Whole genome sequence data of a marine bacterium, Marinobacter adhaerens PBVC038, associated with toxic harmful algal bloom.

Marinobacter adhaerens (PBVC038) was isolated from a harmful algal bloom event caused by the toxic dinoflagellate Pyrodinium bahamense var. compressum (P. bahamense) in Sepanggar Bay, Sabah, Malaysia, in December 2012. Blooms of P. bahamense are frequently linked to paralytic shellfish poisoning, resulting in morbidity and mortality. Prior experimental evidence has implicated the role of symbiotic bacteria in bloom dynamics and the synthesis of biotoxins. The draft genome sequence data of a harmful algal bloom-associated bacterium, Marinobacter adhaerens PBVC038 is presented here. The genome is made up of 21 contigs with an estimated 4,246,508 bases in genome size and a GC content of 57.19%. The raw data files can be retrieved from the National Center for Biotechnology Information (NCBI) under the Bioproject number PRJNA320140. The assessment of bacterial communities associated with harmful algal bloom should be studied more extensively as more data is needed to ascertain the functions of these associated bacteria during a bloom event.

Dataset of genome sequence, de novo assembly, and functional annotation of Ruegeria sp. (PBVC088), a marine bacterium associated with the toxin-producing harmful dinoflagellate, Pyrodinium bahamense var. compressum.

The dataset comprises a whole-genome sequence of Ruegeria sp. PBVC088, a symbiotic (Gram-negative) bacterium associated with Pyrodinium bahamense var. compressum, which has been associated with harmful algal blooms in the coastal waters of west Sabah, Malaysia. Harmful algal blooms contribute to economic losses for the aquaculture industry, as well as human illnesses and fatalities due to paralytic shellfish poisoning. Bacteria-algae dynamics have posited that the interaction is potentially responsible for the toxin production during a toxic harmful algal bloom event. Despite the expanding body of literature on the capabilities of these bacteria to metabolize, produce, and modify toxins autonomously, it has yet to be confirmed that these toxin-producing bacteria are capable of autonomous toxin synthesis. Saxitoxin, a paralytic shellfish poisoning toxin, is produced by a unique biosynthetic pathway, where the genetic basis for the saxitoxin production was first reported in the saxitoxin-producing cyanobacteria strain Cylindrospermopsis raciborskii T3 (NCBI accession no. DQ787200). The genes responsible for saxitoxin biosynthesis in dinoflagellates, have yet to be fully elucidated. The identification of cyanobacteria saxitoxin biosynthesis genes (sxt) may eventually lead to the identification of homologous genes within the dinoflagellates. Previous studies on the diversity of the bacterial communities associated with the same toxic P. bahamense harmful alga has been carried out by using both the culture-dependent 16S ribosomal RNA gene sequence analysis and culture-independent 16S metagenomic sequence analysis. This study extends the knowledge pertaining to the genomic aspect of an associated bacterium isolated from P. bahamense alga by adopting a whole genome sequencing approach. Here, we report the genome sequencing, de novo assembly, and annotation data of a bacterium, Ruegeria sp. PBVC088, associated with harmful alga P. bahamense, which can be referenced by researchers to identify the genes and pathways related to toxin biosynthesis from a much larger data set. The genome of Ruegeria sp. PBVC088 was sequenced using the Illumina MiSeq platform with 250 bp paired-end reads. The number of reads generated from the MiSeq sequencer was 1,135,484, with an estimated coverage of 100X. The estimated genome size for the marine bacterium was computed to be 5.78 Mb. Annotation of the genome predicted 5,689 gene sequences, which were assigned putative functions based on homology to existing protein sequences in public databases. In addition, annotation of genes related to saxitoxin biosynthesis pathway was also performed. Raw fastq reads and the final version of the genome assembly have been deposited in the National Center for Biotechnology Information (NCBI) (BioProject: PRJNA324753, WGS: LZNT00000000, SRA: SRR3646181). The genome data provided here are expected to better understand the genetic processes involved in saxitoxin biosynthesis in marine bacteria associated with dinoflagellates.

Genomic data of two Bacillus and two Pseudomonas strains isolated from the acid mine drainage site at Mamut Copper Mine, Ranau, Malaysia.

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.

Adaptive Strategies of Bacillus thuringiensis Isolated from Acid Mine Drainage Site in Sabah, Malaysia.

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.