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

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

© 2009 Dr. Anusuya Willi

Variation within and between cyanobacterial species and strains affects competition: implications for phytoplankton modelling

Cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii are two harmful species which co-occur and successively dominate in freshwaters globally. Within-species strain variability affects cyanobacterial population responses to environmental conditions, and it is unclear which species/strain would dominate under different environmental conditions. This study applied a Monte Carlo approach to a phytoplankton dynamic growth model to identify how growth variability of multiple strains of these two species affects their competition

Photosynthetic efficiency in Polish and Australian Raphidiopsis raciborskii strains

Raphidiopsis raciborskii, as a potentially toxic, invasive cyanobacteria has attracted great attention. Worldwide distribution could have contributed to its phenotypic plasticity and even the formation of ecotypes adapted to the local environment. To determine mechanisms responsible for the omnipresence of R. raciborskii, photosynthetic efficiency in several strains differing in origin and toxicity has been investigated. Three non-toxic Polish strains and two toxic Australian strains were grown under standardized light and temperature conditions. Concentration of photosynthetic pigments, qualitative and quantitative analysis of carotenoid composition, and photosynthetic performance (chlorophyll fluorescence in vivo) were analysed. No significant differences between strains were observed in the photosystem II quantum efficiency (Fv/Fm), the photochemical (qP) and non-photochemical quenching (NPQ) and dark and light levels of plastoquinone reduction. Nonetheless, a positive correlation between Fv/Fm and overall NPQ was found. The phycocyanin concentration was negatively correlated with the carotenoid concentration in all five examined strains. Furthermore, in four strains roughly one third of pigments consisted of myxoxanthophylls. The ability to accumulate pigments involved both in light harvesting and photoprotection may contribute to the optimization of photosynthetic efficiency of investigated R. raciborskii strains in different environmental conditions. Documented parameters could not be ascribed to the difference in growth conditions, but could result from variations in their genetics

Organellar genomes of giant kelp from the southern hemisphere

ABSTRACTMacrocystis pyrifera is a foundation species that creates kelp forests and supports essential ecosystem services across coastal environments. Over the past half-century, more than 95% of giant kelp forests have declined around Tasmania, Australia, due to climate change, causing a near-complete loss of the ecosystems and services they support. Compared with northern hemisphere giant kelp ecosystems, Australian populations have received little research attention in genomic and other genetic analyses. We present the complete mitochondrial and chloroplast genomes of Macrocystis pyrifera from Tasmania. Both organellar genomes were similar to published Laminariales genomes in length, GC content, gene composition and synteny. A phylogeny constructed by combining protein-coding genes from both genomes showed Tasmanian specimens clustered with M. pyrifera specimens from the northern hemisphere. Genetic differences in protein genes between the Tasmanian M. pyrifera and the northern hemisphere specimens were overall low, but some ribosomal protein genes presented higher values of nonsynonymous mutations. The most divergent gene, the mitochondrial conserved hypothetical protein ORF377, can provide insights into the evolution of the species. This gene has been proposed as a suitable molecular marker for population genetic research in Fucales and may also be helpful for intraspecific studies of M. pyrifera. The complete mitochondrial and chloroplast genomes of Tasmanian M. pyrifera provide important genetic data and critical information for further evolutionary and population studies and for managing these endangered and disappearing populations

Are laboratory growth rate experiments relevant to explaining bloom-forming cyanobacteria distributions at global scale?

Predicting algal population dynamics using models informed by experimental data has been used as a strategy to inform the management and control of harmful cyanobacterial blooms. We selected toxic bloom-forming species Microcystis spp. and Raphidiopsis raciborskii (basionym Cylindrospermopsis raciborskii) for further examination as they dominate in 78 % and 17 %, respectively, of freshwater cyanobacterial blooms (cyanoHABs) reported globally over the past 30 years. Field measurements of cyanoHABs are typically based on biomass accumulation, but laboratory experiments typically measure growth rates, which are an important variable in cyanoHAB models. Our objective was to determine the usefulness of laboratory studies of these cyanoHAB growth rates for simulating the species dominance at a global scale. We synthesized growth responses of M. aeruginosa and R. raciborskii from 20 and 16 culture studies, respectively, to predict growth rates as a function of two environmental variables, light and temperature. Predicted growth rates of R. raciborskii exceeded those of M. aeruginosa at temperatures ≳ 25 °C and light intensities ≳ 150 μmol photons m s. Field observations of biomass accumulation, however, show that M. aeruginosa dominates over R. raciborskii, irrespective of climatic zones. The mismatch between biomass accumulation measured in the field, and what is predicted from growth rate measured in the laboratory, hinders effective use of culture studies to predict formation of cyanoHABs in the natural environment. The usefulness of growth rates measured may therefore be limited, and field experiments should instead be designed to examine key physiological attributes such as colony formation, buoyancy regulation and photoadaptation. Improving prediction of cyanoHABs in a changing climate requires a more effective integration of field and laboratory approaches, and an explicit consideration of strain-level variability

Constitutive toxin production under various nitrogen and phosphorus regimes of three ecotypes of Cylindrospermopsis raciborskii ((Wołoszyńska) Seenayya et Subba Raju)

Cylindrospermopsis raciborskii is a global invasive cyanobacterium, with some ecotypes (i.e. strains) producing the toxin cylindrospermopsin, CYN. Multiple ecotypes can co-exist, complicating prediction of toxin concentrations based on cell concentrations. This study examined the growth response and toxin production of three Australian ecotypes of C. raciborskii, two toxic (CS-505, CS-506) and one non-toxic (CS-510), to a range of nitrogen (N) and phosphorus (P) concentrations. CYN cell quota was constant under all N:P ratios and concentration conditions, indicative of a constitutive response, yet the CYN cell quota was 6-fold higher in CS-506 compared to CS-505. The ecotypes differed in response to dissolved N depletion: there was a 4-fold difference in the number of cells heterocyst mL(-1) between CS-505 and CS-510, while CS-506 did not produce any heterocysts and was unable to grow in N deplete conditions. Growth rates were lower for all ecotypes as [P] increased, indicative of a species with a strategy of P storage rather than increased growth. Presumably this is an adaptation to low and fluctuating P conditions. However, the negative effect of increasing [P] on growth is surprising. In contrast, increasing [N] resulted in higher growth rates across ecotypes. This study highlights the importance of understanding differences in growth and toxin production between ecotypes in response to environmental conditions in order to more effectively predict blooms and toxin yields. (C) 2015 Elsevier B.V. All rights reserved