Genomics—based approaches may assist in the verification and accelerate responsible deployment of marine carbon dioxide removal

Rapid development and deployment of marine carbon dioxide removal (mCDR) approaches will be required to prevent the worst consequences of climate change and meet national treaty obligations under the Paris agreement. However, approaches to monitor the efficacy and environmental safety of mCDR are not being developed with the same intensity as the technology. Verification will be required to convince a sceptical public and regulatory community of the overall benefit of mCDR as well as provide the regulatory community a basis for risk assessments that will be required for at scale deployments. In this perspective, we posit that genomics-based approaches can be used to assess the efficacy of carbon sequestration and monitor for the possibility of unintended consequences. By adopting these approaches, it will be feasible to develop the evidence portfolio necessary to underpin assessments of the risks, benefits and trade-offs involved in responsible deployment of mCDR

Different gene expression response of Polish and Australian Raphidiopsis raciborskii strains to the chill/light stress

R. raciborskii is known for growing under wide ranges of temperature and light. In temperate regions, however, low temperature and high light may serve as a stressful condition for invading tropical populations. The genetic basis of R. raciborskii’s adaptation to this combination of stresses are unknown. In this study, the growth rate and the expression of genes that may be crucial in the response to the chill/light stress of two R. raciborskii strains (differing in their climatic origin and toxicity) exposed to low temperature and high light were examined. Results showed that AMU-DH-30, a non CYN (cylindrospermopsin) producing strain isolated from the temperate region, exhibited under stress the upregulation of genes involved in the protein translation (rbp1, nusG, hflX), membrane fluidity (desA), photosynthetic activity (ccr2 and ftsH), and the accumulation of compatible solutes (asd). In contrast, a CYN producing Australian strain CS-505 was not able to adapt quickly and to continue growth during stress conditions. Intriguingly, CS-505 and AMU-DH-30 had a similar ability to resume growth when the stress conditions subsided. Moreover, in strain CS-505 the cyrB gene was significantly upregulated under the stress conditions. The presented results shed new light on the possible mechanisms involved in the response of R.raciborskii to chill/light stress

Characterisation of the extracellular matrix and adhesive (glyco)proteins of the diatom Phaeodactylum tricornutum

© 2009 Dr. Anusuya Willi

Insights from the global pangenome of Raphidiopsis raciborskii

Anusuya Willis, Jason Woodhouse, and a global network of participants*. Raphidiopsis raciborskii is a species, including both toxic and non-toxic strains. It occurs, and frequently blooms, in freshwater ecosystems across tropical and temperate environments. Local scale studies have shown high physiological and genomic diversity between strains of R. raciborskii, indicating possible rapid adaptation to new environments and resilience to environmental changes. To investigate the global genomic diversity of R. raciborskii we sequenced the full genomes of ~85 strains from 22 countries, spanning the continents Africa, America, Asia, Australia, and Europe. Comparative genomics show a small core genome and a large variable shell genome, suggesting a flexible genome evolution strategy. However, many gene presence/absences appear to be redundant and overall metabolic functions are similar across all genomes. There is a lack of unique features within each cluster and genome structural changes appear haphazard across the genome. These genomes are particularly rich in anti-phage systems, with over 500 CRISPR arrays, suggesting high rates of phage interaction. Speciation is occurring through geographic isolation, and three distinct species clusters were evidenced, indicating taxonomic changes and new species descriptions are needed within Raphidiopsis. The Raphidiopsis global pangenome reveals species with a flexible genome and local adaptation without local functional differences. *global network of participants: Anusuya Willis and Ian Jameson; Australian National Algae Culture Collection, CSIRO, Hobart, TAS, Australia Catharina Alves-de-Souza; Algae Resource Centre, University of North Carolina Wilmington, USA Cecile Bernard and Charlotte Duval; Muséum National d’Histoire Naturelle, Paris, France Masanobu Kawachi and Haruyo Yamaguchi; National Institute for Environmental Studies (NIES), Tsukuba, Japan Ruth N. Levy-Kaplan; Israel National Culture Collection of Algae, Kinneret Limnological Laboratory, Israel Oceanographic & Limnological research, Israel Alescia Cullen and Brett Neilan; University of Newcastle, Australia Maxine A. D. Mowe, Darren C. J. Yeo; National University of Singapore, Singapore Simon M. Mitrovic; University of Technology Sydney, Australia Dariusz Dziga; Laboratory of Metabolomics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland Mikołaj Kokociński; Department of Hydrobiology , Faculty of Biology, Adam Mickiewicz University, Poznań, Poland Jun Yang; Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China Gaetan Burgio: John Curtin School of Medical Research, ANU College of Health and Medicine, The Australia National University, Canberra, Australia Muriel Gugger; Cyanobacteria Culture Collection of Cyanobacteria, Pasteur Culture of Cyanobacteria, Institut Pasteur Institute, Université de Paris, Paris, France Jason Woodhouse; Dept. of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775 Stechlin, German

Defining Cyanobacterial Species: Diversity and Description Through Genomics

Cyanobacteria were the first oxygenic photosynthersizers, evolving ∼3.5 bya, they have since radiated into one of the most diverse and widely distributed phyla of bacteria. Cyanobacterial diversification occurs through ecological adaptation, facilitated by asexual reproduction, homologous recombination and horizontal gene transfer, and selection pressures on ecotypes leading to speciation. Delimiting cyanobacterial species is, thus, fraught with difficulties and a clear taxonomy has not yet been universally accepted. This review discusses diversity and description of cyanobacteria: covering traditional and new methods to define species boundaries and concluding with a focus on the advances made through genomics. Examples from the genera Raphidiopsis, Microcystis, and Prochlorococcus are used throughout. Genome plasticity allows cyanobacteria to rapidly adapt and be resilient to environmental changes, illustrating the means of their persistence, and is an important aspect of their biology. Genomics has revealed generalist and specialist genome strategies, intraspecific diversity, and genome evolution in response to environmental stimuli. New taxonomic definitions will need to account for intraspecific genetic variation, with a species classification that is relevant to a species concept and scientific endeavors. Capturing intraspecific diversity with comparative genomics may provide a new path to species classification. This is demonstrated with two case studies; comparison of available genomes shows differing species delineation of Raphidiopsis and Microcystis. In both genera, species boundaries occur at ∼96% average nucleotide identity (ANI), where homologous recombination is constrained, but speciation of Raphidiopsis raciborskii, R. brookii, and R. curvata has occurred through geographic isolation, whereas available data on Microcystis contain at least 15 species, reflecting, to differing extents, different ecotypes, which may co-exist. Both case studies question the relative importance of species-specific versus habitat specific gene pools as drivers of inter- and intraspecific diversity.No Full Tex

Draft Genome Assembly of Filamentous Brackish Cyanobacterium Limnoraphis robusta Strain CS-951

Griffith Sciences, Griffith School of EnvironmentFull Tex

Differences in cyanobacterial strain responses to light and temperature reflect species plasticity

Microcystis aeruginosa and Cylindrospermopsis raciborskii are two cyanobacterial species that dominate freshwaters globally. Multiple strains of each species with different physiology occur, however, many studies have focused only on one or two strains, limiting our understanding of both strain variation and characterisation of the species. Therefore, in this study we examined the variation in growth and morphology of multiple isolates of both species, isolated from two adjacent Australian reservoirs. Four M. aeruginosa strains (=isolates) (one colony-forming, three single-celled morphology) and eight C. raciborskii isolates (five with straight trichomes, three with coiled trichomes) were cultured individually in a factorial designed experiment with four light intensities (L: 10, 30, 50 and 100 μmol photons m−2 s−1) and two temperatures (T: 20 and 28 °C). The specific growth rate (μ), cell volume, and final cell concentration was measured. The light attenuation coefficient (kj), a measure of self-shading, was calculated. The results showed that the intraspecific variation was greater than the interspecific variation. The μ of all isolates of M. aeruginosa and C. raciborskii ranged from 0.16 to 0.55 d−1 and 0.15 to 0.70 d−1, respectively. However, at a specific light and temperature the mean μ of all M. aeruginosa isolates and C. raciborskii isolates were similar. At the species level, M. aeruginosa had higher growth rates at higher light intensity but lower temperature (L100T20), while straight C. raciborskii had higher growth rates at lower light intensity but higher temperature (L50T28), and coiled C. raciborskii had higher growth rates at higher light intensity and higher temperature (L100T28). The final cell concentrations of M. aeruginosa were higher than C. raciborskii. However, C. raciborskii isolates had greater variation in μ, kj and cell volume than M. aeruginosa. kj varied with light and temperature, and decreased with surface-to-volume ratio within each species. kj was lower for M. aeruginosa compared to C. raciborskii as expected based on cell size, but interestingly, C. raciborskii coiled isolates had lower kj than the straight isolates suggesting lower effect of self-shading. This study highlights the extent of strain variation to environmental conditions and to species variability.Griffith Sciences, Australian Rivers InstituteFull Tex

Adhesive Modular Proteins Occur in the Extracellular Mucilage of the Motile, Pennate Diatom Phaeodactylum tricornutum

AbstractThis Letter reports on adhesive modular proteins recorded by atomic force microscopy on live cells from the extracellular mucilage secreted from, and deposited around, the motile form of the pennate diatom Phaeodactylum tricornutum. This is the first report of modular proteins and their supramolecular assemblies, called adhesive nanofibers (ANFs), to be found on diatoms that use adhesives not only for substratum adhesion, but as a conduit for cell motility. The permanent adhesive pads secreted by Toxarium undulatum, a sessile centric diatom, were previously shown to possess ANFs with a modular protein backbone. Our results reported here suggest that modular proteins may be an important component of diatom adhesives in general, and that diatoms utilize the tensile strength, toughness, and flexibility of ANFs for multiple functions. Significantly, the genome of P. tricornutum has recently been sequenced; this will allow directed searches of the genome to be made for genes with modular protein homologs, and subsequent detailed studies of their molecular structure and function