Studies on Some Anaerobic Rumen Bacteria With Special Reference to Their Endoglucanase Gene

Four strains of Fibrobacter succinogenes (DI, D3, D5 and D6) and 3 strains of Ruminococcus flavefaciens eMD-I, MD-8 and MD-9) were found to be highly fibrolytic, degrading and solubilising Whatman No.1 filter paper strips in Scott and Dehority medium within 16-48 h. Among the 7 bacterial strains, F. succinogenes D3 and R. flavefaciens MD-1 were two of the most active, being able to solubilise the filter paper strip within 16-24 h, and were used for endoglucanase assay. R. flavefaciens MD-1 produced significantly higher endoglucanases activity than F. succinogenes D3 at all incubation periods

Antimicrobial activities of Antarctic soil microbes from Deception island

第6回極域科学シンポジウム[OB] 極域生物圏11月16日（月）　国立極地研究所１階交流アトリウ

Effects of elevated temperature on the tropical soil bacterial diversity

Bacteria are important biological components of soil that play pivotal roles in improving soil quality and maintaining a balanced ecosystem. However, global climate change may have severe impacts on biodiversity and ecosystems including species loss and extinction of plants and animals, including microbes. Thus, it is crucial to determine how elevated temperature may alter soil bacterial diversity and composition. In this study, an in vitro simulated temperature rise experiment was carried out on soils from three sampling sites, referring to S1, S2, and S3 around Sabah, Malaysia. Soils were incubated at 25 °C (control) and 27 °C (simulated warming) with constant parameters in a growth chamber up to 16 months. Total DNA was extracted from microbes in the soil and used for PCR amplification targeting the V3-V4 region of the 16S rRNA gene. These amplicons were sequenced using the MiSeq platform (Illumina, USA). Raw DNA sequences were trimmed, merged, and aligned against the 16S rRNA sequences in the NCBI 16S database. The results showed that the analyzed soils were mainly dominated by Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia. After 16 months of simulated warming, a net decrease of Proteobacteria, Acidobacteria, and Planctomycetes, and an increase of Actinobacteria and Chloroflexi were observed for all three soil samples, indicating that these phyla were highly affected by a temperature rise. At the genus level, Gaiella and Nocardioides exhibited a net increase while Bradyrhizobium, Mycobacterium, Tepidisphaera, and Paludibaculum demonstrated net decrease after 16 months of simulated warming. Knowledge on the changes of soil bacterial diversity patterns as a result of temperature elevation will contribute to select the best intervention strategy to overcome global warming issue in the future

Effects of simulated warming on bacterial diversity and abundance in tropical soils from East Malaysia using open top chambers

The effects of global warming are increasingly evident, where global surface temperatures and atmospheric concentration of carbon dioxide have increased in past decades. Given the role of terrestrial bacteria in various ecological functions, it is important to understand how terrestrial bacteria would respond towards higher environmental temperatures. This study aims to determine soil bacterial diversity in the tropics and their response towards in situ warming using an open-top chamber (OTC). OTCs were set up in areas exposed to sunlight throughout the year in the tropical region in Malaysia. Soil samples were collected every 3 months to monitor changes in bacterial diversity using V3–V4 16S rDNA amplicon sequencing inside the OTCs (treatment plots) and outside the OTCs (control plots). After 12 months of simulated warming, an average increase of 0.81 to 1.15 °C was recorded in treatment plots. Significant changes in the relative abundance of bacterial phyla such as Bacteroidetes and Chloroflexi were reported. Increases in the relative abundance of Actinobacteria were also observed in treatment plots after 12 months. Substantial changes were observed at the genus level, where most bacterial genera decreased in relative abundance after 12 months. This study demonstrated that warming can alter soil bacteria in tropical soils from Kota Kinabalu

Tropical soil bacterial diversity in Sabah, Malaysia

Bacteria are an essential biological component of soil function that plays fundamental roles in biogeochemical cycling, soil quality improvement, habitat-shaping, and ecosystem conservation. It is therefore important to have a good record of soil bacteria in the tropics in order to monitor future changes that may occur due to global warming and other factors. However, extremely limited data are available on the diversity of bacteria in soils in some tropical Borneo regions such as Sabah, Malaysia. This research, therefore, was undertaken to determine the bacterial diversity of soils from various locations in Sabah, Malaysia. Ten soil samples (n=10) were collected around Sabah. 16S rDNA of bacterial DNA extracted from soils were amplified and analysed using the Denaturing Gradient Gel Electrophoresis (DGGE). A total of 100 dominant and well-defined DNA fragments observed in the DGGE gel were extracted, sequenced, and aligned. The results indicated that 93 different bacterial operational taxonomic units (OTUs) representing bacteria from 8 different phyla were present. The most abundant phyla in the analysed Sabah soils were Proteobacteria followed by Acidobacteria, Firmicutes, Actinobacteria, Planctomycetes, Verrucomicrobia, Chloroflexi, and Bacteroidetes. The examined soils of Sabah and Peninsular Malaysia had similar dominant phyla in general, except that the most dominant phylum in Peninsular Malaysia soils is the Acidobacteria instead of Proteobacteria. These baseline data generated from this work are important and can be used to track bacterial diversity shifts due to soil or environmental changes in the future

In silico evaluation of crystallisation potential for conserved hypothetical proteins from the antarctic bacterium, Pedobacter cryoconitis BG5

The genome of Pedobacter cryoconitis BG5 highlighted the presence of conserved hypothetical proteins (HPs) with unique adaptive characteristics. Analysing and annotating the functions of these proteins was indeed essential for determining their suitability for X-ray crystallographic structure determination. The HPs were examined for the presence of transmembrane helices and signal peptides, and their structural and functional characteristics were analyzed using various bioinformatics tools and databases. The analysis revealed twelve conserved HPs with significant thermal stress response functions that met crystallisation criteria. Functional annotation showed that most of the proteins contain domains related to an enzyme or catalytic activity. Furthermore, the physicochemical properties of the shortlisted protein suggest a high probability of crystallisation based on the previously solved crystal structures of proteins with similar features. This early identification of protein eligibility for crystal screening has the potential to significantly reduce the time and cost involved in the structural determination of the unknown proteins in P. cryoconitis BG5

Cloning, expression, and purification of PcBG5HP1, a conserved hypothetical protein related to thermal stress response in antarctic bacterium, Pedobacter cryoconitis BG5

The psychrotolerant bacterium, Pedobacter cryoconitis BG5, has been discovered to encode numerous protein-coding genes that are crucial for thermal adaptation. However, more than 35% of these protein-coding genes for this species are classified as hypothetical proteins (HP). These HPs are proteins whose existence has been predicted, but empirical evidence of their expression in vivo remains lacking. Thus, this research aims to generate a high-quality protein specimen suitable for protein assays and structural biology analyses for future studies. To achieve this, an in vitro analysis was conducted, in which the proteins were cloned, expressed in Escherichia coli, and purified through a two-step purification process. Cultures of P. cryocinitis BG5 cells were retrieved from the glycerol stock and successfully cultivated in LB broth medium at a temperature of 20°C following a three-day incubation period. The targeted gene was successfully amplified, subjected to functional annotation and physicochemical analysis. The targeted genes revealed a 37 kDa conserved HP containing an alcohol and glucose dehydrogenase domain designated as Pcbg5HP1 and annotated with oxidoreductase activity, indicating the bacteria's higher capacity for adaptation to low temperature environments. The recombinant Pcbg5HP1 proteins were successfully overexpressed in their soluble form at 37°C. Subsequently, a soluble protein was obtained through a two-stage purification process involving a column with a his-tag and gel filtration. The identification and validation of the peptide sequences of the purified recombinant protein were successfully achieved through the utilisation of MALDI-TOF-MS analysis. Conclusively, this study has established an efficient workflow to produce high-quality samples of conserved HP from P. cryoconitis BG5, which are well-suited for subsequent protein assays and structural biology analyses

An overview of fermentation in rice winemaking

Rice wine is an alcoholic beverage produced via the fermentation of cereals, primarily rice with starter cultures. It is produced and consumed globally, especially in Asian countries. With the growth of the global rice wine market, the development of high-quality rice wines is gaining increasing interest. This paper reviews and discusses the comprehensive research details of rice wines in different regions, including the selection of starch substrates, comparison of starter cultures’ microbial compositions, compositions of rice wines and its health benefits. The simultaneous saccharification and fermentation (SSF) of rice wine, microorganisms involved in the fermentation, and factors affecting the fermentation process are discussed, thus providing an overview of the rice wine fermentation and the involved study perspectives