Search

Denitrification and nitrate-ammonification are the responsible processes for nitrate removal in the estuaries. Temperature, nitrate and organic carbon availability are key factors controlling a rate of the nitrate reduction processes. This mixed cultures chemostat study investigates the competition ability and their nitrate reduction end-products of the bacteria isolated from an estuary at different temperatures. This study will help us to understand the seasonal nitrate reduction processes in an estuary. The experiments showed that a nitrate-ammonifier was the predominant process in the steady-state chemostat at high temperature. While a facultative denitrifier-nitrate ammonifier was the predominant process at low temperature. However, the main end products of nitrate reduction at high temperature were up to 61% N2 indicating a denitrifier still had an important role in the end products of nitrate reduction in the estuary. The data also showed that a nitrite respiring bacterium reduced nitrite to N2, that responsible for approximately 6-9% of total N2 produced in the culture. This study confirmed that nitrate ammonifiers out-compete denitrifiers at high temperature, however, denitrifiers still had an important role in end products of nitrate reduction. [ABSTRACT FROM AUTHOR]

Certain strains of V. parahaemolyticus carry a gene that encodes a toxin that causes Acute hepatopancreatic necrosis disease (AHPND) in P. vannamei. AHPND attacks shrimp post larvae within 20-30 days after stocking causing up to 100% mortality. The expression of these virulent genes is controlled by the quorum sensing system. This system is inhibited by an anti-quorum sensing (AQS) mechanism. Several Bacillus strains have AQS mechanism by producing AHLLactonase enzyme. Therefore, this study aimed to obtain Bacillus spp. having AQS activity for controlling AHPND. The study was conducted from isolation and selection of Bacillus isolates, as well as determination of AQS activity. From 22 samples consisting of shrimp intestines, water and pond sediment samples, a total of 151 isolates of Bacillus spp. were isolated. The screening test for AQS activity obtained 11 isolates that showed AQS activity on Cromobacterium violaceum. Determination of violacein pigment in liquid cultures of C. violaceum showed the index value of the pigment formation was between 0.025-0.166 and 0.026-0.567 at 24-hour and between 48-hour incubations, respectively. The quantitative analysis of violacein production showed that there were six isolates of Bacillus could inhibit the pigment production more than 75%. The isolates were identified as Bacillus cereus (four isolates), Bacillus thuringiensis (one isolate), and Bacillus velezensis (one isolate), respectively. The molecular analysis had confirmed that the isolates have aiiA genes encoding AHL-lactonase enzyme. These Bacillus isolates have potential application for controlling AHNPD disease. [ABSTRACT FROM AUTHOR]

Paddy field is one of the anthropogenic sources that produce greenhouse gases emission. This study aimed to investigate the impact of methanotrophic and N2Oreducing bacterial inoculation on CH4 and N2O emissions, paddy growth and bacterial community structure in paddy field. Two treatments of 100% synthetic fertilizer (250 kg urea/ha) without biofertilizer and 50% synthetic fertilizer (125 kg urea/ha) with biofertilizer consisted of methanotrophic and N2O-reducing bacteria were applied in the paddy field. Inoculation of methanotrophic and N2O-reducing bacteria was able to reduce CH4 and N2O emission up to 4.19 mg CH4/m2/day and 351.29 µg N2O/m2/day, respectively. Those bacterial applications were also able to increase paddy growth and yield productivity. According to DGGE profile, inoculation of the biofertilizer seemed to have a transient impact on bacterial communities in paddy soil at 36 days after transplanting (DAT) which showed the lowest similarity with all samples (a similarity index of 0.68). DGGE bands successfully excised have closest relative to uncultured bacteria which comprised 5 phyla, i.e. Proteobacteria (Alphaproteobacteria and Deltaproteobacteria), Nitrospirae, Actinobacteria, Firmicutes, and Acidobacteria. In this study, Alphaproteobacteria was the most dominant phylum. We provide basic information for developing the biofertilizer which supports sustainable agriculture. [ABSTRACT FROM AUTHOR]

As a social insect, termite colony consists of three castes, i.e. reproductive, soldier, and worker castes. In their role of cellulose digestion, the worker termites use two sources of cellulolytic enzyme that include cellulases produced by the termite and the gut symbions. Macrotermes gilvus classified in mound builder termite, mostly depend on cellulolytic bacteria for cellulose digestion. This study aims to characterize cellulolytic bacteria of termite gut symbionts of worker M. gilvus and to identify the cellulolytic bacteria based on sequences of 16S ribosomal RNA (rRNA) gene. Cellulolytic bacteria of termite gut were isolated and cultured in CMC (Carboxymethyl cellulose) media. The biochemical characters of bacterial isolates were assayed using Microbact 12A and 12B. Cellulolytic activity was determined based on formation of clear zone and cellulolytic index on CMC plate media. The bacterial isolate that has the highest cellulolytic index was analyzed for its 16S rRNA gene sequences. Four isolates of cellulolytic bacteria were successfully isolated from gut of M. gilvus with aerobic and anaerobic conditions. The highest formation of cellulolytic index (2.5) was revealed by RA2. BLAST-N (Basic Local Alignment Search Tool for Nucleotides) result of 16S rRNA gene sequences of RU4 and RA2 isolates showed that the isolate has similarity with Bacillus megaterium and Paracoccus yeei, respectively. This result indicated that RA2 isolate was P. yeei, a cellulolytic bacterium of a termite gut of M. gilvus. [ABSTRACT FROM AUTHOR]

The research was conducted to study the metagenomic of actinomycetes based on 16S ribosomal RNA (rRNA) and bacterial nifH genes in soil and roots of four rice cultivars. The denaturing gradient gel electrophoresis profile based on 16S rRNA gene showed that the diversity of actinomycetes in roots was higher than soil samples. The profile also showed that the diversity of actinomycetes was similar in four varieties of rice plant and three types of agroecosystem. The profile was partially sequenced and compared to GenBank database indicating their identity with closely related microbes. The blast results showed that 17 bands were closely related ranging from 93% to 100% of maximum identity with five genera of actinomycetes, which is Geodermatophilus, Actinokineospora, Actinoplanes, Streptomyces and Kocuria. Our study found that Streptomyces species in soil and roots of rice plants were more varied than other genera, with a dominance of Streptomyces alboniger and Streptomyces acidiscabies in almost all the samples. Bacterial community analyses based on nifH gene denaturing gradient gel electrophoresis showed that diversity of bacteria in soils which have nifH gene was higher than that in rice plant roots. The profile also showed that the diversity of those bacteria was similar in four varieties of rice plant and three types of agroecosystem. Five bands were closely related with nifH gene from uncultured bacterium clone J50, uncultured bacterium clone clod-38, and uncultured bacterium clone BG2.37 with maximum identity 99%, 98%, and 92%, respectively. The diversity analysis based on 16S rRNA gene differed from nifH gene and may not correlate with each other. The findings indicated the diversity of actinomycetes and several bacterial genomes analyzed here have an ability to fix nitrogen in soil and roots of rice plant. [ABSTRACT FROM AUTHOR]

Bacillus pumilus is a spore-forming bacteria that is rod-shaped, gram positive, and aerobic. B. pumilus produced pumilacidins, known to have toxic effects on epithelial cells. Antibiotics were usually used to treat the disease caused by bacteria. Antibiotic typing test of B. pumilus indigenous from sewage water showed that this isolate was resistant to ampicillin and clindamycin. An alternative way was by application of bacteriophages as biocontrol agents to reduce B. pumilus in environment. The aim of this study were to isolate and characterize B. pumilus bacteriophage isolated from Ciapus River in Bogor, West Java. Bacteriophages infecting B. pumilus were isolated from river water using the double agar overlay method. Phages were defined by plaque morphology, structure, host range, and characteristic of molecular weight protein phage. Phage FBa1, FBa2, and FBa3 had narrow host range and they were specific for infecting B. pumilus. Electron microscope observation showed that phage FBa1 had icosahedral head without tail (166.67 nm in diameter), so it is called phage-like particles. Characterization of phage FBa1 by SDS-PAGE showed five proteins band. Molecular weight of FBa1 proteins was 70.9, 54.9, 33.8, 28.3, and 21.4 kDa. [ABSTRACT FROM AUTHOR]

Tempeh is a well-known Indonesian fermented food made from soybean. During the fermentation process, microorganisms play an important role in the flavor, texture, and nutritional quality of tempeh. Tempeh has been show to have immuno-modulatory and immune-stimulating properties that may also be caused by the microorganisms in tempeh as they interact between the microbial population in the intestinal tract. The objective of this study was to quantify IgA gene expression at both the transcription and translation levels in Sprague Dawley (SD) rats supplemented with tempeh. A total of 6 female SD rats were divided into 3 groups of 2 rats. The first group was the control and was fed a standard diet without tempeh. The second- and third group were fed with a standard diet supplemented with raw and cooked tempeh, respectively. Ileum tissue samples were collected after tempeh supplementation for 28 days. RNA was extracted from ileum samples, and measurement of IgA gene expression was further analyzed using semi quantitative real-time PCR. The concentration of IgA protein was quantiied from ileum lysate using the half sandwich ELISA method. IgA gene expressions in rats supplemented with raw, and with cooked tempeh, were 1.18 and 1.17 fold higher, respectively, compared to the control group. Moreover, IgA protein secretion levels also increased 2.46 and 2.08 fold, respectively, compared to the control group. The result of this study indicates that both raw and cooked tempeh may stimulate IgA secretion, and also that both viable and non-viable microorganisms might stimulate IgA gene expression. [ABSTRACT FROM AUTHOR]

Tempeh is an Indonesian traditional fermented food produced using Rhizopus as a starter culture. In practice, however, the starter culture as well as fermentation processes would yield a polymicrobial fermentation, which generated a unique tempeh flavor and texture. This condition makes Indonesian tempeh as one of the most complex fermented food, while at the same time would make it difficult to scale up tempeh production with uniform quality and consistency. The aim of this study was to compare a number of tempeh microbial communities employing Amplified Ribosomal Intergenic Sequence Analysis (ARISA). Fresh tempeh samples were obtained from tempeh producers in Java and Moluccas. 16S rRNA gene libraries and DNA sequencing were employed to analyze further the nature of bacterial diversity in two selected tempeh samples. The results of our study showed that different tempeh producer possessed different Bacterial ARISA (BARISA) or fungi ARISA (FARISA) profiles. However, BARISA profiles were found to be more discriminative than FARISA, and therefore BARISA would be more useful for tempeh genetic fingerprint or barcoding. [ABSTRACT FROM AUTHOR]