Transcriptomic response of an Antarctic yeast Rhodotorula sp. USM-PSY62 to temperature changes

Aims@#Rhodotorula sp. (USM-PSY62) is a psychrophilic yeast isolated from Antarctic sea ice that grows optimally at 15°C. The inevitable global warming poses many challenges to the microbial community in Antarctica. Therefore, this studywas conceptualized to observe how USM-PSY62 adapted to fluctuations in temperature.@*Methodology and results @#Rhodotorula sp. (USM-PSY62) was grown in YPD broth until the mid-log phase. Then, the culture was transferred to four different temperatures, specifically at 0 °C, 5 °C, 15 °C and 21 °C for 24 h. Then, the RNA was extracted, sequenced and analysed. During cold adaptation, an elevated transcription of the CorA magnesium transporter gene in USM-PSY62 indicated a higher requirement for magnesium ions to gain additional enzyme cofactors or maintain cytoplasmic fluidity. The HepA homologue coding for DNA/RNA helicase was also over-expressed with log fold change 2.89 in cold conditions possibly to reorganize secondary structures of DNA and RNA. An up-regulation of the catalase gene was also observed, reflecting an increment in the concentration of reactive oxygen species and fluctuations in the associated antioxidant system. The YOP1 gene, which encodes a membrane protein associated with protein transport and membrane traffic, was the most down-regulated, with log2 fold change values of -6.93 lower under cold shock conditions. The genes responsible for the structural maintenance of chromosome (SMC) have a -8.80 in expression log2 fold change, indicating the gene was down-regulated when the temperature was shifted to 0 °C. Upon cold shock, the gene for heat shock factor protein 1 (HSF1) was also down-regulated with a log2 fold change value of - 5.86. Hsf1 is a transcriptional regulator which regulates the heat shock responses.@*Conclusion, significance and impact of study: @#In conclusion, the transcriptomic responses demonstrated by Rhodotorula sp. USM-PSY62 characterized critical physiological and biochemical compensatory mechanisms especially cellular processes and signalling, information storage and processing, and metabolism to survive at low and high temperatures. This study provides valuable data for industry, especially in the usage of molecular chaperones.

Unveiling the multifaceted microbial strategies: Insights into ecological adaptations and interactions

@#Microorganisms, such as spanning bacteria, archaea and fungi, were ubiquitous and played pivotal roles in shaping ecosystems. This review offered a comprehensive investigation into the multifaceted strategies employed by microorganisms to thrive and adapt within complex ecological niches. Key themes explored in this review encompassed microbial defence mechanisms, biofilm formation, quorum sensing and altruistic behaviours. Microbial defence mechanisms were scrutinized, with a focus on bacteriocin production. Despite the costs associated with production, bacteriocins served as potent weapons that selectively targeted closely related strains, reducing competition and conferring indirect benefits to the producer's genetic kin. Biofilm formation, a critical facet of microbial survival, was discussed in detail. These structured microbial communities encased in self-secreted extracellular matrices provided structural support and protection, demonstrating their significance in diverse ecological contexts. The review further delved into the evolutionary implications of quorum sensing and altruism within microbial communities. Quorum sensing, a mechanism that allowed population density-dependent communication and cooperation, was revealed as essential for microbial survival. In conclusion, this review enhanced our understanding of the intricate strategies microorganisms employed for survival, adaptation and competition in intricate ecosystems. By shedding light on these mechanisms, it advanced our comprehension of microbial community dynamics and their indispensable roles in diverse environments.

Isolation of thermotolerant xylose-utilizing yeasts for ethanol and xylitol production

Aims@#The implementation of simultaneous saccharification and co-fermentation (SScF) and consolidated bioprocessing (CBP) is highly anticipated for industrial bioethanol applications. Thus, microorganisms capable of utilizing hexose and pentose sugars, as well as thermotolerant, are considered advantageous for optimum ethanol production.@*Methodology and results@#Thermotolerant yeast strains were isolated from wastewater ponds of ethanol-producing facility as well as empty fruit bunch composting area and screened for xylose- and glucose-fermenting ability. Five out of 24 total isolates were able to grow at 40 ºC and were found positive for ethanol production from xylose. Based on their high efficiency of xylose and glucose utilization, two isolates were chosen for further characterization. They were identified as Kluyveromyces marxianus UniMAP 1-1 and Schwanniomyces etchellsii UniMAP 1-7 based on the D1/D2 region of the large subunit ribosomal DNA. The growth kinetics of each isolate on xylose and glucose at 40 °C were determined. The two isolates were able to ferment xylose to ethanol at a maximum concentration between 0.533  0.415 and 1.243  0.246 g/L with concomitant xylitol production between 9.932  0.303 and 12.933  0.505 g/L. Fermentation of glucose to ethanol was also tested for these isolates and the yields were and 0.361 and 0.118 g/g for UniMAP 1-1 and UniMAP 1-7, respectively.@*Conclusion, significance and impact of study@#The potential of these thermotolerant microbes to be used for xylitol and bioethanol production from lignocelluloses are evident from this study.

Characteristics of limestone soil collected from Gunung Lang, Perak and metagenomic analysis of the soil microbial community

Aims: This project was aimed to study the microbial diversity of the limestone soil and its correlation with the environment. Methodology and results: The study was carried out using samples obtained from Gunung Lang, Ipoh, Perak in August 2013. X-ray diffraction analysis of the rock structure confirmed that the samples were of limestone origin. Besides that, soil analysis revealed that this area was fertile and rich in nutrients. It therefore served as a suitable habitat for microorganismal diversity to flourish. This was proven by the 16S rDNA metagenomic analysis which targeted on 16S rDNA variable region V3-V5 using Illumina MiSeq sequencer. Using this approach, a variety of microorganisms was identified and many yet to be characterized microorganisms were detected from this area. Conclusion, significance and impact of study: This is the first study in Malaysia that aimed to study the microbial diversity of limestone soils through metagenomic approach. The study showed that limestone is rich in microbial diversity and it is a place worth looking for novel microbes and genes of interest in biotechnology.

Estimation of Nitrogenase Enzyme Activities and Plant Growth of Legume and Non-legume Inoculated with Diazotrophic Bacteria

Biological Nitrogen Fixation (BNF) process benefits the agriculture sector especially for reducing cost of nitrogen fertilizer. In the process, the diazotrophs convert N2 into ammonia (NH3) which is useable by plants. The BNF process is catalysed by nitrogenase enzyme that involved protons and electrons together with evolution of H2 therefore, the assessment of N2 fixation is also available via H2 production and electron allocation analysis. Thus, the aims of this experiment were to estimate the nitrogenase enzyme activities and observe the influence of diazothrophs on growth of legume (soybean) and non legume (rice) plants. Host plants were inoculated with respective inocula; Bradyrhizobium japonicum (strain 532C) for soybean while Azospirillum brasilense (Sp7) and locally isolated diazotroph (isolate 5) for rice. At harvest, the plants were observed for plant growth parameters, H2 evolution, N2 fixation and electron allocation coefficient (EAC) values. The experiment recorded N2 fixation activities of inoculated soybean plants at 141.2 μmol N2 h-1 g-1 dry weight nodule, and the evolution of H2 at 144.4 μmol H2 h-1 g-1 dry weight nodule. The electron allocation coefficient (EAC) of soybean was recorded at 0.982. For inoculated rice plants, none of the observations was successfully recorded. However, results for chlorophyll contents and plant dry weight of both plants inoculated with respective inocula were similar to the control treatments supplied with full nitrogen fertilization (+N). The experiment clearly showed that inoculation of diazotrophic bacteria could enhance growth of the host plants similar to plants treated with nitrogenous fertilizer due to efficient N2 fixation process