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

Functional Analysis of Conserved Hypothetical Proteins from the Antarctic Bacterium, Pedobacter cryoconitis Strain BG5 Reveals Protein Cold Adaptation and Thermal Tolerance Strategies

Pedobacter cryoconitis BG5 is an obligate psychrophilic bacterium that was first isolated on King George Island, Antarctica. Over the last 50 years, the West Antarctic, including King George Island, has been one of the most rapidly warming places on Earth, hence making it an excellent area to measure the resilience of living species in warmed areas exposed to the constantly changing environment due to climate change. This bacterium encodes a genome of approximately 5694 protein coding genes. However, 35% of the gene models for this species are found to be hypothetical proteins (HP). In this study, three conserved HP genes of P. cryoconitis, designated pcbg5hp1, pcbg5hp2 and pcbg5hp12, were cloned and the proteins were expressed, purified and their functions and structures were evaluated. Real-time quantitative PCR analysis revealed that these genes were expressed constitutively, suggesting a potentially important role where the expression of these genes under an almost constant demand might have some regulatory functions in thermal stress tolerance. Functional analysis showed that these proteins maintained their activities at low and moderate temperatures. Meanwhile, a low citrate synthase aggregation at 43 ◦C in the presence of PCBG5HP1 suggested the characteristics of chaperone activity. Furthermore, our comparative structural analysis demonstrated that the HPs exhibited cold-adapted traits, most notably increased flexibility in their 3D structures compared to their counterparts. Concurrently, the presence of a disulphide bridge and aromatic clusters was attributed to PCBG5HP1’s unusual protein stability and chaperone activity. Thus, this suggested that the HPs examined in this study acquired strategies to maintain a balance between molecular stability and structural flexibility. Conclusively, this study has established the structure– function relationships of the HPs produced by P. cryoconitis and provided crucial experimental evidence indicating their importance in thermal stress response

Characterization of a Putative Antimicrobial Peptide from an Antarctic Bacterium

The search for new antibiotics is a continuous effort since its discovery. Nevertheless, the speed of discovering novels antibiotics cannot match the speed of bacteria acquiring antibiotics resistant. Hence, the search efforts have broadened to include all compounds with antimicrobial activities. The toxin-antitoxin (TA) gene products are the potential antimicrobial compounds worth analyzing. The TA system consists of a set gene found either in the chromosome or plasmid, or both. At the moment, the toxin, a peptide from this system is known to kill some hosts that either encountered stress or have lost the plasmid carrying the TA genes. In a previous study, it was found that an Antarctic bacterium, Cryobacterium sp. SO1 chromosome harbored a putative antimicrobial peptide-coding gene similar to a class II TA, pemK gene. However, it is not clear whether this antimicrobial peptide has cross-species antimicrobial activity. Therefore, this work aims to determine whether this PemK protein has antimicrobial properties or not. The pemKcryobacSo1 gene was ligated to an arabinose-inducible promoter of the Topo pBAD plasmid and used to transform the Escherichia coli TOP10. The cloning of pemK inhibited the growth of the host E. coli TOP10 as the cells failed to grow. This indicated that PemK probably has a cross-species activity inhibited the growth of E. coli apart from its original host Cryobacterium sp. SO1

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