Diversity and dynamics of RNA viruses in equatorial coastal waters

Studies on the ecological effects of marine RNA viruses are critically lacking, despite the fact that viral infections impact health and evolution of individual species, the community structure of populations, and the biogeochemistry of the entire marine ecosystem. In this thesis, using a high-resolution time-series, I uncover a remarkable difference between life-cycles of lytic DNA and RNA phytoplankton viruses with a combination of metagenomics, metatranscriptomics and bioinformatics. The giant DNA viruses, known for lower burst sizes, exhibited low and continuous transcriptional activity, suggesting coexistence with their potential hosts. In contrast, fast-replication RNA viruses, known for high burst sizes, experienced short “bloom and bust” cycles of transcriptional activity which, along with the nutrient limitation, stopped potential bloom formation on two separate instances. Persistent, asymptomatic infections with RNA viruses without an extracellular stage were widely present in the Johor Strait marine ecosystem. Fifty nearly full-length RNA viral genomes and 319 verified RNA viral fragments were discovered using and optimized wet lab protocol and integrated bioinformatic pipeline OrVIT, which through extraction of conserved RdRp domains, produces high-quality phylogenetic trees of RNA viruses. Most recovered sequences clustered within the Sogarnavirus genus, which infects diatoms. Both datasets contained a pool of sequences from dsRNA and ssRNA viruses that infect marine animals, suggesting a possible hazard to aquaculture. This thesis underscores the potential of using an integrated multi-omic approach to capture the complex interplay between viruses and their hosts in marine ecosystems and emphasises the critical importance of phytoplankton RNA viruses in top-down control of blooming, fast-growing phytoplankton populations, especially in eutrophic ecosystems.Doctor of Philosoph

Complete genome sequence of the cyanophage S-PRM1 isolated from Singapore coastal waters

Here, we report the genomic sequence and comparative analysis of the cyanophage S-PRM1 which was recently isolated from Singapore coastal waters using Synechococcus sp. strain WH7803. The genome of 144,311 bp was sequenced using a combination of Illumina and Oxford Nanopore technologies. The calculated OrthoANI (Average Nucleotide Identity by Orthology) values of S-PRM1 were between 65.24% and 89.39% when compared with previously sequenced cyanomyoviruses with the highest identity with cyanophage S-CAM9. Auxiliary metabolic genes (AMGs) involved in photosynthesis, carbon metabolism, phosphate acquisition, DNA biosynthesis were found in the genome of S-PRM1.NRF (Natl Research Foundation, S’pore)Accepted versio

Complete genome sequence of Lelliottia nimipressuralis type strain SGAir0187, isolated from tropical air collected in Singapore

Lelliottia nimipressuralis type strain SGAir0187 was isolated from tropical air samples collected in Singapore. The genome was assembled with an average coverage of 180-fold using Pacific Biosciences long reads and Illumina MiSeq paired-end reads. The genome measures 4.8 Mb and contains 4,424 protein-coding genes, 83 tRNAs, and 25 rRNAs.MOE (Min. of Education, S’pore)Published versio

Complete genome sequence of Acinetobacter indicus type strain SGAir0564 isolated from tropical air collected in Singapore

Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The strain SGAir0564 was isolated from air samples collected in Singapore. The complete genome is 3.1 Mb and was assembled using a combination of short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs, and 21 rRNA subunits.MOE (Min. of Education, S’pore)Published versio

Complete genome sequence of Microbacterium sp. strain SGAir0570, isolated from tropical air collected in Singapore

Microbacterium sp. strain SGAir0570 was isolated from air samples collected in Singapore. Its genome was assembled using single-molecule real-time sequencing and MiSeq short reads. It has one chromosome with a length of 3.38 Mb and one 59.2-kb plasmid. It contains 3,170 protein-coding genes, 48 tRNAs, and 6 rRNAs.MOE (Min. of Education, S’pore)Published versio

Complete genome sequence of Nissabacter sp. strain SGAir0207, isolated from an air sample collected in Singapore

Nissabacter sp. strain SGAir0207 was isolated from a tropical air sample collected in Singapore. Its genome was assembled using a hybrid approach with long and short reads, resulting in one chromosome of 3.9 Mb and 7 plasmids. The complete genome consists of 4,403 protein-coding, 84 tRNA, and 22 rRNA genes.MOE (Min. of Education, S’pore)Published versio