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Articles by issue : Vol 2, No 3 (2008): December 2008
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Articles
Recent Developments in the Bioconversion of Lignocelluloses into Ethanol

KOESNANDAR, ., HELIANTI, IS, NURHAYATI, NIKNIK

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

Ethanol has been commercially produced using sugars derived from sugarcane and corn. Recently, research has been focused on the development of thermotolerant and ethanol-tolerant yeast or bacteria that are able to produce ethanol efficiently, as well as the development of lignocellulosic materials as the carbon sources of fermentation. Utilization of lignocellulosic materials as fermentation substrate is promising since they are available in large amounts, renewable and relatively cheap. A lignocellulose biomass is a complex mixture of carbohydrate polymers. In order to develop an efficient process, there have been many attempts to obtain more efficient ways in the conversion of lignocelluloses to ethanol, including pretreatment, enzymatic hydrolysis of lignocelluloses and direct co-culture fermentation. This paper describes the production process of ethanol from starch-containing material, recent developments on the enzymatic bioconversion of lignocelluloses into sugars and their subsequent fermentation into ethanol and the possible recombination of microbes for the direct conversion of lignocelluloses into ethanol.

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

HUSEN, EDI, WAHYUDI, ARIS TRI, SUWANTO, ANTONIUS, SARASWATI, RASTI

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

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.

Analysis of Pink Pigmented Facultative Methylotroph Bacteria from Human Environments

WATURANGI, DIANA ELIZABETH, KUSUMA, ANDREAS

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

The formation of pink biofilm in wet places are usually correlated with chlorine-resistant pink pigmented facultative methylotrophs (PPFM). In this study we investigated the presence of PPFM bacteria through bacterial isolation and detection of mxaF gene from wet places of human-made environments. A total of eighteen PPFM bacterial isolates were recovered from the formation of biofilm bacterial of four test places such as washstands, bathrooms, and potable water supplies. Confirmation of the isolates through biochemical analysis were done using catalase, oxidase and urease tests. Chlorine-resistance-activity was assayed for all of the isolates. Antibiotic resistance were examined for ampicillin (25 μg), tetracycline (30 μg), kanamycin (30 μg), trimethoprim (1.25 μg), and streptomycin (10 μg) using the agar diffusion method. Genomic DNA was subjected to PCR analysis with primers corresponding to the 5’- and 3’- end conserved segments of the mxaF gene. PCR amplification followed by DNA sequencing of 16S rRNA gene were done for some isolates. We recovered 18 isolates of PPFM bacteria. Biochemical analysis indicated that the isolates were positive for catalase, oxidase, and urease activities. Chlorine-resistance-analysis showed the majority of the isolates were resistant to chlorine. Antibiotic resistance assays showed all of the isolates exhibited resistance to trimethoprim but were sensitive to streptomycin, kanamycin, and tetracycline but were variably resistant to ampicilin. PCR detection using specific primers for the mxaF gene gave a positive result for all of the isolates. DNA sequencing of the 16S rRNA gene of two isolates showed that isolate WD10 had a 98% similarity with the mxaF gene from Methylobacterium lusitanum strain MP2 and isolate WK2 had a 98% similarity to the mxaF gene from Afipia felis strain RD1. The formation of pink biofilm of four wet areas in this study were correlated with the presence of chlorine-resistant PPFM bacteria and we confirmed with the presence of the mxaF gene in all of the isolates. This finding needs to be widely publicized since some PPFM bacteria were known as opportunistic pathogens.

Characteristics of Phosphate-Solubilizing Bacteria Isolated from Acid Soil of Cikopomayak, West Java, Indonesia

WIDIASTUTI, HAPPY

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

Phosphate-solubilizing bacteria were isolated from acid soil from Cikopomayak. Microbiological assay showed that the bacteria were Gram negative, rod-shaped, and lacked red pigment on Pikovskaya medium. Isolate A synthesized red pigment on nutrient agar medium, while isolate B formed slightly red pigment on nutrient agar medium as well as on Voges Proskauer medium. The ratio of clearing zone to colony for isolate A and B were approximately 2.1 and 1.9, respectively. Biochemical assays showed that both isolates A and B utilized glucose, lactose, sucrose, mannitol, glycerol, mannose, urea, indole, and produced catalase, but neither produced amylase and oxidase. The bacteria are identified as Serratia marcescens. The ability to solubilize phosphate decreased or was even lost when subcultured on nutrient agar medium. However, the ability to solubilize phosphate was recovered gradually with the addition of phosphate. The results presented here suggest that the ability to solubilize phosphate and to synthesize the red pigment may be inversely correlated.

Biosynthesis of Polyamide 4, a Biobased and Biodegradable Polymer

SASKIAWAN, IWAN

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

Polyamide 4, which is composed of repeating unit of g-aminobutyric acid (GABA), is a biobased and biodegradable polymer since it can be synthesized from renewable material instead of fossil-based material. GABA is produced by decarboxylation of glutamate (Glu) using glutamate decarboxylase (GAD: EC 4.1.1.15), which is produced by some microorganisms. In this study, enzymatic conversion of GABA from glutamate by Lactococcus lactis and Escherichia coli cell and chemical polymerization of GABA to polyamide 4 were revealed. The results show that GAD activity of E. coli was higher than that of L. lactis. The treatment of E. coli cell by heating and sonication increased the GAD activity and conversion rate of glutamate to GABA was up to 70.5%. The optimum temperature for this conversion is 37ºC. On the other hand, chemical synthesis of polyamide 4 was catalyzed by heating GABA at 215ºC for 2 minutes

Stability of Two Probiotics Bacteria of Goat Milk Yoghurt in Rat Digestive Tract

MAHESWARI, RARAH RATIH ADJIE, WIRYAWAN, I KOMANG GEDE, MADUNINGSIH, GINA LESMANA

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

Increased age will affect the bacterial population of the human digestive tract, in which many bacteria will adapt and colonize different sites. Combining probiotics and prebiotics in what has been called a synbiotic could beneficially affect the host by improving survival and implantation/adhesion of live microbial dietary supplements in the gastrointestinal flora. Probiotic bacteria are expected to survive in the digestive tract to give health effects to the host by balancing the intestinal microflora. The addition of fructo-oligosaccharides is expected to increase viability and growth of probiotics in the digestive tract. The objective of the current research is to investigate the effect of probiotic yoghurt and synbiotic yoghurt of Etawa Breed Cross Saanen (PESA) goats together with fructo-oligosaccharides, on female rats and to study the stability of probiotic bacteria in the digestive tracts. The results showed that synbiotic yoghurt intake had no significant influence (p>0.05) on ration consumption, body weight gain, feed conversion, final body weight and mortality. The synbiotic intake significantly increased the population of Bifidobacterium longum (p

Free-Living Ice-Nucleating Active Bacteria from High Mountain Lake Habitats

YUHANA, MUNTI, HANSELMANN, KURT

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

We collected the culturable heterotrophic bacteria from oligotrophic high mountain lake habitats and tested their capability to induce ice formation. Direct plating was carried out using low-nutrient medium at a temperature of between 3 and 4°C. As many as 84 isolates were recovered from glacial ice and natural biofilm growing on granite rocks surface. Six out of 84 isolates were capable of expressing the ice-nucleation phenotype. After autoclaving the cell suspension at 121°C for 15 min, isolate J78 was still able to retain the ability for ice formation. Heat-stable ice nuclei produced by ice-nucleating active bacteria have potential applications in biotechnology. Characterization of INA bacteria was performed employing live-dead Gram staining and molecular methods. Universal primers for Bacteria (S-D-Bact-0008-b-S-20 and S-D-Bact-1524-a-A-18) were used for PCR to amplify almost the full length of the 16S rRNA genes of selected INA isolates. Restriction fragment length polymorphism analysis resulted in 2 unique patterns, as represented by J43 and J83, respectively. Based on DNA sequencing of 16S rRNA gene, isolate J43 (GeneBank accession no. AJ864852) was closely related to Pseudomonas mephitica (99.2% sequence similarity) and Janthinobacterium lividum (99% similarity), whereas isolate J83 (GeneBank accession no. AJ864859) showed 100% sequence identity to Pseudomonas fluorescens.

Phylogenetic Evidence that Two Submerged-Habitat Fungal Species, Speiropsis pedatospora and Xylomyces chlamydosporus, Belong to the Order Jahnulales Insertae Sedis Dothideomycetes

PRIHATINI, RIRY, BOONYUEN, NATTAWUT, SIVICHAI, SOMSAK

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

The genera Speiropsis and Xylomyces are anomorph fungi. The taxonomic address for the fungi has been unclear. In this study, observation of morphological traits indicates that they have a unique pattern of mycelia with dark-brown to black colour and thick-walled hyphae. The same culture patterns of certain fungi isolated from freshwater habitats in Thailand were selected from BIOTEC Culture Collection (BCC, Thailand), while more species were added from Centraalbureau voor Schimmelcultures (CBS, Netherlands). These fungi were composed of Jahnula spp. (2-celled ascospores), Brachiosphaera tropicalis (hyaline and 4-5 armed conidia), S. pedatospora (hyaline and branches conidia) and Xylomyces sp. (dematiaceous and fusiform chlamydospores). This study was undertaken to confirm the taxonomic address for S. pedatospora and Xylomyces based on phylogenetics relationships as inferred from their ITS rDNA sequence data by using MP (unweighted and successive weighted MP), NJ, ML and Bayesian analysis. Phylogenic analysis revealed that isolates of S. pedatospora (2 strains) was a member of the Order Jahnulales and clustered with Jahnula spp. (5 strains) and B. tropicalis (4 strains) with >82% bootstrap support and 100% posterior probabilities. Four isolates of X. chlamydosporus, X. elegans and X. aquaticus were shown to be polyphyletic within the Jahnulales and Pleoporales. The MP and NJ showed the same topology as in the Jahnulales clade obtained by ML analysis.

Selection of Isolates of Entomopathogenic Fungi and the Bioefficacy of Their Liquid Production against Leptocorisa oratorius Nymphs

HERLINDA, SITI, MULYATI, SRI INDAH, SUWANDI, .

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

Entomopathogenic fungi are fungi pathogenic to insects and are widely used as biocontrol agents for insect pests. The aim of this research was to study the virulence of Beauveria bassiana and Metarhizium sp. isolates and to evaluate the efficacy of liquid production of those fungi against Leptocorisa oratorius (rice bug). Twelve isolates of B. bassiana and five isolates of Metarhizium sp. were used in this research. Selection result of B. bassiana isolates on third-instar rice bug nymphs showed that the isolate KBC caused the highest mortality rate (93%), while the lowest (46%) was caused by the isolate BBY 725. The shortest time needed to produce 50% mortality (Lethal time, LT50) was 3.52 days (isolate KBC). The longest time (10.36 days) was produced by isolate SLSS. The mortality of rice bug nymphs caused by Metarhizium isolates was only 50-62%. The shortest LT50 of Metarhizium (5.75 days) was produced by isolate Mtm, while the longest (7.46 days) was produced by isolate Mpx. Bioefficacy tests on six kinds of liquid formations of entomopathogenic fungi indicated that all were effective, mostly with LT50 d” two days. The mortality rates of rice bug nymphs caused by bioefficacy of fungus liquid production was generally above 85% up to 100%. The liquid media for entomopathogenic fungi performed better compared with solid media (SDA), as indicated by the greater mortality rate and shorter LT50.

The Influence of Oil Concentration, Nitrogen and Phosphorus Composition on Crude Oil Biodegradation by Epyzim and Mixed Cultures of Pseudomonas aeruginosa and Arthrobacter simplex

NOOR, ERLIZA, HARDJITO, LINAWATI

Microbiology Indonesia Vol 2, No 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

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Abstract

Biological methods have gained attention as an alternative treatment for oil degradation in pollution remediation. External and internal factors have a great influence on crude oil biodegradation. This experiment studied the effect of oil concentrations and ratios of Ammonium and Phosphate on oil degradation in mixed cultures of local strains of Pseudomonas aeruginosa and Arthrobacter simplex. The oil degradation ability of this mixed culture was compared to the dormant culture of Epyzim. The increase of oil concentration, from 1, 3, 5 and 10% (w/v), significantly lowered the ability of both cultures to degrade the oil i.e from 83 % for 1% oil concentration to 64% for 10% oil concentration using local strains. The local strains showed better capability compare to the dormant culture. Medium composition was designed by three levels of ammonium concentration (7.6, 37.9 and 75.8 mg l-1) and two levels of phosphate concentration (2.0 and 9.9 mg l-1). The ratio of ammonium to phosphate of 3.8:1.0 in the growth media has resulted the maximum level of oil degradation, i.e 83% and 88%, for dormant and local cultures respectively. The results suggest a potential usage of local microorganisms in degrading crude oil-polluted water.