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Articles by issue : Vol 3, No 3 (2009): December 2009
8
Articles
The Plant – Pathogen Interactions

PRIHATNA, CAHYA ( The Australian National University )

Microbiology Indonesia Vol 3, No 3 (2009): December 2009
Publisher : Indonesian Society for microbiology

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Abstract

Interaction between plants and their pathogens is complex, involving multifaceted recognition of pathogens by the plants and, on the other hand, subtle evasion from the pathogens. Plants perceive pathogens through direct recognition of common molecular patterns in microbes and direct recognition of effectors or their perturbation on cellular components by the pathogens. Recognition of microbe- or pathogen-associated molecular patterns triggers innate immunity that renders plants resistant to most potential microbial pathogens. Recognition-dependant immunity in plants largely relies on polymorphism of resistance gene products that confer specificity towards host-specialised pathogens, which, in turn, induces more specific resistance that is effective against host-specialised pathogens. The deployment of effective resistance involves signalling of pathogen recognition through complex signalling cascades, transcriptional reprogramming, and defence-related genes, which all contribute to an arrest of pathogen growth. Our current insights into effector biology and to which the plants respond, provide a detailed information on the evolutionary arms race between plants and their pathogens. These will lead to an improvement of current strategies for crop improvement and protection.

Analysis of Rumen Microbial Population of Cattle Given Silage and Probiotics Using Terminal Restriction Fragment Length Polymorphism

RIDWAN1, RONI ( Lembaga Ilmu Pengetahuan Indonesia ) , WIDYASTUTI1, YANTYATI ( Lembaga Ilmu Pengetahuan Indonesia ) , BUDIARTI, SRI ( Institut Pertanian Bogor ) , DINOTO, ACHMAD ( Lembaga Ilmu Pengetahuan Indonesia )

Microbiology Indonesia Vol 3, No 3 (2009): December 2009
Publisher : Indonesian Society for microbiology

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Abstract

Rumen ecology is an important observation in evaluating the effectivity of silage and probiotic additives relating to their roles in cattle productivity. The objective of this study was to examine the effects of silage and probiotics on ruminal ecosystems in vivo using a molecular approach. Terminal-restriction fragment-length-polymorphism (T-RFLP) analysis was used to detect changes of ecological communities based on 16S-ribosomal deoxyribonucleic acid (16S-rDNA). Two rumen canulated PO cattle were fed several diets i.e.; (R0) basal diet dry matter basis (Pennisetum purpureum 70% and commercial concentrate 30%), (R1) silage (basal diet fermented using Lactobacillus plantarum BTCC570), (R2) silage + probiotics (L. plantarium Str BTCC531), (R3) Basal diet + probiotics (L. plantarium Str BTCC531). Digesta samples were collected 3 h after feeding for pH and T-RFLP analysis. T-RFLP analysis was performed using the 16S-rDNA amplified from each sample. The lengths of the terminal restriction fragments were analysed after digestion with HhaI, HaeIII and MspI. Results showed the effectivenes of silage and probiotics, given together, on the index of Smith and Wilson evenness applied to T-RFLP ecology data (Evar) with 0.89±0.04 being the highest. The diversity of rumen microorganisms is influenced by individual differences of each animal. T-RFLP analysis has a potency to be used for comparisons of complex bacterial communities, especially to detect changes in community structure in response to different variables and to show rumen bacteria diversity in the rumen.

Bacterial Community Profiles in the Fluid of Four Pitcher Plant Species (Nepenthes spp.) Grown in a Nursery

SIEGARA, ANDREE ( Universitas Katolik Indonesia Atma Jaya ) , YOGIARA, . ( Universitas Katolik Indonesia Atma Jaya )

Microbiology Indonesia Vol 3, No 3 (2009): December 2009
Publisher : Indonesian Society for microbiology

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Abstract

Nepenthes is one of the Indonesian tropical carnivorous plants. The plant has a pitcher-like structure containing fluid for digesting insects. There are many microorganisms growing in the pitcher fluid. Different species of pitcher plants and planting sites could also contribute either to the diversity or the abundance of microorganism inhabiting the pitcher fluid. To assess the bacterial community variation in the fluid of pitcher plants grown in a nursery, amplified ribosomal DNA restriction analysis (ARDRA) was used. Four specimens of N. gracilis, N. truncata, N. veitchii and N. bicalcarata were obtained from Suska Nursery, Ciderum Village, Caringin, Bogor, Indonesia. A total of 191 positive clones were analyzed by using ARDRA. A sum of 124 phylotypes was obtained, comprising 17 in N. gracilis, 7 in N. truncata, 45 in N. veitchii and 55 in N. bicalcarata. It is interesting to note that each specimen harbored unique phylotypes, meaning that no phylotypes generated from one specimen were found in any of other specimens.

Molecular Detection of Dapsone and Rifampicin Resistance on Mycobacterium leprae from Leprosy Patients in East Java

ADRIATY, DINAR ( Universitas Airlangga ) , WAHYUNI, RATNA ( Universitas Airlangga ) , PRAKOESWA, CITA ROSITA S. ( Universitas Airlangga ) , SUSARI, NI PUTU ( Universitas Airlangga ) , AGUSNI, INDROPO ( Universitas Airlangga ) , IZUMI, SHINZO ( Universitas Airlangga )

Microbiology Indonesia Vol 3, No 3 (2009): December 2009
Publisher : Indonesian Society for microbiology

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Abstract

The drug resistant problem of Mycobacterium leprae has been developing since the last decade and this has become a leprosy elimination problem in several countries, including Indonesia. Using biological on molecular methods, it is now possible to test for drug resistant cases in relatively simple and less time consuming ways. The purpose of the study is to analyze theprevalence of drug resistance M. leprae to dapsone and rifampicin in East Java based on the  etection of mutations in the folP and rpoB genes. All samples were obtained from multibacillary leprosy patients in East Java, who have admitted to the Dr Sutomo Hospital Surabaya in 2003-2005. Isolates were analyzed by PCR, and the presence of nucleotide sequence of the folP and rpoB genes from M. leprae were confirmed by direct sequencing. Of 94 specimens which were collected, all were analyzed for their folP and rpoB genome. From 94 isolates, 70 showed a positive result by the folP1-folPR test and 77 out of 94 isolates showed positive by the rpoBF-rpoBR test. From 70 isolates for folP gene examination, there were 3 isolates which had mutation in the amino acid at codon 53; 2 cases Threonin (ACC) became Alanin (GCC) and 1 case Threonin (ACC) became Arginin (AGA). These mutations are responsible to dapsone resistance. For the rpoB gene, no mutation was found. The result suggested that 3 isolates (4.3%), 1 from a new case and 2 from relapse cases in this experiment, were resistant to dapsone and all isolates (100%) were susceptible to rifampicin.

Horizontal Transfer of the “Popcorn-Effect” Strain of Wolbachia from Drosophila melanogaster to Stomoxys calcitrans

KUSMINTARSIH, ENDANG SRIMURNI ( Universitas Jenderal Soedirman )

Microbiology Indonesia Vol 3, No 3 (2009): December 2009
Publisher : Indonesian Society for microbiology

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Abstract

The Wolbachia containing haemolymph from Wolbachia infected Drosophila third/fourth instar larvae was transferred through microinjection into 5-days-old pupae of the blood sucking stable fly, Stomoxys calcitrans. There was no previous record of Wolbachia being present in S. calcitrans. From a total of 682 emerging adults, 236 were females and of these, seven females were tested positive (approximately 3%) for Wolbachia infection. Using electron microscopy, it was shown that Wolbachia were present in the muscle tissues of S. calcitrans.

The Quality of Physic Nut (Jatropha curcas) Seeds Affected by Water Activity and Duration of Storage

DHARMAPUTRA, OKKY SETYAWATI ( Bogor Agricultural University ) , WORANG, RANTJE LILLY ( Institut Pertanian Bogor ) , SYARIEF, RIZAL ( Institut Pertanian Bogor ) , MIFTAHUDIN, . ( Institut Pertanian Bogor )

Microbiology Indonesia Vol 3, No 3 (2009): December 2009
Publisher : Indonesian Society for microbiology

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Abstract

The quality of physic nut (Jatropha curcas) seeds should be maintained during storage, either as seeds for seedlings or oil production to be used for biodiesel. The effects of water activity and duration of storage on the quality, i.e. fungal population, lipid, fatty acid and free fatty acid contents, and viability of physic nut seeds were investigated. The results showed that the moisture content of seeds and total fungal population decreased at low water activities, and increased at high water activities (aw). At aw 0.64, at the beginning of storage and after 20 weeks of storage, total fungal populations were 5.4 x 103 and 1.8 x 102 cfu g-1 dry basis (db), respectively. At aw 0.93, at the beginning of storage and after 20 weeks of storage, total fungal populations were 5.0 x 103 and 3.3 x 106 cfu g-1 db, respectively. At the beginning of storage fungi infecting seeds were field fungi, i.e. Cladosporium sp., Colletotrichum sp., Fusarium semitectum, and F. verticillioides. The population of field fungi decreased with the increase of storage duration. They were replaced by postharvest fungi, i.e. Aspergillus restrictus, A. penicillioides, Eurotium chevalieri, E. rubrum, Penicillium citrinum, P. implicatum and P. oxalicum. Lipid content and viability of seeds decreased with the increase of water activities and seed moisture contents, while free fatty acid contents increased with the increase of water activities and seed moisture contents during storage. Fatty acids of lipid were dominated by unsaturated fatty acids, i.e. oleic and linoleic acids. Physic nut seeds could be stored at aw 0.64-0.75 up to eight weeks when the seeds will be used for seedling, or up to 16 weeks when they will be used for producing oil.

Rapid Detection of Virulence Genes in Vibrio cholerae from Edible Ice in Jakarta

WATURANGI, DIANA E. ( Atma Jaya Catholic University ) , FRANSISCA, MARISA ( Atma Jaya Catholic University )

Microbiology Indonesia Vol 3, No 3 (2009): December 2009
Publisher : Indonesian Society for microbiology

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Abstract

Vibrio cholerae is a bacteria that lives naturally in an aquatic environment. It causes a waterborne disease which is called cholera. Infection of waterborne disease occurs via the fecal-oral route, mostly through drinking water. As we know, ice is made from city water sources and it is commonly used in beverages. Most of publications about V.cholerae come from clinical samples, while little is known about the presence of these bacteria in potable water, especially in ice. In this study, we isolated V. cholerae from ice in Jakarta and continued with detection of the virulence genes. We recovered V. cholerae from ice samples and then continued with detection of virulence genes including toxR, ctxA, ompU, tcpA, ace, zot using multiplex PCR. The results indicated that all of the samples were non-toxigenic strains, but were classified as pathogenic strains because they have at least one of the virulence genes present. The presence of pathogenic V. cholerae in edible ice needs to be emphasized since they have some of the virulence factors and also the class 1 integron.

Antimicrobial Activity of Black Cumin Extracts (Nigella sativa) Against Food Pathogenic and Spoilage Bacteria

YASNI, SEDARNAWATI ( Bogor Agricultural University ) , SYAMSIR, ELVIRA ( Institut Pertanian Bogor ) , DIREJA, EVA H ( PT Jerindo Sari Utama )

Microbiology Indonesia Vol 3, No 3 (2009): December 2009
Publisher : Indonesian Society for microbiology

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Abstract

This study aimed to analyze the antimicrobial activity of black cumin (Nigella sativa) extracts in inhibiting the growth of pathogenic and spoilage bacteria. Black cumin was extracted by using steam distillation, single solvent extraction, and continuous solvent extraction. Ethanol extract was the best extract in inhibiting the growth of bacteria while both aqueous and hexane extracts were less effective as antimicrobial agents. Ethanol extract, essential oil, and ethyl acetate extract have a broad antimicrobial spectrum. The chemical composition of the essential oil was analyzed using a GC-MS technique. The major component of black cumin essential oil was para-cymene, followed by trans-anethole, alloaromadendrene, á-thujene, and thujyl alcohol along with many other components in minor amounts. The Minimum Inhibitory Concentration (MIC) value ofethanol extract in inhibiting the growth of Salmonella typhimurium was 0.084% (w/w), of essential oil in inhibiting the growth of Bacillus cereus was 1.72% (w/w), of ethyl acetate extract in inhibiting the growth of Staphylococcus aureus was 1.88% (w/w) and of methanol extract in inhibiting the growth of Pseudomonas aeruginosa was 1.88% (w/w).