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Articles by issue : Vol 9, No 1 (2015): March 2015
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Articles
Genetic Diversity of Cucumber Mosaic Virus Strain Soybean from Several Areas

DAMAYANTI, TRI ASMIRA, WIYONO, SURYO

Microbiology Indonesia Vol 9, No 1 (2015): March 2015
Publisher : Indonesian Society for microbiology

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Abstract

Cucumber mosaic virus strain soybean (CMV-S) is one of economically important virus infecting soybean in Indonesia. However, it is very few information related with the CMV-S Indonesia isolates. Thus, the aim of present work is to detect and identify CMV-S isolates from different origin. Leaf samples collected from six different soybean fields in Java and North Sumatera. Molecular detection was carried out by reverse transcription polymerase chain reaction (RT-PCR) using specific primer of the coat protein (CP) gene and DNA sequencing. RT-PCR were successfully amplified the entire CP gene size ~657 bp from all samples and encoded 218 amino acids. Analysis of nucleotide and amino acid sequences showed high homology among isolates ranging from 99.5% and 100%. However isolate from Sindang Laut either nucleotides or amino acids showed lower homology to that of five isolates ranging from 89.4%-89.6% and 91.7%, respectively. The differences between CMV-S with other non legume strain found in six amino acid positions in the CP gene, suggesting the differences might related with host specificity. Phylogenetic analysis of amino acid of six isolates to other CMV strain showed that the five CMV-S isolates were in the same cluster, while Sindang Laut isolate was in different cluster together with the non-legume CMV from India. It is indicating the present of genetic variability among CMV-S isolates in Java.

Molecular Phylogeny of Salmonellae: Relationships among Salmonella Species Determined from gyrA, gyrB, parC, and parE Genes

AMARANTINI, CHARIS, SATWIKA, DHIRA

Microbiology Indonesia Vol 9, No 1 (2015): March 2015
Publisher : Indonesian Society for microbiology

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Abstract

Study on molecular characteristics of Salmonella from clinical isolates was done in order to find out its relationship, especially those isolated from Indonesia. Partial sequence of genes belonging to QRDR region, i.e. gyrA, gyrB, parC, and parE were employed. Specific primer pairs covering those genes are used to amplify the bacterial DNA obtained. The amplicons were then analyzed by means of sequencing, and the sequences are analysed bioinformatically to find out similarities and build phylogenetic trees. By comparing all of the phylogenetic tree from QRDR region, this study revealed gyrA as the most suitable gene for rapidly identify member of salmonellae as it gives better separation of samples being analysed. However, the use of parC is recommended as it gives a consistent and reliable value to separate member of Salmonella and other Enterobacter. Further studies are under way to include member of this group, like E. coli, and the use of full sequence of QRDR genes region to verify this report.

Isolation of Oxo-degradable Polyethylene Degrading-Bacteria of Benowo Landfill Soil Surabaya

MUKAMTO, MUKAMTO, RAHAYU, YUNI SRI, LISDIANA, LISA, PRANAMUDA, HARDANING

Microbiology Indonesia Vol 9, No 1 (2015): March 2015
Publisher : Indonesian Society for microbiology

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Abstract

The widespread consumption of oxo-degradable polyethylene plastics in Indonesia is potentially cause pollution. This problem can be overcome by utilize plastic degrading-bacteria as degradation agent. The present study aims to isolate and characterize of oxo-degradable polyethylene degrading-bacteria from Benowo landfill soil Surabaya. Isolation and screening was done by the culture technique and clear zone method. Total abundance of bacteria was calculated based on the Total Plate Count method. Bacterial colonies screening was done based on morphological characteristics and the diameter of clear zone. Four isolates with the largest diameter of clear zone were futher characterized based on cell morphology and physiology biochemistry characters. The results showed the average of total abundance of oxo-degradable polyethylene degrading-bacteria of Benowo landfill was 1.28 x 104 CFU g-1. The four of twelve isolates with the largest diameter of clear zone was indicated the highest degradation capability, that were isolates A221 (0.7 cm), A231 (1 cm), A232 (0.6 cm), and C231 (1.3 cm). Colony morphology characteristics of four isolates were generally shape of circular and irregular; margin of entire and lobate; elevation of flat; optics of opaque; and pigmentation of yellow, greenish and cream. These four isolates were Gram negative with the shape bacilli and cell size range of 3-4 μm. Physiological and biochemical characteristics among the four isolates were resistant to acidic conditions; non-motile; produce catalase enzyme except A231; capable to reduce glucose and mannitol; uncapable to reduce lactose; capable to produce acids, except A232; produce of 2.3-butanediol; unable reduce sodium malonate; and capable to reduce nitrate, except A232 and C231; as well as producing hydrogen sulfide except A221 and A232. The four isolates has similar properties with the genus Mycobacterium.

Administration of Microencapsulated Probiotic at Different Doses to Control Streptococcosis in Tilapia (Oreochromis niloticus)

UTAMI, DIAH AYU SATYARI ( Bogor Agricultural University ) , WIDANARNI, WIDANARNI - ( Bogor Agricultural University ) , SUPRAYUDI, M AGUS ( Bogor Agricultural University )

Microbiology Indonesia Vol 9, No 1 (2015): March 2015
Publisher : Indonesian Society for microbiology

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Abstract

This study aimed to produce microencapsulated probiotic and determine its optimal dose to control streptococcosis in tilapia (Oreochromis niloticus). The probiotic used in this study was Bacillus sp. NP5 RfR that was encapsulated by sterile 10% maltodextrin solution and dried by spray dryer. The experimental fish were reared 28 days and fed by the administration of microencapsulated probiotic in feed with different doses (0,5% (A), 1% (B), and 2% (C)) which were 1010 CFU g-1 as the concentration and control without administration of microencapsulated probiotic, including negative (K-) and positive (K+) control. On day 30, all of the fish except K- were challenged by injecting 0.1 mL/fish  of Streptococcus agalactiae (105 CFU ml-1) by intra-peritoneal (IP) route. This study showed that administration of 0.5% microencapsulated probiotic was effective to control streptococcosis in tilapia with higher post-challenge survival rate, better hematological parameter values, and could inhibit S. agalactiae growth in the host target organs.

16S rRNA-based Metagenomic Analysis of Endophytic Actinomycetes Diversity from Tinospora crispa L. Miers

PRIMANITA, MONA ( Microbiology Study Programme, Graduate School of Bogor Agricultural University, Darmaga Campus, Bogor 16680 ) , WAHYUDI, ARIS TRI ( Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680 ) , LESTARI, YULIN ( Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680 Biopharmaca Research Center, Bogor Agricultural University, Taman Kencana Campus, Bogor 16151 )

Microbiology Indonesia Vol 9, No 1 (2015): March 2015
Publisher : Indonesian Society for microbiology

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Abstract

Endophytic actinomycetes associated with medicinal plants is very important as source of various bioactive compounds. The fact that more than 99% of microbes that exist in nature may have the potency but still unexplored. Published data regarding diversity of endophytic actinomycetes from T. crispa is mainly based on a culturable approach. This paper describes the first reported data regarding metagenomic analysis on the diversity of endophytic actinomycetes from T.crispa based on 16S rRNA gene using PCR-DGGE. There were some similarities amongst endophytic actinomycetes found in stems, roots, and leaves with soil actinomycetes community in the rhizosphere of T. crispa. There were a total of 21 bands found from the DGGE analysis which were interpreted using Phoretix 1D software. Diversity of actinomycetes in the stems, leaves, roots were represented by 17, 16, and 14 bands, respectively. Whereas only 10 bands represented diversity of actinomycetes in the soil rhizosphere. The 12 dominant and or different bands with 180 bp in size were molecularly sequenced. The A4 and A9 bands have 95% and 86% similarities with Williamsia and Streptomyces, respectively. These similarities were less than 97% thus may indicate novel actinomycetes. The other 10 sequenced bands have closed similarity ranging from 97-100% and they were closely related to the genus Streptomyces, Microbacterium, Amycolatopsis, Actinomadura, Actinoplanes, Actinokineospora, Kibdelosporangium, Williamsia and Kocuria. These findings indicate that diversity of actinomycetes can be found associated with T. crispa. 

Antibacterial Activity and Mode of Action of (+)-2,2-Epicytoskyrin A

AGUSTA, ANDRIA, WULANSARI, DEWI, JAMAL, YULIASRI, NURKANTO, ARIEF, PRAPTIWI, PRAPTIWI, FATHONI, AHMAD

Microbiology Indonesia Vol 9, No 1 (2015): March 2015
Publisher : Indonesian Society for microbiology

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Abstract

Antibacterial activity of (+)-2,2-epicytoskyrin A, a main metabolite from culture of fungal endophyte Diaporthe sp. GNBP-10, was investigated against several strains of Gram-positive, Gram-negative bacteria, and one strain of Mycobacterium smegmatis. (+)-2,2-Epicytoskyrin A exhibited prominent activity against Staphylococcus aureus BCC 1452 with minimum inhibitory concentration (MIC) value of 0.06 μg mL-1. The effect of (+)-2,2-epicytoskyrin A treatment to S. aureus, resulted in alteration of bacterial cell membrane with an increase of cation efflux, while the cytoplasmic content was not leaked out and finally resulted in cell damage.