindungan Tanaman Indonesia Journal of Tropical Biodiversity and Biotechnology UNEJ e-Proceeding JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA ANNALES BOGORIENSES Marine Research in Indonesia Biosaintifika: Journal of Biology & Biology Education Menara Perkebunan International Journal of Environment, Engineering, and Education International Journal of Environment, Engineering & Education

Antonius Suwanto dan Meity S. Sinaga . Budi Tjahjono Andi Khaeruni R

Department Of Biology, Faculty Of Mathematics And Natural Sciences, Bogor Agricultural University

Author-ID : 431485

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Control & Systems Engineering Earth & Planetary Sciences Economics, Econometrics & Finance Education Engineering Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics Veterinary

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Isolation and Characterization of Lactic Acid Bacteria from Inasua Ferymon Mahulette; Nisa Rachmania Mubarik; Antonius Suwanto; Widanarni Widanarni
Journal of Tropical Biodiversity and Biotechnology Vol 1, No 2 (2016): December
Publisher : Universitas Gadjah Mada

Inasua is a traditionally product of wet salt fish fermentation produced by Teon, Nila and Serua (TNS) Communities in Central Maluku, Indonesia. The community made this fermented fish to anticipate the lean time when fisherman could not go to sea. The fish that used as inasua raw material is demersal fishes that live around coral reefs, such as Samandar fish (Siganatus guttatus), Gala-gala fish (Lutjanus sp.) and Sikuda fish (Lethrinus ornatus). The objective of the research was to isolate and characterize of bacterial indigenous in Inasua from three producers in Seram Island. The measurement of pH from inasua samples were 5.9, 5.0 and 5.8, respectively. The highest number of lactic acid bacteria was found from Gala – gala inasua was 2,5x107 cfu/g sample. Isolation of all isolates bacteria from inasua showed that a total of 7 isolates of bacteria was obtained from Samadar inasua, 9 isolates from Gala-gala inasua, and 7 isolates from Sikuda inasua. From a total of 23 isolates, only 6 isolates had characteristic as lactic acid bacteria that were Gram positive, negative catalase, and cocci shape. The microscopic characteristics of the isolates are coccid in pairs or uniforms which combine to form tetrads. Carbohydrate utilization test of selected isolate by using API 50 CHB kit indicated that 13 carbohydrates are fermented by these isolates after incubation for 48 hours. The research was concluded that the dominant bacteria in inasua sample is cocci-lactic acid bacteria.Keywords : fermented fish, inasua, lactic acid bacteria, MRSA medium

Molecular Dynamic Simulation for Thermal Stability Properties of Endo β-Mannanase Enzyme Adi Yulandi; A A Hermosaningtyas; Sheila Sutanto; Antonius Suwanto
UNEJ e-Proceeding Indonesian Protein Society (IPS), International Seminar and Workshop 2014
Publisher : UPT Penerbitan Universitas Jember

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Endo β-mannanase or mannanase hydrolyse the β-D-1,4 mannopyranoside linkages in β-mannan intomanno-oligosaccharides. Four mannanases, named MAN1, MAN2, MAN3 and MAN4, were isolated from palm kernel meal waste have potential as thermostable mannanases. Series of enzymatic assay to characterize enzyme properties may affect longer time and higher cost. Homology modeling and molecular dynamic simulation are reliable and faster alternative assay to determine enzyme properties by analyzing enzymes’ three-dimensional structure. The structureswere constructed using homology modeling approach using Modeller. Template 2QHA was chosen for having more than 98% sequence similarity with targets. The homology models and template were simulated using molecular dynamics software GROMACS 4.6 for 10 ns production time each at 300 K, 323 K and 353 K. Both targets share the same (β/α)8 TIM barrel folding type similar to template 2QHA The basic analysis of molecular dynamic simulation (root mean square deviation and root mean square fluctuation) showed that both enzymes were thermostable, albeit compared to template 2QHA amino acid residues substitution in samples contribute for different thermostable profile. However, MAN2 was appeared to be more stable at high temperature than other samples. Keywords: endo β-mananase, homology modeling, molecular dynamic simulation

Isolation and Identification of Ice-Nucleating-Active Bacteria from Indonesian Edible Leafy Plant Poh-Pohan (Pilea glaberina) DIANA ELIZABETH WATURANGI; VICKY MEICY; ANTONIUS SUWANTO
Microbiology Indonesia Vol. 2 No. 1 (2008): April 2008
Publisher : Indonesian Society for microbiology

Two ice-nucleating-active (INA) bacteria (isolates C and 6) were isolated from poh-pohan (Pilea glaberina), an Indonesian edible leafy plant (lalaban). The maximum nucleation temperature of aqueous suspensions of the two isolates is -5 °C. They were classified as a type II ice nucleator. Microscopic and morphological determination showed that these isolates had yellow pigmentation, rod shape, and were Gram negative. Biochemical analysis indicated that the isolates were exhibited catalase activity, but negative in oxidase and indole assays. DNA sequencing of 16SrRNA gene of isolate A3 showed a 94% similarity to Pseudomonas sp. while isolate A4 showed a 97% similarity to Xanthomonas campestris. To our knowledge, this is the first report of INA bacteria isolated from a tropical edible leafy plant.

Role of Bacteria in Tempe Bitter Taste Formation: Microbiological and Molecular Biological Analysis Based on 16S rRNA Gene TATI BARUS; ANTONIUS SUWANTO; ARIS TRI WAHYUDI; HANNY WIJAYA
Microbiology Indonesia Vol. 2 No. 1 (2008): April 2008
Publisher : Indonesian Society for microbiology

Tempe is traditional Indonesian food. It has a variety of tastes, sometimes with a hint of bitterness, which may differ in intensity. The cause of bitterness in tempe has never been reported previously. In this study, the aim is to identify whether bacteria play a role in the formation of bitter tastes in tempe. Sensory tests were carried out in order to determine the scoresof bitter-taste-intensity in tempe. The sensory test on EMP, WJB, CLR, DRG, and MLB tempe shows that EMP tempe has the highest score (2.3) and WJB has the lowest (1.3). It is revealed that the processing method has no impact on the formation of the bitter taste in tempe. Plating analysis, showed that EMP soaking water contained a higher number of Enterobacteria groupbacteria, approximately 103-104 CFU ml-1 and spore-forming bacteria groups, 102 CFU ml-1, compared to WJB. Similarly, other bacteria groups in fresh EMP tempe was 102 CFU g-1 higher than those in fresh WJB tempe. Based on sequencing the16S rRNA gene, the dominant bacteria on PCA media in EMP tempe are Acetobacter indonesiensis, Klebsiella pneumoniae, Bacillus subtilis, and Flavobacterium sp. On the other hand those in WJB tempe were Klebsiella sp., Brevundimonas sp., Bacillus sp., Pseudomonas putida, and Acinetobacter sp. Bacillus, a group of proteolytic bacteria was found 105 CFU m-1 higher in the soaking water of EMP compared to WJB. Nevertheless, the types and numbers of fungi were not significantly different betweentempe types. Accordingly, it is concluded that the difference in the number and the types of bacteria involved in the tempe production process leads to the difference in the bitter taste intensity in both EMP and WJB tempe.

Phenotypic, Metabolic, and Genetic Diversity of the Indonesian Isolates of Rhizopus oligosporus CAHYA PRIHATNA; ANTONIUS SUWANTO
Microbiology Indonesia Vol. 1 No. 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

Fifteen Rhizopus oligosporus isolates were isolated from a number of tempeh samples obtained from Mataram, Jember, and Bogor, Indonesia; and subjected for characterization based on phenotypic, metabolic, and genetic fingerprinting through internal transcribed spacer (ITS) regions and amplified fragment length polymorphism (AFLP). Based on the growth on solid medium, they can be divided into three groups. Firstly, isolates that produced thick mycelia, dumpy sporangiophore, and scarce spores in agar culture, the second group is isolates that produced thin mycelia, stretched sporangiophore, with abundant spores in agar culture. The third group that only comprises one isolate, FB-06, is morphologically intermediate of the first and the second groups. These characters correlated with their range of temperature tolerance. The first group is less tolerant to high temperature (45 oC) compared with the second group, and the third group is the most tolerant to temperature up to 45 oC. Metabolic fingerprinting showed a very high polymorphism. In general, the result may explain a correlation in which isolates obtained from the same locations shared similar patterns. There is no correlation found between metabolic fingerprints and their phenotypic fingerprints. Rhizopus oligosporus readily dominated the niche and utilized nearly all carbon sources given demonstrate the versatile nature of this fungus. ITS regions identification revealed single nucleotide polymorphisms in four representative isolates examined, whereas AFLP fingerprinting determined each of representative isolates as individually unique. Furthermore, this AFLP profile seemed to agree with their phenotypic characters..

Genetic Diversity of Antifungi-Producing Rhizobacteria of Pseudomonas sp. Isolated from Rhizosphere of Soybean Plant SUSILOWATI1 SUSILOWATI1; ARIS TRI WAHYUDI; YULIN LESTARI; SURYO WIYONO; ANTONIUS SUWANTO
Microbiology Indonesia Vol. 4 No. 1 (2010): April 2010
Publisher : Indonesian Society for microbiology

Antifungi-producing rhizobacteria have been recognized playing an important role in plant disease suppression. In our laboratory, 13 indigenous soybeans' rhizobacteria Pseudomonas sp. that showed strong growth inhibition of root pathogenic fungi, Rhizoctonia solani, Fusarium oxysporum and Sclerotium rolfsii, have been isolated from rhizosphere of soybean plant. For further understanding, the genetic diversity of the antifungi-producing Pseudomonas sp. was investigated using Amplified 16S rDNA Restriction Analysis (ARDRA) and 16S rRNA gene sequences analysis. 16S rDNA were amplified by PCR technique and digested with restriction endonuclease HaeIII, RsaI and AluI. Sequences of 16S rRNA gene were analyzed using the BLAST program for similarity searches on sequence databases. ARDRA based dendrogram analysis was carried out by neighbor-joining of TREECON 1.3b software package. ARDRA indicated the variability of Pseudomonas sp. based on the digestion sites. Dendrogram clustering analysis based on the restriction enzymes profile of the amplified rDNA distinguished Pseudomonas sp. into 7 ribotype groups. The sequences of 16S rRNA gene confirmed that the isolates belonging to Pseudomonas sp. and the phylogenetic tree formed 4 clusters. There was a quite overlap among ARDRA groups and 16S rRNA sequence clusters. This finding suggested that antifungal producing Pseudomonas sp. were present in the rhizosphere of soybean plant and the level of genetic diversity exist within these species. Sequence analysis of the 16S rRNA gene of the Pseudomonas sp. with an identical ARDRA pattern confirmed that members of an ARDRA group were closely related to each other.

Evidence for a Link Between Pathogenicity and the Role of ImpBacterial Transport Effector Proteins in Soybean Infection by Xanthomonas axonopodis pv. glycines ANTONIUS SUWANTO; ARIS TRI WAHYUDI; BUDI TJAHJONO
Microbiology Indonesia Vol. 1 No. 2 (2007): August 2007
Publisher : Indonesian Society for microbiology

Xanthomonas axonopodis pv. glycines (Xag) is the causal agent of bacterial pustule disease of soybeans. A nonpathogenic mutant of Xag (M715) was constructed employing transposon mutagenesis which showed similar epiphytic survival in planta to its wild type strain (YR32). The objective of this work was to identify and to analyze genes involved in pathogenicity in Xag YR32. Inverse Polymerase Chain Reaction (IPCR) was used to isolate the DNA flanking transposon insertion. A 1.3 kb flanking DNA fragment was sequenced and analyzed employing BLAST program to study homology, the position of transposon insertion and to predict the structure and function of the gene. One of the Open Reading Frames (ORFs) shared homology with inner membrane proteins (imps) of Xanthomonas axonopodis pv. citri (GenBank accession No. NC 003919). Northern blot analysis revealed that an imps gene was monocistronic and the size of imps mRNA in YR32 was slightly longer than in M715. Reverse Transcriptase- PCR analysis demonstrated that the imps transcript in M715 was much less abundant than in the wild type YR32. Transposon (mini-Tn5-Kmr-Tpr) was determined to be inserted close to the end of C-terminal region of imps gene and might be sufficient to destabilize the imps transcript in M715 and so influence effectors transportation from Xag to plant cell.

The Dynamics of Bacterial Communities During Traditional Nata de Coco Fermentation CECILIA ANNA SEUMAHU; ANTONIUS SUWANTO; DEBORA HADISUSANTO; MAGGY THENAWIJAYA SUHARTONO
Microbiology Indonesia Vol. 1 No. 2 (2007): August 2007
Publisher : Indonesian Society for microbiology

One of the important problems in traditional Nata de Coco (Nata) fermentation is production inconsistency due to strain or genetic variability reflecting mixed microbial communities involved in this process. This research was aimed at examine the population dynamics of the bacterial community during the fermentation processes. Samples were collected daily for six days from fermentation media derived from “good” and “bad” Nata fermentation. We compared the levels of bacterial diversity through amplified 16S-rRNA (ARDRA). DNA was extracted directly from the fermentation media and 16S-rRNA gene was amplified employing Universal Bacterial Primers. The amplicons were cloned into pGEM-T Easy vector, and restriction enzymes HaeIII and RsaI were used to generate ARDRA profiles. ARDRA phylotypes of DNA extracted from the fermentation medium obtained from different Nata qualities were compared. Phylotype profiles demonstrated unique bacterial community profiles for different conditions of Nata quality, which could be developed as a parameter to monitor Nata quality during fermentation. In this research we found that the dynamics of the bacterial population involved in Nata fermentation were a crucial factor for determining traditional Nata quality.

Prospective Use of 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Bacteria for Plant Growth Promotion and Defense against Biotic and Abiotic Stresses in Peat-Soil-Agriculture EDI HUSEN; ARIS TRI WAHYUDI; ANTONIUS SUWANTO; RASTI SARASWATI
Microbiology Indonesia Vol. 2 No. 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

The 1-aminocyclopropane-1-carboxylate (ACC) deaminase (EC4.1.99.4) is an enzyme produced by some soil bacteria to degrade ACC (the immediate precursor of ethylene) to reduce ethylene biosynthesis in higher plants. Increased concentrations of ethylene in plant tissues, which are triggered by various biotic and abiotic stresses, inhibits plant growth and weakens the plant defense against the stressors. Various findings on the successful use of ACC deaminase producing bacteria for plant growth under unfavorable soil conditions are inspiring their use in tropical peat-soil-agriculture, which possesses bio-physical constraints. It has been proven that inoculation of plants with ACC deaminase producing bacteria decreased ethylene inhibition generated by unfavorable environmental conditions, such as nutrient shortage, flooding, drought, high salts, and the presence of heavy metals and organic pollutants. Understanding the mechanisms by which ACC deaminase-producing bacteria act to reduce plant stress and the fitness of bacterial traits with the properties and constraints of peat-soils becomes a key to utilize these bacteria in improving crop productivity. The bacteria may ameliorate plant stress as well as promote plant growth under seasonal bio-physical changes of peat-soils that are usually encountered in the field.

Activity of Proteolytic and Amylolytic Enzymes from Bacillus spp. Isolated from Shrimp Ponds IT JAMILAH; ANJA MERYANDINI; IMAN RUSMANA; ANTONIUS SUWANTO; NISA RACHMANIA MUBARIK
Microbiology Indonesia Vol. 3 No. 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

Accumulation of feed excess in commercial shrimp ponds due to overfeeding could decrease water quality. Protein and starch are the primary components of shrimp feed. This study was conducted to characterize extracellular proteases and amylases of Bacillus spp. isolated from shrimp ponds. 72 proteolytic and amylolytic Bacillus spp. isolates were screened from shrimp ponds in Karawang, West Java. Ten isolates were selected for further characterization for their growth and ability to reduce total suspended solid generated from commercial shrimp feed. Bacillus sp. DA 5.2.3 and L5 showed excellent activity in reducing total suspended solid, by 37 and 30% respectively. Protease and a-amylase activities of Bacillus sp. DA 5.2.3 isolate were consistently higher than that of L5. Maximum total and specific protease activity of DA 5.2.3 isolate was 2.0 U mL-1 and 40.9 U mg-1 respectively, while the activities of the L5 isolate were 2.1 U mL-1 and 23.0 U mg-1 respectively. Based on its 16S rRNA gene sequences, Bacillus sp. DA 5.2.3 showed 99% similarity to Bacillus cereus XHJ-2-6. Bacillus sp. DA 5.2.3 could potentially be applied to maintain water quality by reducing total suspended solid in water columns of shrimp ponds.

Co-Authors . EFRIWATI . Melani . NURHAIMI-HARIS A A Hermosaningtyas A A Hermosaningtyas, A A ADI YULANDI Agus PURWANTARA Agus Purwito Agustin Wydia Gunawan ALINA AKHDIYA RUSMANA AMARILA MALIK AMARILA MALIK Andi Khaeruni Andi Khaeruni ANJA MERYANDINI Anja Meryandini Anja Meryandini ARI SUSILOWATI ARIS TJAHJOLEKSONO Aris Tri Wahyudi ARTINI PANGASTUTI Asmini Budiani Basil J NIKOLAU BIBIANA W LAY Budi Tjahjono Budi Tjahjono BUDI TJAHJONO BUDI TJAHJONO C Hanny Wijaya Cahya Prihatna CAHYA PRIHATNA CECILIA ANNA SEUMAHU DEBORA HADISUSANTO Desniar . DIAH ISKANDRIATI DIANA ELIZABETH WATURANGI Djoko Santoso Dondin Sajuthi DWI SURYANTO Dyah Kusuma Anggraini Edi Husen Edi Husen EDI HUSEN ERNIN HIDAYATI ESTI PUSPITASARI Esti Utarti Eunice Limantara Felicia Kartawidjajaputra Ferymon Mahulette Ferymon Mahulette, Ferymon G. A. Wattimena Gayuh Rahayu Griselda Griselda Griselda, Griselda Hajrial ASWIDINNOO HAJRIAL ASWIDINNOOR Hariyatun, Hariyatun Iman Rusmana Inez H.S. Loeddin Suharsono It Jamilah IVAN HANJAYA JOANITA SADELI KATHARINA JESSICA Kusharyoto, Wien Lilis Nuraida Linda Wati Maggy T Suhartono Maggy T Suhartono MAGGY T. SUHARTONO MAGGY T. SUHARTONO Maggy T. Suhartono MAGGY THENAWIJAYA SUHARTONO Maria Indah Purnamasari Meity S. Sinaga MEITY SURADJI SINAGA MUHAMMAD ZAIRIN Jr. Ni Nyoman Tri Puspaningsih NISA RACHMANIA MUBARIK NURITA TORUAN-MATHIUS NURUL AINI PRIHASTO SETYANTO Prihasto Setyanto QURROTA Aâ€™YUN R. Sapto Hendri Boedi Soesatyo RAHAYU WIDYASTUTI Rasti Saraswati RASTI SARASWATI Rasti Saraswati RASTI SARASWATI RATIH DEWI HASTUTI RATNA SETYANINGSIH RATNA SETYANINGSIH RIDWAN AFFANDI ROB HARLING ROHANI CINTA BADIA GINTING Sheila Sutanto Sheila Sutanto, Sheila Suryo Wiyono SUSAN SOKA SUSILOWATI1 SUSILOWATI1 Tan Watumesa Agustina TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN Tati Barus TEMMY DESILIYARNI TRESNAWATI PURWADARIA VICKY MEICY WALTER ERDELEN Widanarni Widanarni Yogiara Yogiara YULIN LESTARI YUSMINAH HALA

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