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The decline of the freshwater prawn, Macrobrachium spp. in rivers can be attributed to overfishing, habitat loss and pollution. In order to offset the pressure, a community-based stock enhancement project was initiated by Borneo Marine Research Institute (BMRI), University Malaysia Sabah, to increase the number of Macrobrachium spp. in Petagas River, Putatan, Sabah. This study was conducted to determine the distribution and abundance of different life stages of the freshwater prawn, Macrobrachium spp. following stocking programme. The different life stages of the freshwater prawns were caught using hand net and modified prawn trap. A total of 539 specimens were caught and separated into postlarvae (PL), juvenile and adult. Abundance of PL (53.47%) was found at the downstream region of Petagas River, juvenile (18.06%) was found at the midstream region while adult prawn (81.63%) was found at the upstream region. The distribution of PL prawn was found to be increased with increasing salinities (R2=0.95) while for juvenile (R2= 0.98) and adult prawns (R2=0.921) were inversely correlated. The CPUE of PL, juvenile and adult were positively correlated with the increase of stocking juvenile following stocking programme with R2=0.89, R2=0.73 and R2=0.87 accordingly. The stock enhancement programme is suggested to be implemented continuously to improve the population of Macrobrachium spp. in the Petagas River. This study will provide baseline information on the effectiveness of stock enhancement programme of freshwater prawn especially in Malaysia.

During a harmful algal bloom (HAB), the seawater contains a high abundance of microorganisms and elemental ions. Such components can interfere with RNA isolation, leading to RNA degradation. The complex HAB seawater property makes isolating high-quality RNA for metatranscriptomic sequencing difficult, which is required for effective RNA sequencing and transcriptome profiling. This study used three isolation techniques to find the optimal strategy for isolating total RNA from bloom samples. One of the isolation techniques was the phenol-chloroform extraction method, which uses organic solvents to isolate RNA. The remaining two isolation techniques used the same commercial RNA extraction kit, TransZol Up Plus RNA kit (TransGen Biotech, China). One followed the extraction kit’s protocol, while the other modified the protocol. Total RNA was extracted from three seawater samples of three occasions of HAB in Sepanggar Bay. The most effective approach used to extract high-quality RNA from the environmental samples of the HABs was the TransZol Up Plus RNA kit, with modified protocol. Results of the modified protocol generated a high-purity total RNA, ranging from 2.081 to 2.474 for both the absorbance ratios A260/280 and A260/230. The RNA integrity number value ranged from 6.2 to 7.6. All of the samples resulted in concentrations up to 91 ng/µl. We concluded that the modified protocol of TransZol Up Plus RNA kit yielded the highest quality total RNA for metatranscriptome next-generation sequencing (NGS). Apart from NGS, the high-quality RNA can also be used for various downstream applications, including real-time PCR, RNA cloning, and RNA microarray analysis.

Using Palm Oil Mill Effluent (POME) as a medium for culturing oleaginous yeast is advantageous for simultaneous lipid production and waste removal. The organic compounds in POME can be utilised as a nutrient source for yeast growth. Rhodotorula toruloides yeast was cultivated in filtered and unfiltered raw POME as growth media in this study. The yeast growth, pH changes in media, lipid production and removal of chemical oxygen demand (COD) of Rhodotorula toruloides cultivated in POME were examined and compared to Rhodotorula toruloides grown in yeast peptone dextrose (YPD) control media. The COD level of filtered POME was reduced by nearly 50% after filtration. The biomass concentration of Rhodotorula toruloides in filtered POME surpassed the other media in the following order: filtered POME > YPD > unfiltered POME (152 mg/ml > 121 mg/ml > 37 mg/ml). The filtered POME was found favourable for yeast growth due to the minimal amount of colloidal particles and suspended solids. Meanwhile, the lipid production (4.51 %) in filtered POME was 4.8-fold higher than in control media. The water analysis indicated about 43% of COD reduction, signifying the ability of Rhodotorula toruloides to utilise nutrient components present in POME for growth. This study provides insightful knowledge on the utilisation of oleaginous yeast for simultaneous green waste disposal and sustainable microbial oil production.

The dataset comprises a whole-genome sequence of

The adaptive process in bacteria is driven by specific genetic elements which regulate phenotypic characteristics such as tolerance to high metal ion concentrations and the secretion of protective biofilms. Extreme environments such as those associated with heavy metal pollution and extremes of acidity offer opportunities to study the adaptive mechanisms of microorganisms. This study focused on the genome analysis of Bacillus thuringiensis (Bt MCMY1), a gram positive rod shaped bacterium isolated from an acid mine drainage site in Sabah, Malaysia by using a combination of Single Molecule Real Time DNA Sequencing, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The genome size of Bt MCMY1 was determined to be 5,458,152 bases which was encoded on a single chromosome. Analysis of the genome revealed genes associated with resistance to Copper, Mercury, Arsenic, Cobalt, Zinc, Cadmium and Aluminum. Evidence from SEM and FTIR indicated that the bacterial colonies form distinct films which bear the signature of polyhydroxyalkanoates (PHA) and this finding was supported by the genome data indicating the presence of a genetic pathway associated with the biosynthesis of PHAs. This is the first report of a Bacillus sp. isolated from an acid mine drainage site in Sabah, Malaysia and the genome sequence will provide insights into the manner in which B. thuringiensis adapts to acid mine drainage.

The genomic data of four bacteria strains isolated from the abandoned Mamut Copper Mine, an Acid Mine Drainage (AMD) site is presented in this report. Two of these strains belong to the genus Bacillus, while the other two belong to the genus Pseudomonas. The draft genome size of Pseudomonas sp. strain MCMY3 was 6,396,595 bp (GC: 63.3%), Bacillus sp. strain MCMY6 was 6,815,573 bp (GC: 35.2%), Bacillus sp. strain MCMY13 was 5,559,059 bp (GC: 35.5%) and Pseudomonas sp. strain MCMY15 was 7,381,777 bp (GC: 64.8%). These four genomes contained 493, 495, 495 and 579 annotated subsystems, respectively. The sequence data are available at GenBank sequence read archive with accessions numbers SRX7859406, SRX7859404, SRX7859405 and SRX7293032 for strains MCMY3, MCMY6, MCMY13 and MCMY15, respectively.

Taxonomic clarification of Kappaphycus alvarezii, Kappaphycus striatus and Eucheuma denticulatum based on standard DNA barcodes has proven to be useful as the phenotypic plasticity of the species can confound traditional taxonomic approaches. Molecular characterization of each isolate is time-consuming and a painstaking task as multiple runs of PCR amplification needs to be carried out and the identity of the isolates is only known after sequencing of the PCR amplicons. In this study, we have developed a simple, efficient and reproducible one-step polymerase chain reaction (PCR) based method for the identification of the three eucheumatoid species, K. alvarezii, K. striatus and E. denticulatum. Based on the nuclear ribosomal internal transcribed spacer (ITS) sequence, all the available genetic polymorphisms were reviewed and three primers were designed. The combination of these primers in the same PCR reaction results in a specific amplicon of distinct size ranging from approximately 140-400 bp to be produced for each of the three red algal species. The proposed method is found to be an effective and practical tool to aid in the selection of the desired seaweed seedlings even before they are cultivated and also the identification of commercial cultivars accurately.

The division Rhodophyta includes members from the commercially important genera Kappaphycus and Eucheuma. The efficient cultivation of seaweeds depends upon the development of genomic molecular markers which can be applied to detect varietal differences and select strains which exhibit ideal growth characteristics. We developed 117 single loci DNA markers from shotgun genomic libraries derived from Kappaphycus alvarezii, Kappaphycus striatus and Eucheuma denticulatum and tested them across twelve phenotypes which are commercially cultured in Sabah, Malaysia. Sixteen of the markers amplified across all varieties of Kappaphycus implying a shared genetic identity. Eight of the markers could successfully differentiate between varieties of Eucheuma and Kappaphycus on the basis of DNA fingerprinting profiles. These markers will serve as resource for the identification and selection of red algae for commercial cultivation and their application can be extended to marker assisted selection (MAS) and hybrid development.

Bacillus thuringiensis is a type of Gram positive and rod shaped bacterium that is found in a wide range of habitats. Despite the intensive studies conducted on this bacterium, most of the information available are related to its pathogenic characteristics, with only a limited number of publications mentioning its ability to survive in extreme environments. Recently, a B. thuringiensis MCMY1 strain was successfully isolated from a copper contaminated site in Mamut Copper Mine, Sabah. This study aimed to conduct a comparative genomic analysis by using the genome sequence of MCMY1 strain published in GenBank (PRJNA374601) as a target genome for comparison with other available B. thuringiensis genomes at the GenBank. Whole genome alignment, Fragment all-against-all comparison analysis, phylogenetic reconstruction and specific copper genes comparison were applied to all forty-five B. thuringiensis genomes to reveal the molecular adaptation to copper tolerance. The comparative results indicated that B. thuringiensis MCMY1 strain is closely related to strain Bt407 and strain IS5056. This strain harbors almost all available copper genes annotated from the forty-five B. thuringiensis genomes, except for the gene for Magnesium and cobalt efflux protein (CorC) which plays an indirect role in reducing the oxidative stress that caused by copper and other metal ions. Furthermore, the findings also showed that the Copper resistance gene family, CopABCDZ and its repressor (CsoR) are conserved in almost all sequenced genomes but the presence of the genes for Cytoplasmic copper homeostasis protein (CutC) and CorC across the sample genomes are highly inconsonant. The variation of these genes across the B. thuringiensis genomes suggests that each strain may have adapted to their specific ecological niche. However, further investigations will be need to support this preliminary hypothesis.

The adaptive process in bacteria is driven by specific genetic elements which regulate phenotypic characteristics such as tolerance to high metal ion concentrations and the secretion of protective biofilms. Extreme environments such as those associated with heavy metal pollution and extremes of acidity offer opportunities to study the adaptive mechanisms of microorganisms. This study focused on the genome analysis of Bacillus thuringiensis (Bt MCMY1), a gram positive rod shaped bacterium isolated from an acid mine drainage site in Sabah, Malaysia by using a combination of Single Molecule Real Time DNA Sequencing, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The genome size of Bt MCMY1 was determined to be 5,458,152 bases which was encoded on a single chromosome. Analysis of the genome revealed genes associated with resistance to Copper, Mercury, Arsenic, Cobalt, Zinc, Cadmium and Aluminum. Evidence from SEM and FTIR indicated that the bacterial colonies form distinct films which bear the signature of polyhydroxyalkanoates (PHA) and this finding was supported by the genome data indicating the presence of a genetic pathway associated with the biosynthesis of PHAs. This is the first report of a Bacillus sp. isolated from an acid mine drainage site in Sabah, Malaysia and the genome sequence will provide insights into the manner in which B. thuringiensis adapts to acid mine drainage.

Morphological and molecular studies were carried on an undescribed species of Kappaphycus (AS 12) from Sabah, Malaysia. The species displays unique and different physical characters from Kappaphycus alvarezii , K. striatus , K. malesianus and Eucheuma denticulatum in terms of branching patterns, thalli texture and colors. The phylogenetic position of this plant was inferred by cox 2-3 spacer, intergenic transcribed spacer (ITS) region and RuBisCo spacer. Based on the results from this study, it is clear that the specimen AS 12 pointed to significant differences from K. alvarezii , K. striatus , K. malesianus and E. denticulatum as supported by both morphological and molecular analyses.

Dinoflagellates are eukaryotic microorganisms that represent a group of single-celled algae composed of a highly diversified phylum that is well known for displaying an amazing range of ecological adaptation. Cochlodinium polykrikoides is an unarmored dinoflagellate species belonging to the Family Gymnodiniaceae. It is one of the causative agents for harmful algal blooms occurring in the west coast of Sabah, which result in massive economic damages to the aquaculture and mariculture industries. The limited availability of information pertaining to the genetics of C. polykrikoides raises the need for an in-depth study into the expression mechanisms and regulation of the genes of this microorganism. However, isolation of good quality and intact RNA samples from C. polykrikoides seems to be quite a challenge for molecular biologists. Rapid degradation of freshly isolated RNA samples is a bottleneck for researchers to conduct studies on the gene expression and regulation patterns, which requires intact and high-quality RNA samples. In this study, an attempt to establish the best protocol for isolation of good quality and intact RNA from C. polykrikoides was carried out by testing four different total RNA isolation protocols. We conclude that the RNA isolation protocol using the TRIzol reagent produced the best results among the methods tried. The information from this study will allow further research pertaining to the molecular aspects of C. polykrikoides to be conducted with much ease in the future.