Publications
Chapters
Červený, J, Šalagovič, J, Muzika, F, Šafránek, D & Schreiber, I 2019, 'Influence of Circadian Clocks on Optimal Regime of Central C-N Metabolism of Cyanobacteria' in Cyanobacteria, Elsevier, pp. 193-206.
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Malik, S, Liu, C-G, Zhao, X-Q & Mehmood, MA 2019, 'Long-Chain Liquid Biofuels' in Comprehensive Biotechnology, Elsevier, pp. 101-109.
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The rate at which fossil fuels are being consumed today has never been so high in human history. In addition to rapid depletion of the reserves for fossil fuels, the increased consumption also results in the enhanced carbon emissions, raising serious environmental concerns. Therefore, a significant amount of efforts has been devoted to developing fossil fuel alternatives, which are sustainable and environmentally friendly. The first-generation biofuels such as fuel ethanol and biodiesel have been produced through fermentation and enzymatic catalysis from grains and sugarcane and vegetable oils. Due to low energy density, these fuels are not compatible with jet engines, which require energy-rich long-chain fuels that can be produced through microbial platforms either by the manipulation of resident metabolic pathways or engineering the novel ones. However, currently, the production of such fuels is not commercially feasible due to low product yields, fuel-induced toxicity, and complex extraction processes. This article discusses strategies employed to enhance the carbon assimilation pathways of host organisms for directing the metabolic flux more effectively toward the synthesis of desired biofuels via natural or synthetic pathways, along with remodeling of metabolic pathways to achieve the enhanced titer and productivity, and the feasibility of designing biofuel secretion systems are also addressed.
Ngo, HH, Vo, HNP, Guo, W, Bui, X-T, Nguyen, PD, Nguyen, TMH & Zhang, X 2019, 'Advances of Photobioreactors in Wastewater Treatment: Engineering Aspects, Applications and Future Perspectives' in Bui, X-T, Chiemchaisri, C, Fujioka, T & Varjani, S (eds), Energy, Environment, and Sustainability, Springer Singapore, Germany, pp. 297-329.
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The photobioreactor is an efficient artificial system in terms of biomass cultivation and removing pollutants. Compared to other conventional technologies, its design and operational processes are superior. Therefore, the photobioreactor specifically targets and tailors for the increasing demand for biomass and stringent pollutants removal standards. Since the early 1950s, there has been a variety of photobioreactor types, and these have been addressing the different technical issues over time and others more recently. As well, diverse applications of the photobioreactor process are becoming more widespread, and this opens for a good opportunity for future sustainable developments. This book chapter discusses advances being made in photobioreactor technology, encompassing: (1) modelling; (2) designs and classifications; (3) applications and (4) future perspectives.
Shahid, A, Malik, S, Alam, MA, Nahid, N & Mehmood, MA 2019, 'The Culture Technology for Freshwater and Marine Microalgae' in Microalgae Biotechnology for Development of Biofuel and Wastewater Treatment, Springer Singapore, pp. 21-44.
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Microalgae are promising eco-friendly source of food, feed, biofuels, and chemicals. There has been substantial progress at the lab and industrial scales to develop efficient and sustainable microalgae culturing techniques. However, several constraints must be addressed to make the overall process economically viable. Chemo-genetics elements can play a pivotal role in achieving the commercial goals because microalgae grow more efficiently in high concentrations of essential nutrients like nitrogen, phosphorus, and carbon in addition to enhance by-product formation. Moreover, alteration in culturing conditions also activates lipid accumulation. Recent strategies have combined these approaches to enhance lipid accumulation and along with enhanced biomass productivity. It is necessary to optimize inoculum production and culture management to avoid contamination, especially at commercial scales. Furthermore, prevailing outdoor conditions of rainfall, variable temperature, and irradiation, which are entirely different from small lab-scale facilities, pose additional challenges during outdoor cultivation. This chapter highlights the nutritional requirements of culturing media and their impact along with possible challenges on microalgae cultivation to ensure the stable and high productivities of large-scale cultures. Media recycling not only reduces the dependency on freshwater but also increases the economic viability of the process. Recent advances regarding media recycling and strategies to control biological contaminants are also discussed.
Suggett, DJ & Moore, CM 2019, 'Fluorometry for Biological Sensing' in Encyclopedia of Ocean Sciences, Third Edition: Volume 1-5, p. V5-87-V5-93.
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Light-absorbing pigments cause many marine organisms to naturally fluoresce, a phenomenon whereby light is emitted at a longer wavelength following light absorption at a shorter wavelength. Fluorescence provides a relatively unobtrusive signature of organism abundance and physiology; consequently, a wide variety of fluorescence techniques are now routinely employed in marine biological investigations. Important technological advances throughout the last 20 years have enabled exploration of the taxonomy and physiology of marine organisms with increasing complexity. In particular, the intracellular use of fluorescent tags, molecules, and dyes that covalently bind to sensing biomolecules. However, many such techniques require samples to be removed from nature. Most widespread for assaying biology in situ exploits the fluorescence emitted from chlorophyll a, the predominant light harvesting pigment inherent to all (micro)algae, cyanobacteria, and aquatic vascular plants. Measurements of chlorophyll a fluorescence were introduced in the 1960s to improve estimates of phytoplankton abundance. By the 1990s, this field had evolved to enable the physiology and productivity of primary producers to be examined at scales from the single cell to entire ocean basins. Current remote sensing algorithms concentrate on better describing the relationship between primary productivity and natural fluorescence that is emitted from solar excitation. While several major challenges exist in achieving this goal, such approaches provide great promise for accurately characterizing the role of marine primary productivity during this period of extreme climate change.
Journal articles
Achlatis, M, Pernice, M, Green, K, de Goeij, JM, Guagliardo, P, Kilburn, MR, Hoegh-Guldberg, O & Dove, S 2019, 'Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter', Proceedings of the Royal Society B: Biological Sciences, vol. 286, no. 1916, pp. 20192153-20192153.
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Aguilar, C, Raina, J-B, Fôret, S, Hayward, DC, Lapeyre, B, Bourne, DG & Miller, DJ 2019, 'Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress', BMC Genomics, vol. 20, no. 1.
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Akyol, S, Ben Nissan, B, Karacan, I, Yetmez, M, Gokce, H, Suggett, DJ & Oktar, FN 2019, 'Morphology, characterization, and conversion of the corals Goniopora spp. and Porites cylindrica to hydroxyapatite', Journal of the Australian Ceramic Society, vol. 55, no. 3, pp. 893-901.
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© 2019, Australian Ceramic Society. The aim of this study is to obtain pure natural hydroxyapatite (HAp) and tricalcium phosphate (TCP) from a Goniopora spp. and from hump coral (Porites cylindrica), both sourced from Australia. Due to the nature of the conversion process, commercial coralline HAp has retained coral or CaCO3, and the structure possesses both nano- and mesopores within the interpore trabeculae resulting in high dissolution rates. To overcome these limitations, a newly patented coral double-conversion technique has been developed. The current technique involves a two-stage application route where in the first-stage complete conversion of coral to pure HAp is achieved. In the second stage, a sol-gel-derived HAp nanocoating is directly applied to cover the meso- and nanopores within the intrapore material, while maintaining the large pores. Here, we specifically investigated the morphological changes and characterized these corals prior to and after conversion. For this purpose, four groups designated as C0, C1, C2, and C3 were used. C0 is Porites, Goniopora, and cylindrica; the original coral is calcium carbonate with aragonite structure that contains proteins and polysaccharides. C1 is coral cleaned under ultrasound in bleach diluted with water. C2 is coral converted to hydroxyapatite (HAp) by hydrothermal treatment method at 200 °C under pressure in the presence of ammonium biphosphate. C3 is obtained by coating C2 with sol-gel alkoxide-derived nanohydroxyapatite to obtain a more bioactive osteoconductive material and improve mechanical properties. All groups were characterized by XRD, EDAX, DTA/TGA, and SEM. The results showed that the biaxial strengths of the C2 and C3 were significantly higher than the original coral. The work also showed the advantages of the hydrothermal conversion method and the effect of the nanocoating which is expected to improve the final bioactivity through microstructural changes of the surfaces.
Armbrecht, LH, Coolen, MJL, Lejzerowicz, F, George, SC, Negandhi, K, Suzuki, Y, Young, J, Foster, NR, Armand, LK, Cooper, A, Ostrowski, M, Focardi, A, Stat, M, Moreau, JW & Weyrich, LS 2019, 'Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation', Earth-Science Reviews, vol. 196, pp. 102887-102887.
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© 2019 Elsevier B.V. The study of ancient DNA (aDNA) from sediments (sedaDNA) offers great potential for paleoclimate interpretation, and has recently been applied as a tool to characterise past marine life and environments from deep ocean sediments over geological timescales. Using sedaDNA, palaeo-communities have been detected, including prokaryotes and eukaryotes that do not fossilise, thereby revolutionising the scope of marine micropalaeontological research. However, many studies to date have not reported on the measures taken to prove the authenticity of sedaDNA-derived data from which conclusions are drawn. aDNA is highly fragmented and degraded and extremely sensitive to contamination by non-target environmental DNA. Contamination risks are particularly high on research vessels, drilling ships and platforms, where logistics and facilities do not yet allow for sterile sediment coring, and due consideration needs to be given to sample processing and analysis following aDNA guidelines. This review clarifies the use of aDNA terminology, discusses common pitfalls and highlights the urgency behind adopting new standards for marine sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sedaDNA research into International Ocean Discovery Program (IODP) operations. Currently available installations aboard drilling ships and platforms are reviewed, improvements suggested, analytical approaches detailed, and the controls and documentation necessary to support the authenticity of aDNA retrieved from deep-sea sediment cores is outlined. Beyond practical considerations, concepts relevant to the study of past marine biodiversity based on sedaDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.
Bodachivskyi, I, Kuzhiumparambil, U & Bradley G. Williams, D 2019, 'High Yielding Acid‐Catalysed Hydrolysis of Cellulosic Polysaccharides and Native Biomass into Low Molecular Weight Sugars in Mixed Ionic Liquid Systems', ChemistryOpen, vol. 8, no. 10, pp. 1316-1324.
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Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'A Systematic Study of Metal Triflates in Catalytic Transformations of Glucose in Water and Methanol: Identifying the Interplay of Brønsted and Lewis Acidity', ChemSusChem, vol. 12, no. 14, pp. 3208-3208.
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Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'A Systematic Study of Metal Triflates in Catalytic Transformations of Glucose in Water and Methanol: Identifying the Interplay of Brønsted and Lewis Acidity', ChemSusChem, vol. 12, no. 14, pp. 3263-3270.
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Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'Acid‐Catalysed Conversion of Carbohydrates into Furan‐Type Molecules in Zinc Chloride Hydrate', ChemPlusChem, vol. 84, no. 4, pp. 352-357.
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Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'Metal triflates are tunable acidic catalysts for high yielding conversion of cellulosic biomass into ethyl levulinate', Fuel Processing Technology, vol. 195, pp. 106159-106159.
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© 2019 Metal triflates and their mixtures with Brønsted acids are excellent catalysts for the selective and high yielding transformation of microcrystalline cellulose into ethyl levulinate, in ethanol, producing synergistic catalyst effects in some instances. The pretreatment of raw and unrefined cellulosic materials with a deep eutectic solvent enables similarly excellent catalysed conversion thereof into ethyl levulinate in superb yield (up to 75%) and selectivity (up to 88%). When using fermentation-derived ethanol, the product possesses 100% renewable content.
Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'The role of the molecular formula of ZnCl2·nH2O on its catalyst activity: a systematic study of zinc chloride hydrates in the catalytic valorisation of cellulosic biomass', Catalysis Science & Technology, vol. 9, no. 17, pp. 4693-4701.
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We show the efficient and direct transformation of a range of low value cellulosic substrates such as lignocellulose and algal biomass, into higher value chemicals, including low molecular weight reducing saccharides and furanoid products.
Bretherton, L, Poulton, AJ, Lawson, T, Rukminasari, N, Balestreri, C, Schroeder, D, Mark Moore, C & Suggett, DJ 2019, 'Day length as a key factor moderating the response of coccolithophore growth to elevated pCO2', Limnology and Oceanography, vol. 64, no. 3, pp. 1284-1296.
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Buapet, P, Mohammadi, NS, Pernice, M, Kumar, M, Kuzhiumparambil, U & Ralph, PJ 2019, 'Excess copper promotes photoinhibition and modulates the expression of antioxidant-related genes in Zostera muelleri', Aquatic Toxicology, vol. 207, pp. 91-100.
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© 2018 Elsevier B.V. Copper (Cu) is an essential micronutrient for plants and as such is vital to many metabolic processes. Nevertheless, when present at elevated concentrations, Cu can exert toxic effects on plants by disrupting protein functions and promoting oxidative stress. Due to their proximity to the urbanised estuaries, seagrasses are vulnerable to chemical contamination via industrial runoff, waste discharges and leachates. Zostera muelleri is a common seagrass species that forms habitats in the intertidal areas along the temperate coast of Australia. Previous studies have shown the detrimental effects of Cu exposure on photosynthetic efficiency of Z. muelleri. The present study focuses on the impacts of sublethal Cu exposure on the physiological and molecular responses. By means of a single addition, plants were exposed to 250 and 500 μg Cu L−1 (corresponding to 3.9 and 7.8 μM, respectively) as well as uncontaminated artificial seawater (control) for 7 days. Chlorophyll fluorescence parameters, measured as the effective quantum yield (ϕPSII), the maximum quantum yield (Fv/Fm) and non-photochemical quenching (NPQ) were assessed daily, while Cu accumulation in leaf tissue, total reactive oxygen species (ROS) and the expression of genes involved in antioxidant activities and trace metal binding were determined after 1, 3 and 7 days of exposure. Z. muelleri accumulated Cu in the leaf tissue in a concentration-dependent manner and the bioaccumulation was saturated by day 3. Cu exposure resulted in an acute suppression of ϕPSII and Fv/Fm. These two parameters also showed a concentration- and time-dependent decline. NPQ increased sharply during the first few days before subsequently decreasing towards the end of the experiment. Cu accumulation induced oxidative stress in Z. muelleri as an elevated level of ROS was detected on day 7. Lower Cu concentration promoted an up-regulation of genes encoding Cu/Zn-superoxide dismutase (Cu/Zn-sod), ascorbate p...
Camp, EF, Edmondson, J, Doheny, A, Rumney, J, Grima, AJ, Huete, A & Suggett, DJ 2019, 'Mangrove lagoons of the Great Barrier Reef support coral populations persisting under extreme environmental conditions', Marine Ecology Progress Series, vol. 625, pp. 1-14.
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© The authors 2019. Global degradation of coral reefs has increased the urgency of identifying stress-tolerant coral populations, to enhance understanding of the biology driving stress tolerance, as well as identifying stocks of stress-hardened populations to aid reef rehabilitation. Surprisingly, scientists are continually discovering that naturally extreme environments house established coral populations adapted to grow within extreme abiotic conditions comparable to seawater conditions predicted over the coming century. Such environments include inshore mangrove lagoons that carry previously unrecognised ecosystem service value for corals, spanning from refuge to stress preconditioning. However, the existence of such hot-spots of resilience on the Great Barrier Reef (GBR) remains entirely unknown. Here we describe, for the first time, 2 extreme GBR mangrove lagoons (Woody Isles and Howick Island), exposing taxonomically diverse coral communities (34 species, 7 growth morphologies) to regular extreme low pH (<7.6), low oxygen (<1 mg l−1) and highly variable temperature range (>7°C) conditions. Coral cover was typically low (<5%), but highly patchy and included established colonies (>0.5 m diameter), with net photosynthesis and calcification rates of 2 dominant coral species (Acropora millepora, Porites lutea) reduced (20−30%), and respiration enhanced (11−35%), in the mangrove lagoon relative to adjacent reefs. Further analysis revealed that physiological plasticity (photosynthetic ‘strategy’) and flexibility of Symbiodiniaceae taxa associations appear crucial in supporting coral capacity to thrive from reef to lagoon. Prevalence of corals within these extreme conditions on the GBR (and elsewhere) increasingly challenge our understanding of coral resilience to stressors, and highlight the need to study unfavourable coral environments to better resolve mechanisms of stress tolerance.
Cardona, T, Sánchez‐Baracaldo, P, Rutherford, AW & Larkum, AW 2019, 'Early Archean origin of Photosystem
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Carney, RL, Labbate, M, Siboni, N, Tagg, KA, Mitrovic, SM & Seymour, JR 2019, 'Urban beaches are environmental hotspots for antibiotic resistance following rainfall', Water Research, vol. 167, pp. 115081-115081.
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© 2019 Elsevier Ltd To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.
Chmelík, D, Hrouzek, P, Fedorko, J, Vu, DL, Urajová, P, Mareš, J & Červený, J 2019, 'Accumulation of cyanobacterial oxadiazine nocuolin A is enhanced by temperature shift during cultivation and is promoted by bacterial co-habitants in the culture', Algal Research, vol. 44, pp. 101673-101673.
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© 2019 Elsevier B.V. Proper setting of cultivation conditions is essential for production of high-value compounds in microbial biotechnology. The present study characterizes photoautotrophic growth and capacity to accumulate the antiproliferative secondary metabolite Nocuolin A (NoA) in cyanobacterium Nostoc sp. CCAP 1453/38. As the cyanobacterial culture was found to be non-axenic, the bacteria accompanying the culture were characterized, then the growth demands and NoA production in the Nostoc-bacterial consortium were determined, and finally an axenic strain was prepared. For the purposes of growth characterization, the culture was maintained in a quasi-continuous regime under various light intensities, temperatures, and inorganic carbon concentrations in a small-scale laboratory photobioreactor. The maximum biomass growth rate obtained was 0.10 h−1 (doubling time Dt = 6.93 h). Following optimal growth conditions were identified: temperature of 35 °C, light intensity 600 μmol(photons) m−2 s−1, and 2500 ppm CO2 in the sparging gas. As the temperature optima for the biomass production and for NoA accumulation differed, biphasic cultivation for maximal NoA yield was designed, leading to a three times more effective cultivation procedure compared to batch culture maintained at a temperature optimal for NoA production. The increased NoA accumulation at reduced temperature that correlated with enhanced expression of NoA biosynthetic genes after the temperature shift suggested its regulation occurs at the expression level. It has further been shown that NoA production is reduced in axenic culture, which indicates that it is also triggered by presence of bacteria. This study shows an example of how a biphasic cultivation mode with different temperatures can be used in high-value compound production processes. It also brings direct evidence that cyanobacterial strain axenization can lead to a rapid decrease in production of valuable compounds and that non-axenic strain...
Clifton, J, Osman, EO, Suggett, DJ & Smith, DJ 2019, 'WITHDRAWN: Resolving conservation and development tensions in a small island state: A governance analysis of Curieuse Marine National Park, Seychelles', Marine Policy, pp. 103650-103650.
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Coleman, MA, Clark, JS, Doblin, MA, Bishop, MJ & Kelaher, BP 2019, 'Genetic differentiation between estuarine and open coast ecotypes of a dominant ecosystem engineer', Marine and Freshwater Research, vol. 70, no. 7, pp. 977-977.
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Commault, AS, Fabris, M, Kuzhiumparambil, U, Adriaans, J, Pernice, M & Ralph, PJ 2019, 'Methyl jasmonate treatment affects the regulation of the 2-C-methyl-D-erythritol 4-phosphate pathway and early steps of the triterpenoid biosynthesis in Chlamydomonas reinhardtii', Algal Research, vol. 39, pp. 101462-101462.
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© 2019 Elsevier B.V. Terpenoids are a large and diverse class of naturally occurring metabolites serving many industrial applications and natural roles. Economically important terpenoids are often produced in low abundance from their natural sources, making their industrial-scale production challenging or uneconomical, therefore engineered microorganisms are frequently used as heterologous production platforms. Photosynthetic microorganisms, such as the green alga Chlamydomonas reinhardtii, represent promising systems to produce terpenoids in a cost-effective and sustainable manner, but knowledge about the regulation of their terpenoid metabolism remains limited. Here we report on the investigation of the phytohormone methyl jasmonate (MeJA) as elicitor of algal terpenoid synthesis. We treated C. reinhardtii cells in mid-exponential growth phase with three different concentrations of MeJA (0.05, 0.5 and 1 mM). The highest concentration of MeJA affected the photosynthetic activity of the cells, arrested the growth and up-regulated key genes of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, leading to a significant increase in intermediates of this pathway, squalene and (S)-2,3-epoxysqualene, while the abundance of cycloartenol, and two main sterols (ergosterol and 7-dehydroporiferasterol) decreased. These data suggest the redirection of the carbon flux towards the synthesis of yet uncharacterised triterpenoid secondary metabolites upon MeJA treatment. Our results offer important new insights into the regulation of the triterpenoid metabolism in C. reinhardtii and raise important questions on hormonal signalling in microalgae. Phytohormone treatment is tested for the first time in algae, where it holds great potential for identifying key transcriptional regulators of the MEP pathway as targets for future metabolic engineering studies for improve production of high-value triterpenoids.
Curson, ARJ, Williams, BT, Pinchbeck, BJ, Sims, LP, Martínez, AB, Rivera, PPL, Kumaresan, D, Mercadé, E, Spurgin, LG, Carrión, O, Moxon, S, Cattolico, RA, Kuzhiumparambil, U, Guagliardo, P, Clode, PL, Raina, J-B & Todd, JD 2019, 'Author Correction: DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton', Nature Microbiology, vol. 4, no. 3, pp. 540-542.
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In the version of this Letter originally published, the Methods incorrectly stated that all phytoplankton cultures were sampled in mid-exponential phase. The low-nitrogen cultures were sampled in early stationary phase and at the point at which Fv/Fm values decreased, to indicate that cultures were experiencing low-nitrogen conditions. All other phytoplankton cultures were sampled in exponential phase. Growth and Fv/Fm data are provided here on high- and low-nitrogen cultures (Figs 1, 2 and 3) to clarify and support this correction. The Methods also stated that cell counting was done using a Beckman Multisizer 3 Coulter Counter, but a CASY Model TT Cell Counter was used.
Deschaseaux, E, O'Brien, J, Siboni, N, Petrou, K & Seymour, JR 2019, 'Shifts in dimethylated sulfur concentrations and microbiome composition in the red-tide causing dinoflagellate <i>Alexandrium minutum</i> during a simulated marine heatwave', Biogeosciences, vol. 16, no. 22, pp. 4377-4391.
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Dukic, E, Herdean, A, Cheregi, O, Sharma, A, Nziengui, H, Dmitruk, D, Solymosi, K, Pribil, M & Spetea, C 2019, 'K+ and Cl− channels/transporters independently fine-tune photosynthesis in plants', Scientific Reports, vol. 9, no. 1.
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Espinoza-Vergara, G, Noorian, P, Silva-Valenzuela, CA, Raymond, BBA, Allen, C, Hoque, MM, Sun, S, Johnson, MS, Pernice, M, Kjelleberg, S, Djordjevic, SP, Labbate, M, Camilli, A & McDougald, D 2019, 'Vibrio cholerae residing in food vacuoles expelled by protozoa are more infectious in vivo', Nature Microbiology, vol. 4, no. 12, pp. 2466-2474.
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© 2019, The Author(s), under exclusive licence to Springer Nature Limited. Vibrio cholerae interacts with many organisms in the environment, including heterotrophic protists (protozoa). Several species of protozoa have been reported to release undigested bacteria in expelled food vacuoles (EFVs) when feeding on some pathogens. While the production of EFVs has been reported, their biological role as a vector for the transmission of pathogens remains unknown. Here we report that ciliated protozoa release EFVs containing V. cholerae. The EFVs are stable, the cells inside them are protected from multiple stresses, and large numbers of cells escape when incubated at 37 °C or in the presence of nutrients. We show that OmpU, a major outer membrane protein positively regulated by ToxR, has a role in the production of EFVs. Notably, cells released from EFVs have growth and colonization advantages over planktonic cells both in vitro and in vivo. Our results suggest that EFVs facilitate V. cholerae survival in the environment, enhancing their infectious potential and may contribute to the dissemination of epidemic V. cholerae strains. These results improve our understanding of the mechanisms of persistence and the modes of transmission of V. cholerae and may further apply to other opportunistic pathogens that have been shown to be released by protists in EFVs.
Fisher, A, Wangpraseurt, D, Larkum, AWD, Johnson, M, Kühl, M, Chen, M, Wong, HL & Burns, BP 2019, 'Correlation of bio-optical properties with photosynthetic pigment and microorganism distribution in microbial mats from Hamelin Pool, Australia', FEMS Microbiology Ecology, vol. 95, no. 1.
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© FEMS 2018. All rights reserved. Microbial mats and stromatolites are widespread in Hamelin Pool, Shark Bay, however the phototrophic capacity of these systems is unknown. This study has determined the optical properties and light-harvesting potential of these mats with light microsensors. These characteristics were linked via a combination of 16S rDNA sequencing, pigment analyses and hyperspectral imaging. Local scalar irradiance was elevated over the incident downwelling irradiance by 1.5-fold, suggesting light trapping and strong scattering by the mats. Visible light (400-700 nm) penetrated to a depth of 2 mm, whereas near-infrared light (700-800 nm) penetrated to at least 6 mm. Chlorophyll a and bacteriochlorophyll a (Bchl a) were found to be the dominant photosynthetic pigments present, with BChl a peaking at the subsurface (2-4 mm). Detailed 16S rDNA analyses revealed the presence of putative Chl f-containing Halomicronema sp. and photosynthetic members primarily decreased from the mat surface down to a depth of 6 mm. Data indicated high abundances of some pigments and phototrophic organisms in deeper layers of the mats (6-16 mm). It is proposed that the photosynthetic bacteria present in this system undergo unique adaptations to lower light conditions below the mat surface, and that phototrophic metabolisms are major contributors to ecosystem function.
Ganesan, M, Trivedi, N, Gupta, V, Madhav, SV, Radhakrishna Reddy, C & Levine, IA 2019, 'Seaweed resources in India – current status of diversity and cultivation: prospects and challenges', Botanica Marina, vol. 62, no. 5, pp. 463-482.
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Gardner, SG, Camp, EF, Smith, DJ, Kahlke, T, Osman, EO, Gendron, G, Hume, BCC, Pogoreutz, C, Voolstra, CR & Suggett, DJ 2019, 'Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave', Ecology and Evolution, vol. 9, no. 3, pp. 938-956.
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Gleason, FH, Larkum, AWD, Raven, JA, Manohar, CS & Lilje, O 2019, 'Ecological implications of recently discovered and poorly studied sources of energy for the growth of true fungi especially in extreme environments', Fungal Ecology, vol. 39, pp. 380-387.
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© 2018 Rhodopsin transmembrane proton pumps (fuelled by visible light which is absorbed by retinal (carotenoid) chromophores) exist in all three domains of living species and in all groups of true fungi studied. Light driven proton and sodium pumps are likely to be essential for some marine fungi, especially hypersaline tolerant and endolithic species. Rhodopsin macromolecular machines, using visible light, drive metabolic reactions in addition to those provided by aerobic respiration, providing extra energy needed for the maintenance and growth of fungi, especially in euphotic environments where oxygen concentration is limited. In addition, dissimilatory nitrate and metal oxide reduction can provide sources of energy for fungi in the absence of oxygen, for example, in fungal species growing in marine sediments. Finally, the oxidation of elemental sulphur, iron and manganese can be a source of energy. Some fungi are, therefore, lithotrophs and photoheterotrophs. The ecological implications of these latter processes are discussed.
GOH, CJ, PARK, D, LEE, JS, DAVEY, PA, PERNICE, M, RALPH, PJ & HAHN, Y 2019, 'Zostera virus T – a novel virus of the genus Tepovirus identified in the eelgrass, Zostera muelleri', Acta virologica, vol. 63, no. 04, pp. 366-372.
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Analysis of a transcriptome dataset obtained from tissue samples of the eelgrass Zostera muelleri, an aquatic flowering plant species of the family Zosteraceae, yielded three genome sequence contigs of a novel RNA virus. Sequence comparison and phylogenetic analysis revealed that the novel RNA virus, named Zostera virus T (ZoVT), belongs to the genus Tepovirus of the family Betaflexiviridae. The three genome contigs of ZoVT showed 88.2‒97.2% nucleotide sequence identity to each other, indicating that they descended from a common ancestor. The ZoVT genome contains three open reading frames (ORFs): ORF1 encodes a 1816 amino acid (aa) replicase (REP) with RNA-dependent RNA polymerase (RdRp) activity; ORF2, a 398 aa movement protein (MP); and ORF3, a 240 aa coat protein (CP). The phylogenetic analysis using REP sequences of ZoVT and other Betaflexiviridae viruses showed that Prunus virus T is the closest known virus to ZoVT, whereas potato virus T, the type species of the genus Tepovirus, is the second closest virus. Genome sequences of ZoVT, which is the third tepovirus species identified to date, may be useful for investigating the evolution and molecular biology of tepoviruses. Keywords: Zostera virus T; Tepovirus; Betaflexiviridae; eelgrass; Zostera muelleri.
Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunensse, T, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015–2016 heatwave', Coral Reefs, vol. 38, no. 4, pp. 815-830.
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© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. High-latitude coral communities are distinct from their tropical counterparts, and how they respond to recent heat wave events that have decimated tropical reefs remains unknown. In Australia, the 2016 El Niño resulted in the largest global mass coral bleaching event to date, reaching as far south as Sydney Harbour (~ 34°S). Coral bleaching was observed for the first time (affecting ca., 60% of all corals) as sea surface temperatures in Sydney Harbour remained > 2 °C above the long-term mean summer maxima, enabling us to examine whether high-latitude corals bleached in a manner described for tropical corals. Responses of the geographically cosmopolitan Plesiastrea versipora and southerly restricted Coscinaraea mcneilli were contrasted across two harbour sites, both in situ and among samples-maintained ex situ in aquaria continually supplied with Sydney Harbour seawater. While both coral taxa hosted the same species of microalgal endosymbiont (Breviolum spp; formerly clade B), only P. versipora bleached both in situ and ex situ via pronounced losses of endosymbiont cells. Both species displayed very different metabolic responses (growth, photosynthesis, respiration and calcification) and bleaching susceptibilities under elevated temperatures. Bacterial microbiome profiling, however, revealed a convergence of bacterial community composition across coral species throughout the bleaching. Corals species found in temperate regions, including the generalist P. versipora, will therefore likely be highly susceptible to future change as heat waves grow in frequency and severity unless their thermal thresholds increase. Our observations provide further evidence that high-latitude systems are susceptible to community reorganisation under climate change.
Gray, R, Jones, HA, Hitchcock, JN, Hardwick, L, Pepper, D, Lugg, A, Seymour, JR & Mitrovic, SM 2019, 'Mitigation of cold‐water thermal pollution downstream of a large dam with the use of a novel thermal curtain', River Research and Applications, vol. 35, no. 7, pp. 855-866.
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Green, TJ, Siboni, N, King, WL, Labbate, M, Seymour, JR & Raftos, D 2019, 'Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event', Microbial Ecology, vol. 77, no. 3, pp. 736-747.
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© 2018, Springer Science+Business Media, LLC, part of Springer Nature. Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.
Hewson, I, Sullivan, B, Jackson, EW, Xu, Q, Long, H, Lin, C, Quijano Cardé, EM, Seymour, J, Siboni, N, Jones, MRL & Sewell, MA 2019, 'Perspective: Something Old, Something New? Review of Wasting and Other Mortality in Asteroidea (Echinodermata)', Frontiers in Marine Science, vol. 6.
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Hurtado-McCormick, V, Kahlke, T, Petrou, K, Jeffries, T, Ralph, PJ & Seymour, JR 2019, 'Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome', Frontiers in Microbiology, vol. 10, no. MAY.
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Jain, D, Ghonse, SS, Trivedi, T, Fernandes, GL, Menezes, LD, Damare, SR, Mamatha, SS, Kumar, S & Gupta, V 2019, 'CO2 fixation and production of biodiesel by Chlorella vulgaris NIOCCV under mixotrophic cultivation', Bioresource Technology, vol. 273, pp. 672-676.
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Jaramillo-Madrid, AC, Ashworth, J, Fabris, M & Ralph, PJ 2019, 'Phytosterol biosynthesis and production by diatoms (Bacillariophyceae)', Phytochemistry, vol. 163, pp. 46-57.
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© 2019 Elsevier Ltd Diatoms are abundant unicellular marine photosynthetic algae that have genetically diversified their physiology and metabolism while adapting to numerous environments. The metabolic repertoire of diatoms presents opportunities to characterise the biosynthesis and production of new and potentially valuable microalgal compounds, including sterols. Sterols of plant origin, known as phytosterols, have been studied for health benefits including demonstrated cholesterol-lowering properties. In this review we summarise sterol diversity, the unique metabolic features of sterol biosynthesis in diatoms, and prospects for the extraction of diatom phytosterols in comparison to existing sources. We also review biotechnological efforts to manipulate diatom biosynthesis, including culture conditions and avenues for the rational engineering of metabolism and cellular regulation.
Kahlke, T & Ralph, PJ 2019, '
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Kim, M, Pernice, M, Watson-Lazowski, A, Guagliardo, P, Kilburn, MR, Larkum, AWD, Raven, JA & Ralph, PJ 2019, 'Effect of reduced irradiance on 13C uptake, gene expression and protein activity of the seagrass Zostera muelleri', Marine Environmental Research, vol. 149, pp. 80-89.
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Photosynthesis in the seagrass Zostera muelleri remains poorly understood. We investigated the effect of reduced irradiance on the incorporation of 13C, gene expression of photosynthetic, photorespiratory and intermediates recycling genes as well as the enzymatic content and activity of Rubisco and PEPC within Z. muelleri. Following 48 h of reduced irradiance, we found that i) there was a ∼7 fold reduction in 13C incorporation in above ground tissue, ii) a significant down regulation of photosynthetic, photorespiratory and intermediates recycling genes and iii) no significant difference in enzyme activity and content. We propose that Z. muelleri is able to alter its physiology in order to reduce the amount of C lost through photorespiration to compensate for the reduced carbon assimilation as a result of reduced irradiance. In addition, the first estimated rate constant (Kcat) and maximum rates of carboxylation (Vcmax) of Rubisco is reported for the first time for Z. muelleri.
King, WL, Jenkins, C, Go, J, Siboni, N, Seymour, JR & Labbate, M 2019, 'Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event', Microbial Ecology, vol. 77, no. 2, pp. 502-512.
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© 2018, Springer Science+Business Media, LLC, part of Springer Nature. The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013–2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1–V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.
King, WL, Jenkins, C, Seymour, JR & Labbate, M 2019, 'Oyster disease in a changing environment: Decrypting the link between pathogen, microbiome and environment', Marine Environmental Research, vol. 143, pp. 124-140.
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© 2018 Elsevier Ltd Shifting environmental conditions are known to be important triggers of oyster diseases. The mechanism(s) behind these synergistic effects (interplay between host, environment and pathogen/s) are often not clear, although there is evidence that shifts in environmental conditions can affect oyster immunity, and pathogen growth and virulence. However, the impact of shifting environmental parameters on the oyster microbiome and how this affects oyster health and susceptibility to infectious pathogens remains understudied. In this review, we summarise the major diseases afflicting oysters with a focus on the role of environmental factors that can catalyse or amplify disease outbreaks. We also consider the potential role of the oyster microbiome in buffering or augmenting oyster disease outbreaks and suggest that a deeper understanding of the oyster microbiome, its links to the environment and its effect on oyster health and disease susceptibility, is required to develop new frameworks for the prevention and management of oyster diseases.
King, WL, Siboni, N, Kahlke, T, Green, TJ, Labbate, M & Seymour, JR 2019, 'A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event', Frontiers in Microbiology, vol. 10, pp. 2907-2907.
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© Copyright © 2019 King, Siboni, Kahlke, Green, Labbate and Seymour. The Vibrio genus is notable for including several pathogens of marine animals and humans, yet characterization of Vibrio diversity using routine 16S rRNA sequencing methods is often constrained by poor resolution beyond the genus level. Here, a new high throughput sequencing approach targeting the heat shock protein (hsp60) as a phylogenetic marker was developed to more precisely discriminate members of the Vibrio genus in environmental samples. The utility of this new assay was tested using mock communities constructed from known dilutions of Vibrio isolates. Relative to standard and Vibrio-specific 16S rRNA sequencing assays, the hsp60 assay delivered high levels of fidelity with the mock community composition at the species level, including discrimination of species within the Vibrio harveyi clade. This assay was subsequently applied to characterize Vibrio community composition in seawater and delivered substantially improved taxonomic resolution of Vibrio species compared to 16S rRNA analysis. Finally, this assay was applied to examine patterns in the Vibrio community within oysters during a Pacific oyster mortality event. In these oysters, the hsp60 assay identified species-level Vibrio community shifts prior to disease onset, pinpointing V. harveyi as a putative pathogen. Given that shifts in the Vibrio community can precede, cause, and follow disease onset in numerous marine organisms, there is a need for an accurate high throughput assay for defining Vibrio community composition in natural samples. This Vibrio-centric hsp60 sequencing assay offers the potential for precise high throughput characterization of Vibrio diversity, providing an enhanced platform for dissecting Vibrio dynamics in the environment.
King, WL, Siboni, N, Williams, NLR, Kahlke, T, Nguyen, KV, Jenkins, C, Dove, M, O’Connor, W, Seymour, JR & Labbate, M 2019, 'Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease', Frontiers in Microbiology, vol. 10, no. MAR.
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Copyright © 2019 King, Siboni, Williams, Kahlke, Nguyen, Jenkins, Dove, O’Connor, Seymour and Labbate. Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or de...
Kloten, V, Neumann, MHD, Di Pasquale, F, Sprenger-Haussels, M, Shaffer, JM, Schlumpberger, M, Herdean, A, Betsou, F, Ammerlaan, W, af Hällström, T, Serkkola, E, Forsman, T, Lianidou, E, Sjöback, R, Kubista, M, Bender, S, Lampignano, R, Krahn, T & Schlange, T 2019, 'Multicenter Evaluation of Circulating Plasma MicroRNA Extraction Technologies for the Development of Clinically Feasible Reverse Transcription Quantitative PCR and Next-Generation Sequencing Analytical Work Flows', Clinical Chemistry, vol. 65, no. 9, pp. 1132-1140.
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Kretzschmar, AL, Larsson, ME, Hoppenrath, M, Doblin, MA & Murray, SA 2019, 'Characterisation of Two Toxic Gambierdiscus spp. (Gonyaulacales, Dinophyceae) from the Great Barrier Reef (Australia): G. lewisii sp. nov. and G. holmesii sp. nov.', Protist, vol. 170, no. 6, pp. 125699-125699. © 2019 Elsevier GmbH Ciguatera fish poisoning (CFP) is a human illness caused via consumption of seafood contaminated with neurotoxins produced by some species from the epiphytic dinoflagellate genus Gambierdiscus. In this study, we describe two new species of Gambierdiscus isolated from Heron Island in the Southern Great Barrier Reef, Queensland, Australia. These new species were analysed using light microscopy, scanning electron microscopy, and phylogenetic analyses of nuclear encoded ribosomal ITS, SSU as well as D1-D3 and D8-D10 of the LSU gene regions. Gambierdiscus lewisii sp. nov. (Po, 3′, 0a, 7″, 6c,? s, 5‴, 0p, 2′‴) is distinguished by its strong reticulate-foveate ornamentation and is genetically distinct from its sister species, G. pacificus. Gambierdiscus holmesii sp. nov. (Po, 3′, 0a, 7″, 6c, 6s?, 5‴, 0p, 2′‴) is morphologically distinct from the genetically similar species G. silvae because of a strongly ventrally displaced apical pore complex and a characteristic fold at the anterior edge of the sulcus. Both G. lewisii and G. holmesii produce putative Maitotoxin-(44-Methylgambierone) and compounds which show ciguatoxin and maitotoxin-like activities. Identification of two new Gambierdiscus species will enable us to more accurately assess the risk of CFP in Australia and internationally. Larsson, ME, Harwood, TD, Lewis, RJ, S. W. A., H & Doblin, MA 2019, 'Toxicological characterization of Fukuyoa paulensis (Dinophyceae) from temperate Australia', Phycological Research, vol. 67, no. 1, pp. 65-71. Larsson, ME, Smith, KF & Doblin, MA 2019, 'First description of the environmental niche of the epibenthic dinoflagellate species Coolia palmyrensis, C. malayensis, and C. tropicalis (Dinophyceae) from Eastern Australia', Journal of Phycology, vol. 55, no. 3, pp. 565-577. Lawson, CA, Possell, M, Seymour, JR, Raina, J-B & Suggett, DJ 2019, 'Coral endosymbionts (Symbiodiniaceae) emit species-specific volatilomes that shift when exposed to thermal stress', Scientific Reports, vol. 9, no. 1. Leggat, WP, Camp, EF, Suggett, DJ, Heron, SF, Fordyce, AJ, Gardner, S, Deakin, L, Turner, M, Beeching, LJ, Kuzhiumparambil, U, Eakin, CM & Ainsworth, TD 2019, 'Rapid Coral Decay Is Associated with Marine Heatwave Mortality Events on Reefs', Current Biology, vol. 29, no. 16, pp. 2723-2730.e4. © 2019 Elsevier Ltd Due to climate change, coral reefs are now being subjected to extreme marine heatwave (MHW) conditions. Leggat et al. show that large-scale mortality due to MHWs and microbial colonization leads to a previously undescribed rapid dissolution of the coral skeleton. Liang, J, Mondal, AK, Wang, D & Iacopi, F 2019, 'Graphene‐Based Planar Microsupercapacitors: Recent Advances and Future Challenges', Advanced Materials Technologies, vol. 4, no. 1, pp. 1800200-1800200. Lohr, KE, Camp, EF, Kuzhiumparambil, U, Lutz, A, Leggat, W, Patterson, JT & Suggett, DJ 2019, 'Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling', Journal of Experimental Biology, vol. 222, no. 8. Macreadie, PI, Atwood, TB, Seymour, JR, Fontes, MLS, Sanderman, J, Nielsen, DA & Connolly, RM 2019, 'Vulnerability of seagrass blue carbon to microbial attack following exposure to warming and oxygen', Science of The Total Environment, vol. 686, pp. 264-275. © 2019 Seagrass meadows store globally-significant quantities of organic ‘blue’ carbon. These blue carbon stocks are potentially vulnerable to anthropogenic stressors (e.g. coastal development, climate change). Here, we tested the impact of oxygen exposure and warming (major consequences of human disturbance) on rates of microbial carbon break-down in seagrass sediments. Active microbes occurred throughout seagrass sediment profiles, but deep, ancient sediments (~5000 yrs. old) contained only 3% of the abundance of active microbes as young, surface sediments (<2 yrs. old). Metagenomic analysis revealed that microbial community structure and function changed with depth, with a shift from proteobacteria and high levels of genes involved in sulfur cycling in the near surface samples, to a higher proportion of firmicutes and euraracheota and genes involved in methanogenesis at depth. Ancient carbon consisted almost entirely (97%) of carbon considered ‘thermally recalcitrant’, and therefore presumably inaccessible to microbial attack. Experimental warming had little impact on carbon; however, exposure of ancient sediments to oxygen increased microbial abundance, carbon uptake and sediment carbon turnover (34–38 fold). Overall, this study provides detailed characterization of seagrass blue carbon (chemical stability, age, associated microbes) and suggests that environmental disturbances that expose coastal sediments to oxygen (e.g. dredging) have the capacity to diminish seagrass sediment carbon stocks by facilitating microbial remineralisation. Mantri, VA, Ganesan, M, Gupta, V, Krishnan, P & Siddhanta, AK 2019, 'An overview on agarophyte trade in India and need for policy interventions', Journal of Applied Phycology, vol. 31, no. 5, pp. 3011-3023. McInnes, AS, Laczka, OF, Baker, KG, Larsson, ME, Robinson, CM, Clark, JS, Laiolo, L, Alvarez, M, Laverock, B, Kremer, CT, van Sebille, E & Doblin, MA 2019, 'Live cell analysis at sea reveals divergent thermal performance between photosynthetic ocean microbial eukaryote populations', The ISME Journal, vol. 13, no. 5, pp. 1374-1378. Meunier, V, Bonnet, S, Pernice, M, Benavides, M, Lorrain, A, Grosso, O, Lambert, C & Houlbrèque, F 2019, 'Bleaching forces coral’s heterotrophy on diazotrophs and Synechococcus', The ISME Journal, vol. 13, no. 11, pp. 2882-2886. Moore, LR, Huang, T, Ostrowski, M, Mazard, S, Kumar, SS, Gamage, HKAH, Brown, MV, Messer, LF, Seymour, JR & Paulsen, IT 2019, 'Unicellular Cyanobacteria Are Important Components of Phytoplankton Communities in Australia’s Northern Oceanic Ecoregions', Frontiers in Microbiology, vol. 9, no. JAN. © 2019 Moore, Huang, Ostrowski, Mazard, Kumar, Gamage, Brown, Messer, Seymour and Paulsen. The tropical marine environments of northern Australia encompasses a diverse range of geomorphological and oceanographic conditions and high levels of productivity and nitrogen fixation. However, efforts to characterize phytoplankton assemblages in these waters have been restricted to studies using microscopic and pigment analyses, leading to the current consensus that this region is dominated by large diatoms, dinoflagellates, and the marine cyanobacterium Trichodesmium. During an oceanographic transect from the Arafura Sea through the Torres Strait to the Coral Sea, we characterized prokaryotic and eukaryotic phytoplankton communities in surface waters using a combination of flow cytometry and Illumina based 16S and 18S ribosomal RNA amplicon sequencing. Similar to observations in other marine regions around Australian, phytoplankton assemblages throughout this entire region were rich in unicellular picocyanobacterial primary producers while picoeukaryotic phytoplankton formed a consistent, though smaller proportion of the photosynthetic biomass. Major taxonomic groups displayed distinct biogeographic patterns linked to oceanographic and nutrient conditions. Unicellular picocyanobacteria dominated in both flow cytometric abundance and carbon biomass, with members of the Synechococcus genus dominating in the shallower Arafura Sea and Torres Strait where chlorophyll a was relatively higher (averaging 0.4 ± 0.2 mg m-3), and Prochlorococcus dominating in the oligotrophic Coral Sea where chlorophyll a averaged 0.13 ± 0.07 mg m-3. Consistent with previous microscopic and pigment-based observations, we found from sequence analysis that a variety of diatoms (Bacillariophyceae) exhibited high relative abundance in the Arafura Sea and Torres Strait, while dinoflagellates (Dinophyceae) and prymnesiophytes (Prymnesiophyceae) were more abundant in the Coral Sea. Ordination a... Mote, S, Schönberg, CHL, Samaai, T, Gupta, V & Ingole, B 2019, 'A new clionaid sponge infests live corals on the west coast of India (Porifera, Demospongiae, Clionaida)', Systematics and Biodiversity, vol. 17, no. 2, pp. 190-206. Müller, S, Zavřel, T & Červený, J 2019, 'Towards a quantitative assessment of inorganic carbon cycling in photosynthetic microorganisms', Engineering in Life Sciences, vol. 19, no. 12, pp. 955-967. Nguyen, LN, Labeeuw, L, Commault, AS, Emmerton, B, Ralph, PJ, Johir, MAH, Guo, W, Ngo, HH & Nghiem, LD 2019, 'Validation of a cationic polyacrylamide flocculant for the harvesting fresh and seawater microalgal biomass', Environmental Technology & Innovation, vol. 16, pp. 100466-100466. © 2019 Elsevier B.V. A simple, efficient, and fast settling flocculation technique to harvest microalgal biomass was demonstrated using a proprietary cationic polyacrylamide flocculant for a freshwater (Chlorella vulgaris) and a marine (Phaeodactylum tricornutum) microalgal culture at their mid-stationary growth phase. The optimal flocculant doses were 18.9 and 13.7 mg/g of dry algal biomass for C. vulgaris and P. tricornutum, respectively (equivalent to 7 g per m3 of algal culture for both species). The obtained optimal dose was well corroborated with changes in cell surface charge, and culture solution optical density and turbidity. At the optimal dose, charge neutralization of 64 and 86% was observed for C. vulgaris and P. tricornutum algal cells, respectively. Algae recovery was independent of the culture solution pH in the range of pH 6 to 9. Algal biomass recovery was achieved of 100 and 90% for C vulgaris and P. tricornutum respectively, and over 98% medium recovery was achievable by simple decanting. Pereira, RRC, Scanes, E, Parker, L, Byrne, M, Cole, VJ & Ross, PM 2019, 'Restoring the flat oyster Ostrea angasi in the face of a changing climate', Marine Ecology Progress Series, vol. 625, pp. 27-39. Across the globe, restoration efforts are stemming the loss of native oyster reefs and the ecosystem services they provide, but these efforts will need to consider climate change in order to be sustainable. South-eastern Australia is the focus of restoring the once abundant oyster Ostrea angasi. This region is also a climate change ‘hot spot’ where the ocean is warming rapidly, with the potential to be exacerbated by marine heatwaves and coastal acidification. In this study, the impact of near-future (~2050) elevated temperature and pCO2 on O. angasi was determined and considered in context with concerns for the long-term sustainability of oyster reef restoration efforts. Oysters were exposed to ambient and elevated pCO2 concentrations (mean ± SE: 408 ± 19.8 and 1070 ± 53.4 μatm) and ambient and elevated temperatures (22.78 ± 0.17 and 25.73 ± 0.21°C) for 10 wk in outdoor flow-through mesocosms. Shell growth, condition index, standard metabolic rate (SMR), extracellular pH and survival were measured. Elevated temperature caused high mortality (36%) and decreased the condition of oysters (33%). Elevated pCO2 increased SMR almost 4-fold and lowered the extracellular pH of O. angasi by a mean 0.29 pH units. In combination, elevated pCO2 and temperature ameliorated effects on SMR and survivorship of oysters. O. angasi appears to be living near the limits of its thermal tolerance. Restoration projects will need to account for the temperature sensitivity of this species and its changing habitat to ‘climate proof’ long-term restoration efforts. Pernice, M & Hughes, DJ 2019, 'Forecasting global coral bleaching', Nature Climate Change, vol. 9, no. 11, pp. 803-804. Phong Vo, HN, Le, GK, Hong Nguyen, TM, Bui, X-T, Nguyen, KH, Rene, ER, Vo, TDH, Thanh Cao, N-D & Mohan, R 2019, 'Acetaminophen micropollutant: Historical and current occurrences, toxicity, removal strategies and transformation pathways in different environments', Chemosphere, vol. 236, pp. 124391-124391. Pollier, J, Vancaester, E, Kuzhiumparambil, U, Vickers, CE, Vandepoele, K, Goossens, A & Fabris, M 2019, 'A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis', Nature Microbiology, vol. 4, no. 2, pp. 226-233. Steroids are essential triterpenoid molecules that are present in all eukaryotes and modulate the fluidity and flexibility of cell membranes. Steroids also serve as signalling molecules that are crucial for growth, development and differentiation of multicellular organisms1-3. The steroid biosynthetic pathway is highly conserved and is key in eukaryote evolution4-7. The flavoprotein squalene epoxidase (SQE) catalyses the first oxygenation reaction in this pathway and is rate limiting. However, despite its conservation in animals, plants and fungi, several phylogenetically widely distributed eukaryote genomes lack an SQE-encoding gene7,8. Here, we discovered and characterized an alternative SQE (AltSQE) belonging to the fatty acid hydroxylase superfamily. AltSQE was identified through screening of a gene library of the diatom Phaeodactylum tricornutum in a SQE-deficient yeast. In accordance with its divergent protein structure and need for cofactors, we found that AltSQE is insensitive to the conventional SQE inhibitor terbinafine. AltSQE is present in many eukaryotic lineages but is mutually exclusive with SQE and shows a patchy distribution within monophyletic clades. Our discovery provides an alternative element for the conserved steroid biosynthesis pathway, raises questions about eukaryote metabolic evolution and opens routes to develop selective SQE inhibitors to control hazardous organisms. Raina, J-B, Fernandez, V, Lambert, B, Stocker, R & Seymour, JR 2019, 'The role of microbial motility and chemotaxis in symbiosis', Nature Reviews Microbiology, vol. 17, no. 5, pp. 284-294. © 2019, Springer Nature Limited. Many symbiotic relationships rely on the acquisition of microbial partners from the environment. However, the mechanisms by which microbial symbionts find and colonize their hosts are often unknown. We propose that the acquisition of environmental symbionts often necessitates active migration and colonization by the symbionts through motility and chemotaxis. The pivotal role of these behaviours in the onset and maintenance of symbiotic interactions is well established in a small number of model systems but remains largely overlooked for the many symbioses that involve the recruitment of microbial partners from the environment. In this Review, we highlight when, where and how chemotaxis and motility can enable symbiont recruitment and propose that these symbiont behaviours are important across a wide range of hosts and environments. Ramarajan, M, Fabris, M, Abbriano, RM, Pernice, M & Ralph, PJ 2019, 'Novel endogenous promoters for genetic engineering of the marine microalga Nannochloropsis gaditana CCMP526', Algal Research, vol. 44, pp. 101708-101708. © 2019 Elsevier B.V. Nannochloropsis is a marine microalga from the Eustigmatophyceae stramenopile lineage that has been studied extensively due to a broad range of industrial applications, mostly related to their oil and pigment production. However, tools to genetically engineer members of this group, and therefore further understand and maximise their industrial potential are still limited. In order to expand the potential industrial uses of this organism, several molecular tools, including gene promoters of different strength, are needed. A comprehensive and diverse set of well-characterized promoters is key to a number of genetic engineering and synthetic biology applications, such as the assembly of complex biological functions or entire metabolic pathways. In this study, we measured the promoter activity of three endogenous constitutive promoters from N. gaditana genes EPPSII (Nga02101); HSP90 (Nga00934); ATPase (Nga06354.1) in driving the expression of a Sh ble- mVenus fluorescent reporter fusion protein. Through a combined approach that includes flow cytometry, RT-qPCR and immunoblotting, we profiled the activity of these promoters at both the transcript and protein level. Two promoters HSP90 (Nga00934) and EPPSII (Nga02101) outperformed the widely used β-tubulin promoter, exhibiting 4.5 and 3.1-fold higher mVenus fluorescence, respectively. A third promoter ATPase (Nga06354.1) was also able to drive the expression of transgenes, albeit at lower levels. We show that the new promoters identified in this study are valuable tools, which can be used for genetic engineering and functional genetics studies in N. gaditana. Rinke, C, Rubino, F, Messer, LF, Youssef, N, Parks, DH, Chuvochina, M, Brown, M, Jeffries, T, Tyson, GW, Seymour, JR & Hugenholtz, P 2019, 'A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)', The ISME Journal, vol. 13, no. 3, pp. 663-675. Scanes, E, Wood, H & Ross, P 2019, 'Microplastics detected in haemolymph of the Sydney rock oyster Saccostrea glomerata', Marine Pollution Bulletin, vol. 149, pp. 110537-110537. Plastic waste is ubiquitous in marine environments. Despite the sheer volume of plastic waste, it remains relatively unknown how marine invertebrates will interact with microplastics (plastic <1 mm). Microplastics (<2 μm) were ingested by the economically and ecologically significant Sydney rock oyster Saccostrea glomerata and translocated to the haemolymph, perhaps via phagocytosis. The presence of microplastics in the haemolymph indicates that filter feeding S. glomerata can ingest and accumulate microplastics which are prevalent in the environment. This research shows microplastics can enter marine molluscs and highlights the need to monitor microplastics in the marine environment and aquaculture to safeguard the seafood industry. Segečová, A, Pérez-Bueno, ML, Barón, M, Červený, J & Roitsch, TG 2019, 'Noninvasive determination of toxic stress biomarkers by high-throughput screening of photoautotrophic cell suspension cultures with multicolor fluorescence imaging', Plant Methods, vol. 15, no. 1. Background:With increasing pollution, herbicide application and interest in plant phenotyping, sensors capturing early responses to toxic stress are demanded for screening susceptible or resistant plant varieties. Standard toxicity tests on plants are laborious, demanding in terms of space and material, and the measurement of growth-inhibition based endpoints takes relatively long time. The aim of this work was to explore the potential of photoautotrophic cell suspension cultures for high-throughput early toxicity screening based on imaging techniques. The investigation of the universal potential of fluorescence imaging methods involved testing of three toxicants with different modes of action (DCMU, glyphosate and chromium). Results:The increased pace of testing was achieved by using non-destructive imaging methods-multicolor fluorescence (MCF) and chlorophyll fluorescence (ChlF). These methods detected the negative effects of the toxicants earlier than it was reflected in plant growth inhibition (decrease in leaf area and final dry weight). Moreover, more subtle and transient effects not resulting in growth inhibition could be detected by fluorescence. The pace and sensitivity of stress detection was further enhanced by using photoautotrophic cell suspension cultures. These reacted sooner, more pronouncedly and to lower concentrations of the tested toxicants than the plants. Toxicant-specific stress signatures were observed as a combination of MCF and ChlF parameters and timing of the response. Principal component analysis was found to be useful for reduction of the collected multidimensional data sets to a few informative parameters allowing comparison of the toxicant signatures. Conclusions:Photoautotrophic cell suspension cultures have proved to be useful for rapid high-throughput screening of toxic stress and display a potential for employment as an alternative to tests on whole plants. The MCF and ChlF methods are capable of distinguishing early stress sig... Seguro, I, Marca, AD, Painting, SJ, Shutler, JD, Suggett, DJ & Kaiser, J 2019, 'High-resolution net and gross biological production during a Celtic Sea spring bloom', Progress in Oceanography, vol. 177, pp. 101885-101885. © 2017 The Authors Shelf seas represent only 10% of the ocean area, but support up to 30% of all oceanic primary production. There are few measurements of shelf-sea biological production at high spatial and temporal resolution in such heterogeneous and physically dynamic systems. Here, we use dissolved oxygen-to-argon (O2/Ar) ratios and oxygen triple isotopes (16O, 17O, 18O) to estimate net and gross biological production in the Celtic Sea during spring 2015. O2/Ar ratios were measured continuously using a shipboard membrane inlet mass spectrometer (MIMS). Additional discrete water samples from CTD hydrocasts were used to measure O2/Ar depth profiles and the δ(17O) and δ(18O) values of dissolved O2. These high-resolution data were combined with wind-speed based gas exchange parameterisations to calculate biologically driven air-sea oxygen fluxes. After correction for disequilibrium terms and diapycnal diffusion, these fluxes yielded estimates of net community (N(O2/Ar)) and gross O2 production (G(17O)). N(O2/Ar) was spatially heterogeneous and showed predominantly autotrophic conditions, with an average of (33 ± 41) mmol m−2 d−1. G(17O) showed high variability between 0 and 424 mmol m−2 d−1. The ratio of N(O2/Ar) to G(17O), ƒ(O2), was (0.18 ± 0.03) corresponding to 0.34 ± 0.06 in carbon equivalents. We also observed rapid temporal changes in N(O2/Ar), e.g. an increase of 80 mmol m−2 d−1 in <6 h during the spring bloom, highlighting the importance of high-resolution biological production measurements. Such measurements will help reconcile the differences between satellite and in situ productivity observations, and improve our understanding of the biological carbon pump. Serrano, O, Lovelock, CE, B. Atwood, T, Macreadie, PI, Canto, R, Phinn, S, Arias-Ortiz, A, Bai, L, Baldock, J, Bedulli, C, Carnell, P, Connolly, RM, Donaldson, P, Esteban, A, Ewers Lewis, CJ, Eyre, BD, Hayes, MA, Horwitz, P, Hutley, LB, Kavazos, CRJ, Kelleway, JJ, Kendrick, GA, Kilminster, K, Lafratta, A, Lee, S, Lavery, PS, Maher, DT, Marbà, N, Masque, P, Mateo, MA, Mount, R, Ralph, PJ, Roelfsema, C, Rozaimi, M, Ruhon, R, Salinas, C, Samper-Villarreal, J, Sanderman, J, J. Sanders, C, Santos, I, Sharples, C, Steven, ADL, Cannard, T, Trevathan-Tackett, SM & Duarte, CM 2019, 'Australian vegetated coastal ecosystems as global hotspots for climate change mitigation', Nature Communications, vol. 10, no. 1, p. 4313. Shah Mohammadi, N, Buapet, P, Pernice, M, Signal, B, Kahlke, T, Hardke, L & Ralph, PJ 2019, 'Transcriptome profiling analysis of the seagrass, Zostera muelleri under copper stress', Marine Pollution Bulletin, vol. 149, pp. 110556-110556. Copper (Cu) in an essential trace metal but it can also contaminate coastal waters at high concentrations mainly from agricultural run-off and mining activities which are detrimental to marine organisms including seagrasses. The molecular mechanisms driving Cu toxicity in seagrasses are not clearly understood yet. Here, we investigated the molecular responses of the Australian seagrass, Z. muelleri at the whole transcriptomic level after 7 days of exposure to 250 μg Cu L-1 and 500 μg Cu L-1. The leaf-specific whole transcriptome results showed a concentration-dependent disturbance in chloroplast function, regulatory stress responses and defense mechanisms. This study provided new insights into the responses of seagrasses to trace metal stress and reports possible candidate genes which can be considered as biomarkers to improve conservation and management of seagrass meadows. Shahid, A, Ishfaq, M, Ahmad, MS, Malik, S, Farooq, M, Hui, Z, Batawi, AH, Shafi, ME, Aloqbi, AA, Gull, M & Mehmood, MA 2019, 'Bioenergy potential of the residual microalgal biomass produced in city wastewater assessed through pyrolysis, kinetics and thermodynamics study to design algal biorefinery', Bioresource Technology, vol. 289, pp. 121701-121701. The suitability of integrating biological and thermal transformation of microalgal biomass to design a biorefinery was studied. The mixed cultivation of Chlorella sp. and Bracteacoccus sp. in city wastewater produced 12 g L-1 of biomass (0.77 g L-1 day-1) and removed nitrates and phosphates by 68% and 75%, respectively. Microalgae outcompeted the contaminating microbes by raising the pH of wastewater to 9.93. The lipid-free residual biomass was pyrolyzed at four heating rates (10, 20, 30, 40 °C min-1) which showed a three-stage pyrolysis. The activation energies (182-256 kJ mol-1) and their corresponding lower enthalpies at the conversional fractions from 0.2 to 0.6 indicated that product formation was being favored. The values of pre-exponential factors (1015-17 s-1), Gibbs free energy (159-190 kJ mol-1) and entropy (43-81 J mol-1) showed efficient pyrolysis. The data may lead to establish a robust microalgal biorefinery to produce biomass and energy along with primary treatment of city wastewater. Smith, MH, Schrag, CH, Chandarana, SP, Cobb, JG, Matthews, TW, Mckenzie, CD & Matthews, JL 2019, 'Novel Plate Design to Improve Mandibular and Maxillary Reconstruction with the Osteocutaneous Fibula Flap', Plastic and Reconstructive Surgery - Global Open, vol. 7, no. 1, pp. e2094-e2094. Sproles, AE, Oakley, CA, Matthews, JL, Peng, L, Owen, JG, Grossman, AR, Weis, VM & Davy, SK 2019, 'Proteomics quantifies protein expression changes in a model cnidarian colonised by a thermally tolerant but suboptimal symbiont', The ISME Journal, vol. 13, no. 9, pp. 2334-2345. Suggett, DJ, Camp, EF, Edmondson, J, Boström‐Einarsson, L, Ramler, V, Lohr, K & Patterson, JT 2019, 'Optimizing return‐on‐effort for coral nursery and outplanting practices to aid restoration of the Great Barrier Reef', Restoration Ecology, vol. 27, no. 3, pp. 683-693. Sukačová, K, Búzová, D, Trávníček, P, Červený, J, Vítězová, M & Vítěz, T 2019, 'Optimization of microalgal growth and cultivation parameters for increasing bioenergy potential: Case study using the oleaginous microalga Chlorella pyrenoidosa Chick (IPPAS C2)', Algal Research, vol. 40, pp. 101519-101519. © 2019 The aim of the presented research was application of optimized cultivation conditions for lipid production using the oleaginous microalga Chlorella pyrenoidosa Chick (IPPAS C2), followed by an assessment of the bioenergy potential of lipid-rich biomass and biomethane production. The optimization of cultivation parameters led to an increase in lipid production. The average and maximum lipid production for C. pyrenoidosa was 101 ± 22 mg.L −1 .D −1 and 126 mg.L −1 .D −1 , respectively. The average calorific value of the lipid rich-biomass was 27.56 ± 0.93 MJ.kg −1 . However, the recorded biomethane yield of 0.16 ± 0.006 m 3 .kg −1 VS, caused probably by low digestibility of C. pyrenoidosa and by short hydraulic retention time during anaerobic digestion, was interpreted as low. However, the high lipid content along with high calorific value indicated an increased bioenergy potential of microalgal biomass cultivated under the optimized cultivation parameters. Sutherland, DL & Ralph, PJ 2019, 'Microalgal bioremediation of emerging contaminants - Opportunities and challenges', Water Research, vol. 164, pp. 114921-114921. © 2019 Emerging contaminants (ECs) are primarily synthetic organic chemicals that have a focus of increasing attention due to either increased awareness of their potential risks to humans and aquatic biota, or only recently been detected in the aquatic environment or drinking water supplies, through improved analytical techniques. Many ECs have no regulatory standards due to the lack of information on the effects of chronic exposure. Pharmaceuticals, personal care products, pesticides and flame retardants are some of the most frequently detected ECs in aquatic environments, with over 200 individual compounds identified, to date. Current wastewater treatment is ineffective at removing ECs and there is a vital need for the development of efficient, cost-effective EC treatment systems that can be applied to a range of scales and wastewater types. Microalgae have demonstrated potential for detoxifying organic and inorganic pollutants, with a number of large-scale wastewater treatment microalgal technologies already developed. There are three main pathways that microalgae can bioremediate ECs; bioadsorption, bio-uptake and biodegradation. Microalgal bioadsorption occurs when ECs are either adsorbed to cell wall components, or onto organic substances excreted by the cells, while bio-uptake involves the active transport of the contaminant into the cell, where it binds to intracellular proteins and other compounds. Microalgal biodegradation of ECs involves the transformation of complex compounds into simpler breakdown molecules through catalytic metabolic degradation. Biodegradation provides one of the most promising technologies for the remediation of contaminants of concern as it can transform the contaminant to less toxic compounds rather than act as a biofilter. Further research is needed to exploit microalgal species for EC bioremediation properties, such as increased bioadsorption, enhanced biodegrading enzymes and optimised growth conditions. When couple... Thomson, ACG, Trevathan‐Tackett, SM, Maher, DT, Ralph, PJ & Macreadie, PI 2019, 'Bioturbator‐stimulated loss of seagrass sediment carbon stocks', Limnology and Oceanography, vol. 64, no. 1, pp. 342-356. Trevathan-Tackett, SM, Sherman, CDH, Huggett, MJ, Campbell, AH, Laverock, B, Hurtado-McCormick, V, Seymour, JR, Firl, A, Messer, LF, Ainsworth, TD, Negandhi, KL, Daffonchio, D, Egan, S, Engelen, AH, Fusi, M, Thomas, T, Vann, L, Hernandez-Agreda, A, Gan, HM, Marzinelli, EM, Steinberg, PD, Hardtke, L & Macreadie, PI 2019, 'A horizon scan of priorities for coastal marine microbiome research', Nature Ecology & Evolution, vol. 3, no. 11, pp. 1509-1520. © 2019, The Author(s), under exclusive licence to Springer Nature Limited. Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth’s climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the ‘microbiome’) and the environment or their hosts — termed the ‘holobiont’. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research. Trivedi, T, Jain, D, Mulla, NSS, Mamatha, SS, Damare, SR, Sreepada, RA, Kumar, S & Gupta, V 2019, 'Improvement in biomass, lipid production and biodiesel properties of a euryhaline Chlorella vulgaris NIOCCV on mixotrophic cultivation in wastewater from a fish processing plant', Renewable Energy, vol. 139, pp. 326-335. Verma, A, Kohli, GS, Harwood, DT, Ralph, PJ & Murray, SA 2019, 'Transcriptomic investigation into polyketide toxin synthesis in Ostreopsis (Dinophyceae) species', Environmental Microbiology, vol. 21, no. 11, pp. 4196-4211. Vo, HNP, Koottatep, T, Chapagain, SK, Panuvatvanich, A, Polprasert, C, Nguyen, TMH, Chaiwong, C & Nguyen, NL 2019, 'Removal and monitoring acetaminophen-contaminated hospital wastewater by vertical flow constructed wetland and peroxidase enzymes', Journal of Environmental Management, vol. 250, pp. 109526-109526. © 2019 Elsevier Ltd Hospital wastewater contains acetaminophen (ACT) and nutrient, which need adequate removal and monitoring to prevent impact to environment and community. This study developed a pilot scale vertical flow constructed wetland (CW) to (1) remove high-dose ACT and pollutants in hospital wastewater and (2) identify the correlation of peroxidase enzyme extruded by Scirpus validus and pollutants removal efficiency. By that correlation, a low-cost method to monitor pollutants removal was drawn. Plants, such as Scirpus validus, generated peroxidase enzymes to alleviate pollutants’ stress. Results showed that the CW removed 3.5 to 6 logs of initial concentration 10 mg ACT/L to a recommended level for drinking water. The CW eliminated COD, TKN and TP efficiently, meeting the wastewater discharged standards of Thailand and Vietnam. By various multivariable regression models, concentrations of ACT in CW effluent and enzymes in S. validus exhibited a significant correlation (p < 0.01, R2 = 68.3%). These findings suggested that (i) vertical flow CW could remove high-dose ACT and nutrient and (ii) peroxidase enzymes generated in S. validus, such as soluble and covalent ones, could track ACT removal efficiency. This would help to reduce facilities and analytical cost of micro-pollutants. Vo, HNP, Ngo, HH, Guo, W, Liu, Y, Chang, SW, Nguyen, DD, Nguyen, PD, Bui, XT & Ren, J 2019, 'Identification of the pollutants’ removal and mechanism by microalgae in saline wastewater', Bioresource Technology, vol. 275, pp. 44-52. © 2018 Elsevier Ltd This study investigated the growth dynamics of a freshwater and marine microalgae with supported biochemical performance in saline wastewater, the pollutants assimilation by a developed method, and the mechanism of salinity's effect to pollutants assimilation. Maximal biomass yield was 400–500 mg/L at 0.1–1% salinity while the TOC, NO3−-N, PO43−-P were eliminated 39.5–92.1%, 23–97.4% and 7–30.6%, respectively. The biomass yield and pollutants removal efficiencies reduced significantly when salinity rose from 0.1 to 5%. The freshwater Chlorella vulgaris performed its best with a focus on TOC removal at 0.1% salinity. The marine Chlorella sp. was prominent for removing NO3−-N at 0.1–1% salinity. Through the developed method, the freshwater C. vulgaris competed to the marine microalgae referring to pollutants assimilation up to 5% salinity. This study unveiled the mechanism of salinity's effect with evidence of salt layer formation and salt accumulation in microalgae. Vo, HNP, Ngo, HH, Guo, W, Nguyen, TMH, Liu, Y, Liu, Y, Nguyen, DD & Chang, SW 2019, 'A critical review on designs and applications of microalgae-based photobioreactors for pollutants treatment', Science of The Total Environment, vol. 651, no. Pt 1, pp. 1549-1568. © 2018 Elsevier B.V. The development of the photobioreactors (PBs) is recently noticeable as cutting-edge technology while the correlation of PBs' engineered elements such as modellings, configurations, biomass yields, operating conditions and pollutants removal efficiency still remains complex and unclear. A systematic understanding of PBs is therefore essential. This critical review study is to: (1) describe the modelling approaches and differentiate the outcomes; (2) review and update the novel technical issues of PBs' types; (3) study microalgae growth and control determined by PBs types with comparison made; (4) progress and compare the efficiencies of contaminants removal given by PBs' types and (5) identify the future perspectives of PBs. It is found that Monod model's shortcoming in internal substrate utilization is well fixed by modified Droop model. The corroborated data also remarks an array of PBs' types consisting of flat plate, column, tubular, soft-frame and hybrid configuration in which soft-frame and hybrid are the latest versions with higher flexibility, performance and smaller foot-print. Flat plate PBs is observed with biomass yield being 5 to 20 times higher than other PBs types while soft-frame and membrane PBs can also remove pharmaceutical and personal care products (PPCPs) up to 100%. Looking at an opportunity for PBs in sustainable development, the flat plate PBs are applicable in PB-based architectures and infrastructures indicating an encouraging revenue-raising potential. Wangpraseurt, D, Lichtenberg, M, Jacques, SL, Larkum, AWD & Kühl, M 2019, 'Optical Properties of Corals Distort Variable Chlorophyll Fluorescence Measurements', Plant Physiology, vol. 179, no. 4, pp. 1608-1619. © 2019 American Society of Plant Biologists. All rights reserved. Pulse-amplitude–modulated (PAM) fluorimetry is widely used in photobiological studies of corals, as it rapidly provides numerous photosynthetic parameters to assess coral ecophysiology. Coral optics studies have revealed the presence of light gradients in corals, which are strongly affected by light scattering in coral tissue and skeleton. We investigated whether coral optics affects variable chlorophyll (Chl) fluorescence measurements and derived photosynthetic parameters by developing planar hydrogel slabs with immobilized microalgae and with bulk optical properties similar to those of different types of corals. Our results show that PAM-based measurements of photosynthetic parameters differed substantially between hydrogels with different degrees of light scattering but identical microalgal density, yielding deviations in apparent maximal electron transport rates by a factor of 2. Furthermore, system settings such as the measuring light intensity affected F0, Fm, and Fv/Fm in hydrogels with identical light absorption but different degrees of light scattering. Likewise, differences in microalgal density affected variable Chl fluorescence parameters, where higher algal densities led to greater Fv/Fm values and relative electron transport rates. These results have important implications for the use of variable Chl fluorimetry in ecophysiological studies of coral stress and photosynthesis, as well as other optically dense systems such as plant tissue and biofilms. Wu, S, Gu, W, Huang, A, Li, Y, Kumar, M, Lim, PE, Huan, L, Gao, S & Wang, G 2019, 'Elevated CO2 improves both lipid accumulation and growth rate in the glucose-6-phosphate dehydrogenase engineered Phaeodactylum tricornutum', Microbial Cell Factories, vol. 18, no. 1. Zapata, J, Meynard, A, Anguita, C, Espinoza, C, Alvear, P, Kumar, M & Contreras‐Porcia, L 2019, 'Non‐Random Distribution and Ecophysiological Differentiation of Pyropia Species (Bangiales, Rhodophyta) Through Environmental Gradients', Journal of Phycology, vol. 55, no. 5, pp. 1140-1153. Zavřel, T, Faizi, M, Loureiro, C, Poschmann, G, Stühler, K, Sinetova, M, Zorina, A, Steuer, R & Červený, J 2019, 'Quantitative insights into the cyanobacterial cell economy', eLife, vol. 8. Zhu, Y, Suggett, DJ, Liu, C, He, J, Lin, L, Le, F, Ishizaka, J, Goes, J & Hao, Q 2019, 'Primary Productivity Dynamics in the Summer Arctic Ocean Confirms Broad Regulation of the Electron Requirement for Carbon Fixation by Light-Phytoplankton Community Interaction', Frontiers in Marine Science, vol. 6. Zizka, A, Silvestro, D, Andermann, T, Azevedo, J, Duarte Ritter, C, Edler, D, Farooq, H, Herdean, A, Ariza, M, Scharn, R, Svantesson, S, Wengström, N, Zizka, V & Antonelli, A 2019, '
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Conferences
Awan, Z, Kahlke, T, Ralph, P & Kennedy, P 1970, 'Chemical Named Entity Recognition with Deep Contextualized Neural Embeddings', Proceedings of the 11th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management, 11th International Conference on Knowledge Discovery and Information Retrieval, SCITEPRESS - Science and Technology Publications, Austria, pp. 135-144.
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Copyright © 2019 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved Chemical named entity recognition (ChemNER) is a preliminary step in chemical information extraction pipelines. ChemNER has been approached using rule-based, dictionary-based, and feature-engineered based machine learning, and more recently also deep learning based methods. Traditional word-embeddings, like word2vec and Glove, are inherently problematic because they ignore the context in which an entity appears. Contextualized embeddings called embedded language models (ELMo) have been recently introduced to represent contextual information of a word in its embedding space. In this work, we quantify the impact of contextualized embeddings for ChemNER by using Bi-LSTM-CRF (bidirectional long short term memory networks - conditional random fields) networks. We benchmarked our approach using four well-known corpora for chemical named entity recognition. Our results show that incorporation of ELMo results in statistically significant improvements in F1 score in all of the tested datasets.
Nguyen, VK, King, WL, Siboni, N, Mahbub, KR, Dove, M, O’connor, W, Seymour, J & Labbate, M 1970, 'The sydney rock oyster microbiome is influenced by local environmental parameters and QX disease resistance', Fish & Shellfish Immunology, Elsevier BV, pp. 438-438.
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Schreiber, I, Muzika, F & Červený, J 1970, 'Reaction Networks, Oscillatory Motifs and Parameter Estimation in Biochemical Systems', HYBRID SYSTEMS BIOLOGY (HSB 2019), 6th International Workshop on Hybrid Systems Biology (HSB), Springer International Publishing, Charles Univ, Fac Math & Phys, Prague, CZECH REPUBLIC, pp. 30-41.
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UTS acknowledges the Gadigal people of the Eora Nation, the Boorooberongal people of the Dharug Nation, the Bidiagal people and the Gamaygal people, upon whose ancestral lands our university stands. We would also like to pay respect to the Elders both past and present, acknowledging them as the traditional custodians of knowledge for these lands.