Shotgun metagenomic analysis of microbial communities in the surface waters of the Eastern South China Sea

Aims: The South China Sea (SCS) harbours a rich biodiversity. However, few studies have been published on its diverse communities, particularly its microbial counterparts. As key players behind many of the vital processes carried out in the ocean, microbes are the focus of this study, placing particular emphasis on community composition, structure, and function. Methodology and results: By employing next generation shotgun sequencing technologies (Illumina HiSeq2000), we assessed the taxonomic structure and functional diversity of the prokaryotic communities in surface waters collected from 3 representative sites in the Eastern SCS: Sarawak (Kuching), Sabah (Kota Kinabalu), and Philippines (Manila). Comparisons were undertaken to similar studies from coastal and open ocean environments. All 3 locations were dominated by members of the Proteobacteria (Alpha- and Gamma-) and Cyanobacteria (Synechococcus sp. and Prochlorococcus sp.). The highest proportion of Gammaproteobacteria was found in Sarawak, representing an approximate 20% of total sequences. Archaeal assemblages were made up largely of Euryarchaeota and unclassified sequences, while Crenarchaeota and Thaumarchaeota were present in much smaller proportions, except in the Philippines where Thaumarchaeota made up almost 40% of the entire taxa. Conclusion, significance and impact of study: The majority of the microbial communities adhered to a core set of functional genes across the different locations. However, differences existed particularly in Sarawak waters which are hypothesized to be due to local environmental parameters such as riverine influence. The results obtained from this study provide the first comparison of prokaryotic communities in the surface waters of the eastern SCS and will serve as a good platform for prospective studies in the field of environmental science.

Screening of endophytic fungi for biofuel feedstock production using palm oil mill effluent as a carbon source

Aims: Palm oil mill effluent (POME) is a major agricultural waste product of Malaysia. The aim of this study was to identify endophytic fungi capable of producing biofuel feedstock utilizing POME. Methodology and results: Endophytes were isolated from the Nipah palm tree, Nypa fruticans, and exposed to different POME concentrations (25%, 50% and 75%), with and without the addition of nutrients. The utilization of glucose was measured using the Dinitrosalicylic Acid assay whereas the lipid content in the fungal cells was extracted using the Bligh and Dyer method with slight modifications. Three endophytic fungi that displayed the highest growth on POME were identified using ITS 1 and 4 primers and found to be related to Pestalotiopsis sp., Lasiodiplodia theobromae and Rhizoctonia bataticola. Nutrient addition caused an average increase of 8 times in biomass, indicating nitrogen requirement for cell proliferation. The highest POME concentration (75%) resulted in lower biomass yield. Furthermore, all fungal samples in high POME concentration and nutrient conditions showed a decrease in lipids accumulated per milligram of biomass whereby lipid synthesis was enhanced under nitrogen limitation (25% without nutrients). Conclusion, significance and impact of study: In conclusion, all fungal samples can be classified as oleaginous microorganisms with Pestalotipsis sp. being the most efficient (up to 70% of its biomass). This is to our knowledge the first study that shows the potential use of Pestalotiopsis sp., L. theobromae and R. bataticola for the utilisation of POME as biofuel feedstock and could in the future potentially provide an alternative approach to the treatment of POME with value-added effect.

Role of bacterial communities in coral’s defence against a causative agent of coral bleaching: Vibrio coralliilyticus

Aims: Different studies have shown that members of the Vibrio such as Vibrio coralliilyticus and Vibrio shiloi are opportunistic pathogens which can cause coral lysis. The aims of this study were to assess whether this results of the virulence of V. coralliilyticus are transmittable to Acropora hyacinthus and Porites lobata, and what role the microbiome of the corals plays during exposure to V. coralliilyticus. Methodology and results: In laboratory-based experiments, we examined the impact of V. coralliilyticus (ATCC BAA- 450) to the microbiome of Acropora hyacinthus and Porites lobata. A. hyacinthus and P. lobata were exposed to ampicillin, V. coralliilyticus, and a combination of both. Results indicate a resistance of A. hyacinthus to V. coralliilyticus through the microbiome and underpin the importance of the microbiome for the coral’s health. Conclusion, significance and impact study: Further studies are needed to identify the bacteria responsible for the coral resistance and could in future lead to the development of a probiotic treatment or prevention of bleaching for sensitive corals.