Murray, SA, Ruvindy, R, Kohli, GS, Anderson, DM & Brosnahan, ML 2019, 'Evaluation of sxtA and rDNA qPCR assays through monitoring of an inshore bloom of Alexandrium catenella Group 1.', Scientific reports, vol. 9, no. 1.View/Download from: UTS OPUS or Publisher's site
Alexandrium catenella (formerly A. tamarense Group 1, or A. fundyense) is the leading cause of Paralytic Shellfish Poisoning in North and South America, Europe, Africa, Australia and Asia. The quantification of A.catenella via sxtA, a gene involved in Paralytic Shellfish Toxin synthesis, may be a promising approach, but has not been evaluated in situ on blooms of A. catenella, in which cell abundances may vary from not detectable to in the order of 106 cells L-1. In this study, we compared sxtA assay performance to a qPCR assay targeted to a species-specific region of ribosomal DNA (rDNA) and an established fluorescent in situ hybridization (FISH) microscopy method. Passing-Bablok regression analyses revealed the sxtA assay to overestimate abundances when <5 cell equivalents A. catenella DNA were analysed, but otherwise was closer to microscopy estimates than the rDNA assay, which overestimated abundance across the full range of concentrations analysed, indicative of a copy number difference between the bloom population and a culture used for assay calibration a priori. In contrast, the sxtA assay performed more consistently, indicating less copy number variation. The sxtA assay was generally reliable, fast and effective in quantifying A. catenella and was predictive of PST contamination of shellfish.
Verma, A, Barua, A, Ruvindy, R, Savela, H, Ajani, PA & Murray, SA 2019, 'The Genetic Basis of Toxin Biosynthesis in Dinoflagellates.', Microorganisms, vol. 7, no. 8.View/Download from: UTS OPUS or Publisher's site
In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.
Ruvindy, R, Bolch, CJ, MacKenzie, L, Smith, KF & Murray, SA 2018, 'qPCR Assays for the Detection and Quantification of Multiple Paralytic Shellfish Toxin-Producing Species of Alexandrium.', Frontiers in microbiology, vol. 9.View/Download from: UTS OPUS or Publisher's site
Paralytic shellfish toxin producing dinoflagellates have negatively impacted the shellfish aquaculture industry worldwide, including in Australia and New Zealand. Morphologically identical cryptic species of dinoflagellates that may differ in toxicity, in particular, species of the former Alexandrium tamarense species complex, co-occur in Australia, as they do in multiple regions in Asia and Europe. To understand the dynamics and the ecological drivers of the growth of each species in the field, accurate quantification at the species level is crucial. We have developed the first quantitative polymerase chain reaction (qPCR) primers for A. australiense, and new primers targeting A. ostenfeldii, A. catenella, and A. pacificum. We showed that our new primers for A. pacificum are more specific than previously published primer pairs. These assays can be used to quantify planktonic cells and cysts in the water column and in sediment samples with limits of detection of 2 cells/L for the A. catenella and A. australiense assays, 2 cells/L and 1 cyst/mg sediment for the A. pacificum assay, and 1 cells/L for the A. ostenfeldii assay, and efficiencies of >90%. We utilized these assays to discriminate and quantify co-occurring A. catenella, A. pacificum, and A. australiense in samples from the east coast of Tasmania, Australia.
White, RA, Wong, HL, Ruvindy, R, Neilan, BA & Burns, BP 2018, 'Viral communities of Shark Bay modern stromatolites', Frontiers in Microbiology, vol. 9, no. JUN.View/Download from: UTS OPUS or Publisher's site
© 2018 White, Wong, Ruvindy, Neilan and Burns. Single stranded DNA viruses have been previously shown to populate the oceans on a global scale, and are endemic in microbialites of both marine and freshwater systems. We undertook for the first time direct viral metagenomic shotgun sequencing to explore the diversity of viruses in the modern stromatolites of Shark Bay Australia. The data indicate that Shark Bay marine stromatolites have similar diversity of ssDNA viruses to that of Highbourne Cay, Bahamas. ssDNA viruses in cluster uniquely in Shark Bay and Highbourne Cay, potentially due to enrichment by phi29-mediated amplification bias. Further, pyrosequencing data was assembled from the Shark Bay systems into two putative viral genomes that are related to Genomoviridae family of ssDNA viruses. In addition, the cellular fraction was shown to be enriched for antiviral defense genes including CRISPR-Cas, BREX (bacteriophage exclusion), and DISARM (defense island system associated with restriction-modification), a potentially novel finding for these systems. This is the first evidence for viruses in the Shark Bay stromatolites, and these viruses may play key roles in modulating microbial diversity as well as potentially impacting ecosystem function through infection and the recycling of key nutrients.
Ruvindy, R, White, RA, Neilan, BA & Burns, BP 2016, 'Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics', ISME Journal, vol. 10, pp. 183-196.View/Download from: Publisher's site
Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.The ISME Journal advance online publication, 29 May 2015; doi:10.1038/ismej.2015.87.
Hallegraeff, G, Bolch, C, Condie, S, Dorantes-Aranda, J, Murray, SA, Quinlan, R, Ruvindy, R, Turnbull, A, Ugalde, S & Wilson, K 2016, 'Unprecedented Alexandrium blooms in a previously low biotoxin risk area of Tasmania, Australia.', Proceedings of the 17th International Conference on Harmful Algae, 17th International Conference on Harmful Algae, ICHA, Brazil, pp. 38-41.View/Download from: UTS OPUS
During October 2012, a shipment of blue mussels (Mytilus galloprovincialis) from the poorly monitored east coast of Tasmania, Australia, was tested by Japanese import authorities and found to be contaminated with unacceptable levels of Paralytic Shellfish Toxins (PSTs; 10 mg/kg). Subsequently local oysters, scallops, clams, the viscera of abalone and rock lobsters were also found to be contaminated. This led to a global product recall and loss to the local economy of AUD 23M. Following low toxicity during 2013 and 2014 and implementation of minimal shellfish farm closures, a more severe bloom event occurred during July-November 2015 and again June-September 2016 (up to 300,000 Alexandrium cells/L; 24 mg/kg PST in mussels, 6 mg/kg in Crassostrea gigas oysters), also causing 4 human illnesses resulting in hospitalization after consumption of wild shellfish. While Alexandrium tamarense had been detected in low concentrations in southeastern Australia since 1987, all cultured strains belonged to the mostly non-toxic group 5 (now designated A. australiense; detected since 1987) and weakly toxic group 4 (A. pacificum; detected in 1997).
In contrast, the 2012 to 2016 outbreaks were dominated by highly toxic group 1 (A. fundyense) never
detected previously in the Australian region. Molecular analyses suggest that A. fundyense may have been a cryptic ribotype previously present in Tasmania, but newly stimulated by altered water column stratification
conditions driven by changing rainfall and temperature patterns. Increased seafood and plankton monitoring of the area now include the implementation of Alexandrium qPCR, routine Neogen™ immunological and HPLC PST tests, but ultimately may also drive change in harvesting strategies and aquaculture species selection by the local seafood industry.
Ruvindy, R, Ajani, PA & Murray, S 2018, Microalgal Community Composition Assessment in Warringah Lagoons 2017-2018. A report to Warringah Council, August 2018., pp. 1-29, Sydney, Australia.View/Download from: UTS OPUS