Publications

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-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.

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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Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known, however, about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most other invertebrates. Here, we examine the cellular capacity for direct processing of DOM, and the fate of the processed matter, inside a dinoflagellate-hosting bioeroding sponge that is prominent on Indo-Pacific coral reefs. Integrating transmission electron microscopy with nanoscale secondary ion mass spectrometry, we track 15 N- and 13 C-enriched DOM over time at the individual cell level of an intact sponge holobiont. We show initial high enrichment in the filter-feeding cells of the sponge, providing visual evidence of their capacity to process DOM through pinocytosis without mediation of resident bacteria. Subsequent enrichment of the endosymbiotic dinoflagellates also suggests sharing of host nitrogenous wastes. Our results shed light on the physiological mechanism behind the ecologically important ability of sponges to cycle DOM via the recently described sponge loop.

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.

Bates, H, Zavafer, A, Szabó, M & Ralph, PJ 2019, 'A guide to Open-JIP, a low-cost open-source chlorophyll fluorometer', Photosynthesis Research, vol. 142, no. 3, pp. 361-368.
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© 2019, Springer Nature B.V. Chlorophyll a fluorescence is the most widely used method to study photosynthesis and plant stress. While several commercial fluorometers are available, there is a need for a low-cost and highly customisable chlorophyll fluorometer. Such a device would aid in performing high-throughput assessment of photosynthesis, as these instruments can be mass-produced. Novel investigations into photosynthesis can also be performed as a result of the user’s ability to modify the devices functionality for their specific needs. Motivated by this, we present an open-source chlorophyll fluorometer based on the Kautsky induction curve (OJIP). The instrument consists of low-cost, easy-to-acquire electrical components and an open-source microcontroller (Arduino Mega) whose performance is equivalent to that of commercial instruments. Two 3D printable Open-JIP configurations are presented, one for higher plants and the other for microalgae cells in suspension. Directions for its construction are presented and the instrument is benchmarked against widely used commercial chlorophyll fluorometers.

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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AbstractIonic media comprising 1‐butyl‐3‐methylimidazolium chloride and the acidic deep eutectic solvent choline chloride/oxalic acid as co‐solvent‐catalyst, very efficiently convert various cellulosic substrates, including native cellulosic biomass, into water‐soluble carbohydrates. The optimum reaction systems yield a narrow range of low molecular weight carbohydrates directly from cellulose, lignocellulose, or algal saccharides, in high yields and selectivities up to 98 %. Cellulose possesses significant potential as a renewable platform from which to generate large volumes of green replacements to many petrochemical products. Within this goal, the production of low molecular weight saccharides from cellulosic substances is the key to success. Native cellulose and lignocellulosic feedstocks are less accessible for such transformations and depolymerisation of polysaccharides remains a primary challenge to be overcome. In this study, we identify the catalytic activity associated with selected deep eutectic solvents that favours the hydrolysis of polysaccharides and develop reaction conditions to improve the outcomes of desirable low molecular weight sugars. We successfully apply the chemistry to raw bulk, non‐pretreated cellulosic substances.

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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AbstractInvited for this month′s cover is the group of Prof. Bradley Williams at the University of Technology Sydney. The image depicts the manifold products that can be selected in transformations of glucose through manipulation of the Brønsted or Lewis acidity of the catalyst. The Full Paper itself is available at 10.1002/cssc.201900292.

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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AbstractThe specific type of acidity associated with the given metal trifloromethanesulfonates (Brønsted or Lewis acidity) dramatically influences the course of reactions, and it is possible to select for disaccharides, fructose, methyl glucosides, or methyl levulinate. Glucose is transformed into a range of value‐added molecules in water and methanol under the action of acidic metal triflates as catalysts, including their analogous Brønsted acid‐assisted or Brønsted base‐modified systems. A systematic study is presented of a range of metal triflates in methanol and water, pinning down the preferred conditions to select for each product.

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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AbstractAcid‐catalysed conversion of biomass, specifically cellulose, holds promise to create value‐added, renewable replacements for many petrochemical products. We investigated an unusual acid‐catalysed transformation of cellulose and cellobiose in the biphasic solvent system zinc chloride hydrate (ionic liquid)/anisole. Here, furyl hydroxymethyl ketone and furfural are obtained as major products, which are valuable but less commonly formed in high yields in transformations of cellulosic substrates. We explored this chemistry in small‐scale model reactions and applied the optimised methods to the conversion of cellulose in bench‐scale processes. The optimum reaction system and preferred reaction conditions are defined to select for highly desirable furanoid products in the highest known yields (up to 46 %) directly from cellulose or cellobiose. The method avoids the use of added catalysts: the ionic solvent zinc chloride hydrate possesses the intrinsic acidity required for the hydrolysis and chemical transformation steps. The process involves inexpensive media for the catalytic conversion of cellulose into high‐value products under mild processing conditions.

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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AbstractThe fate of coccolithophores in the future oceans remains uncertain, in part due to key factors having not been standardized across experiments. A potentially moderating role for differences in day length (photoperiod) remains largely unexplored. We therefore cultured four different geographical isolates of the species Emiliania huxleyi, as well as two additional species, Gephyrocapsa oceanica (tropical) and Coccolithus braarudii (temperate), to test for interactive effects of pCO2 with the light : dark (L : D) cycle. We confirmed a general regulatory effect of photoperiod on the pCO2 response, whereby growth and particulate inorganic carbon and particulate organic carbon (PIC : POC) ratios were reduced with elevated pCO2 under 14 : 10 h L : D, but these reductions were dampened under continuous (24 h) light. The dynamics underpinning this pattern generally differed for the temperate vs. tropical isolates. Reductions in PIC : POC with elevated pCO2 for tropical taxa were largely through reduced calcification and enhanced photosynthesis under 14 : 10 h L : D, with differences dampened under continuous light. In contrast, reduced PIC : POC for temperate strains reflected increases of photosynthesis that outpaced increases in calcification rates under 14 : 10 h L : D, with both responses again dampened under continuous light. A multivariate analysis of 35 past studies of E. huxleyi further demonstrated that differences in photoperiod account for as much as 40% (strain B11/92) to 55% (strain NZEH) of ...

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 II', Geobiology, vol. 17, no. 2, pp. 127-150.
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AbstractPhotosystem II is a photochemical reaction center that catalyzes the light‐driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale, we hypothesize that this early Archean photosystem was capable of water oxidation to oxygen and had already evolved protection mechanisms against the formation of reactive oxygen species. This would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

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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Temperate intertidal shores globally are often dominated by habitat-forming seaweeds, but our knowledge of these systems is heavily biased towards northern hemisphere species. Rocky intertidal shores throughout Australia and New Zealand are dominated by a single monotypic species, Hormosira banksii. This species plays a key role in facilitating biodiversity on both rocky shores and estuarine habitats, yet we know little about the processes that structure populations. Herein we characterise the genetic diversity and structure of Hormosira and demonstrate strong restrictions to gene flow over small spatial scales, as well as between estuarine and open coast populations. Estuarine ecotypes were often genetically unique from nearby open coast populations, possibly due to extant reduced gene flow between habitats, founder effects and coastal geomorphology. Deviations from random mating in many locations suggest complex demographic processes are at play within shores, including clonality in estuarine populations. Strong isolation by distance in Hormosira suggests that spatial management of intertidal habitats will necessitate a network of broad-scale protection. Understanding patterns of genetic diversity and gene flow in this important ecosystem engineer will enhance the ability to manage, conserve and restore this key species into the future.

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 Alexandrium minutum during a simulated marine heatwave', Biogeosciences, vol. 16, no. 22, pp. 4377-4391.
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Abstract. The biogenic sulfur compounds dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) are produced andtransformed by diverse populations of marine microorganisms and havesubstantial physiological, ecological and biogeochemical importance spanningorganism to global scales. Understanding the production and transformationdynamics of these compounds under shifting environmental conditions isimportant for predicting their roles in a changing ocean. Here, we reportthe physiological and biochemical response of a robust strain ofAlexandrium minutum, a dinoflagellate with the highest reported intracellular DMSP content,exposed to a 6 d increase in temperature mimicking mild and extremecoastal marine heatwave conditions (+4 and +12 ∘C). Under mild temperature increases (+4 ∘C), A. minutum growth wasenhanced, with no measurable physiological stress response. However, under avery acute increase in temperature (+12 ∘C) triggering thermalstress, A. minutum growth declined, photosynthetic efficiency (FV∕FM) wasimpaired, and enhanced oxidative stress was observed. These physiologicalresponses indicative of thermal stress were accompanied by increased DMS andDMSO concentrations followed by decreased DMSP concentration. At thistemperature extreme, we observed a cascading stress response in A. minutum, which wasinitiated 6 h after the start of the experiment by a spike in DMS and DMSOconcentrations and a rapid decrease in FV∕FM. This was followed byan increase in reactive oxygen species (ROS) and an abrupt decline in DMSand DMSO on day 2 of the experiment. A subsequent decrease in DMSP coupledwith a decline in the growth rate of both A. minutum and its associated totalbacterial assemblage coincided with a shift in the composition of the A. minutummicrobiome. Specifically, an increase in the relative abundance of the operational taxonomic units (OTUs)matching Oceanicaulis (17.0 %), Phycisphaeraceae ...

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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AbstractIn variable light environments, plants adjust light use in photosynthetic electron transport and photoprotective dissipation in the thylakoid membrane. In this respect, roles of the K+/H+ antiporter KEA3, the Cl− channel/transporter CLCe and the voltage-dependent Cl− channel VCCN1 have been unraveled in Arabidopsis thaliana. Here we report that they independently adjust photosynthesis on the basis of analyses using single and higher order loss-of-function mutants. In short experiments of photosynthetic response on transition from dark to low light, we reveal a sequential functioning of VCCN1 and CLCe in the activation of photoprotection and of KEA3 in its downregulation to a low steady state while adjusting the electron transport. On transition from low to high light, VCCN1 accelerates the activation of photoprotection, whereas KEA3 slows it down on transition from high to low light. Based on parallel electrochromic band shift measurements, the mechanism behind is that VCCN1 builds up a pH gradient across the thylakoid membrane, whereas KEA3 dissipates this gradient, which affects photoprotection. CLCe regulates photosynthesis by a pH-independent mechanism likely involving Cl− homeostasis. Nevertheless, all genotypes grow well in alternating high and low light. Taken together, the three studied ion channels/transporters function independently in adjusting photosynthesis to the light environment.

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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Abstract Seaweeds are an integral part of coastal ecosystems and offer invaluable ecosystem services supporting the life of many marine forms. The economic value of seaweeds significantly contributes to the sustainable development of rural coastal regions. Seaweeds are consumed as food in some Asian countries, but their utilization for production of phycocolloids is widespread across the globe, with an estimated value of more than one billion US$. In India, seaweeds have been utilized exclusively for the production of phycocolloids but recently they are used for the production of plant growth stimulants for agricultural applications. The domestic agar and alginate industry totally depends on the supplies from natural seaweed beds with some occasional imports. The recent success achieved in both upstream and downstream technologies in production and processing of seaweeds has boosted the prospects for commercialization of seaweed resources in the country. The present article briefly appraises the current status of Indian seaweed resources and their utilization, as well as developments in seaweed farming technologies, the status of seaweed industry and recent efforts to transform seaweed farming into a social enterprise. It also highlights the challenges encountered for mainstreaming these resources so as to evolve into a marine industry.

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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AbstractRepeat marine heat wave‐induced mass coral bleaching has decimated reefs in Seychelles for 35 years, but how coral‐associated microbial diversity (microalgal endosymbionts of the family Symbiodiniaceae and bacterial communities) potentially underpins broad‐scale bleaching dynamics remains unknown. We assessed microbiome composition during the 2016 heat wave peak at two contrasting reef sites (clear vs. turbid) in Seychelles, for key coral species considered bleaching sensitive (Acropora muricata, Acropora gemmifera) or tolerant (Porites lutea, Coelastrea aspera). For all species and sites, we sampled bleached versus unbleached colonies to examine how microbiomes align with heat stress susceptibility. Over 30% of all corals bleached in 2016, half of which were from Acropora sp. and Pocillopora sp. mass bleaching that largely transitioned to mortality by 2017. Symbiodiniaceae ITS2‐sequencing revealed that the two Acropora sp. and P. lutea generally associated with C3z/C3 and C15 types, respectively, whereas C. aspera exhibited a plastic association with multiple D types and two C3z types. 16S rRNA gene sequencing revealed that bacterial communities were coral host‐specific, largely through differences in the most abundant families, Hahellaceae (comprising Endozoicomonas), Rhodospirillaceae, and Rhodobacteraceae. Both Acropora sp. exhibited lower bacterial diversity, species richness, and community evenness compared to more bleaching‐resistant P. lutea and C. aspera. Different bleaching susceptibility among coral species was thus consistent with distinct microbiome commun...

Gide, TN, Quek, C, Menzies, AM, Tasker, AT, Shang, P, Holst, J, Madore, J, Lim, SY, Velickovic, R, Wongchenko, M, Yan, Y, Lo, S, Carlino, MS, Guminski, A, Saw, RPM, Pang, A, McGuire, HM, Palendira, U, Thompson, JF, Rizos, H, Silva, IPD, Batten, M, Scolyer, RA, Long, GV & Wilmott, JS 2019, 'Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy', Cancer Cell, vol. 35, no. 2, pp. 238-255.e6.
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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.

Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunesse, TC, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Correction to: Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015–2016 heatwave', Coral Reefs, vol. 38, no. 4, pp. 877-877.
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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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AbstractHypolimnial releases from dams during periods of thermal stratification modify the downstream riverine thermal regime by decreasing water temperature and reducing natural diel thermal variability. This cold‐water thermal pollution in rivers can persist for hundreds of kilometres downstream of dams and impact important ecological processes such as fish spawning. To mitigate this problem, a first‐of‐its‐kind thermal curtain was fitted to the large bottom release Burrendong Dam on the Macquarie River, Australia. The thermal curtain acts by directing warmer, near‐surface epilimnial water to the low‐level hypolimnial offtake. This study aimed to test the efficacy of the thermal curtain by measuring temperatures before and after the curtains installation, quantifying the magnitude and extent of cold‐water thermal pollution along the Macquarie River downstream of Burrendong Dam. Epilimnial releases with use of the curtain increased diel temperature ranges and the mean monthly water temperature below the dam. Epilimnial releases with use of the curtain increased diel temperature ranges from 0.9°C to 2.5°C and reduced the difference between the mean monthly water temperature of an upstream control and a downstream site by up to 3.5°C. A comparison of the monthly temperature means along the river, indicated that thermal recovery, whereby temperatures returned to within the natural range of upstream temperatures occurred 45 km downstream of the dam during summer when the thermal curtain was deployed, compared with approximately 200 km prior to deployment of the curtain. Our study suggests that the use of thermal curtains can reduce cold‐water thermal pollution and improve ecological outcomes for river ecosystems downstream of dams.

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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Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify “core microbiome” members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with “core” taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenviron...

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, 'BASTA – Taxonomic classification of sequences and sequence bins using last common ancestor estimations', Methods in Ecology and Evolution, vol. 10, no. 1, pp. 100-103.
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AbstractIdentification of the taxonomic origin of a DNA sequence is crucial for many sequencing projects, e.g. metagenomics studies, identification of contaminations in whole genome sequencing projects and filtering of organisms of interest in marker‐gene based community analyses.Last common ancestor algorithms are powerful approaches to estimate the taxonomy of a given sequence and have been widely used for classification of next‐generation sequencing (NGS) reads, also known as 2nd generation sequencing reads.Here, we present BASTA (https://github.com/timkahlke/BASTA), a basic sequence taxonomy annotator, which extends last common ancestor estimations from sequencing reads to any kind of nucleotide or amino acid sequence utilizing NCBI taxonomies of user‐defined best hits.BASTA can be configured to use the output of many common sequence comparison tools, e.g. BLAST and Diamond, in conjunction with either provided or user‐defined target sequence databases.

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...

Kligyte, G, Baumber, A, Van der Bijl-Brouwer, M, Dowd, C, Hazell, N, Le Hunte, B, Newton, M, Roebuck, D & Pratt, S 2019, '“Stepping in and stepping out”: Enabling creative third spaces through transdisciplinary partnerships', International Journal for Students as Partners, vol. 3, no. 1, pp. 5-21.
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This article explores how transformative higher education approaches can be fostered through an integration of the concepts of third space, Students as Partners (SaP), and transdisciplinarity in practical contexts. We describe a collaborative enquiry that engaged staff and students in a reflexive dialogue centred on the concepts of mutual learning, liminality, emergence, and creativity as enacted in the curriculum of a transdisciplinary undergraduate degree, the Bachelor of Creative Intelligence and Innovation (BCII) at the University of Technology Sydney in Australia. The key insights that emerged through this enquiry were: third spaces in curriculum can be enabled but not constructed, all parties need to embrace uncertainty and a mutual learning mindset, and that “stepping in and out” of such fluid liminal spaces can stimulate creativity. Based on our experience and exploration, we offer some practical recommendations to those seeking to create similar enabling conditions for third spaces in their own undergraduate programs.

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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Abstract BACKGROUND In human body fluids, microRNA (miRNA) can be found as circulating cell-free miRNA (cfmiRNA), as well as secreted into extracellular vesicles (EVmiRNA). miRNAs are being intensively evaluated as minimally invasive liquid biopsy biomarkers in patients with cancer. The growing interest in developing clinical assays for circulating miRNA necessitates careful consideration of confounding effects of preanalytical and analytical parameters. METHODS By using reverse transcription quantitative real-time PCR and next-generation sequencing (NGS), we compared extraction efficiencies of 5 different protocols for cfmiRNA and 2 protocols for EVmiRNA isolation in a multicentric manner. The efficiency of the different extraction methods was evaluated by measuring exogenously spiked cel-miR-39 and 6 targeted miRNAs in plasma from 20 healthy individuals. RESULTS There were significant differences between the tested methods. Although column-based extraction methods were highly effective for the isolation of endogenous miRNA, phenol extraction combined with column-based miRNA purification and ultracentrifugation resulted in lower quality and quantity of isolated miRNA. Among all extraction methods, the ubiquitously expressed miR-16 was represented with high abundance when compared with other targeted miRNAs. In addition, the use of miR-16 as an endogenous control for normalization of quantification cycle values resulted in a decreased variability of column-based cfmiRNA extraction methods. Cluster analysis of normalized NGS counts clearly indicated a method-dependent bias.

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.
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© 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.
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SUMMARYDinoflagellates of the genus Gambierdiscus are known to produce neurotoxins that cause the human illness ciguatera, a tropical and sub‐tropical fish poisoning. Some species from the Gambierdiscus genus were recently re‐classified into a new genus, Fukuyoa based on their phylogenetic and morphological divergence, however, little is known about their distribution, ecology and toxicology. Here we report the first occurrence of F. paulensis in the temperate coastal waters of eastern Australia and characterize its toxicology. Liquid chromatography–tandem mass spectrometry (LC–MS/MS) did not detect the presence of ciguatoxins, however, a putative maitotoxin congener (MTX‐3) was present. Similarly, high maitotoxin‐like activity was detected in High Performance Liquid Chromatography (HPLC) fractionated cell extracts using a Ca2+ influx bioassay on a Fluorescent Imaging Plate Reader (FLIPR), but no ciguatoxin‐like activity was detected.

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.
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Environmental variables such as temperature, salinity, and irradiance are significant drivers of microalgal growth and distribution. Therefore, understanding how these variables influence fitness of potentially toxic microalgal species is particularly important. In this study, strains of the potentially harmful epibenthic dinoflagellate species Coolia palmyrensis, C. malayensis, and C. tropicalis were isolated from coastal shallow water habitats on the east coast of Australia and identified using the D1‐D3 region of the large subunit (LSU) ribosomal DNA (rDNA). To determine the environmental niche of each taxon, growth was measured across a gradient of temperature (15–30°C), salinity (20–38), and irradiance (10–200 μmol photons · m−2 · s−1). Specific growth rates of Coolia tropicalis were highest under warm temperatures (27°C), low salinities (ca. 23), and intermediate irradiance levels (150 μmol photons · m−2 · s−1), while C. malayensis showed the highest growth at moderate temperatures (24°C) and irradiance levels (150 μmol photons · m−2 · s−1) and growth rates were consistent across the range of salinity levels tested (20–38). Coolia palmyrensis had the highest growth rate of all species tested and favored moderate temperatures (24°C), oceanic salinity (35), and high irradiance (>200 μmol photons · m−2 · s−1). This is the first study to characterize the environmental niche of species from the benthic harmful algal bloom genus

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.
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AbstractBiogenic volatile organic compounds (BVOCs) influence organism fitness by promoting stress resistance and regulating trophic interactions. Studies examining BVOC emissions have predominantly focussed on terrestrial ecosystems and atmospheric chemistry – surprisingly, highly productive marine ecosystems remain largely overlooked. Here we examined the volatilome (total BVOCs) of the microalgal endosymbionts of reef invertebrates, Symbiodiniaceae. We used GC-MS to characterise five species (Symbiodinium linucheae, Breviolum psygmophilum, Durusdinium trenchii, Effrenium voratum, Fugacium kawagutii) under steady-state growth. A diverse range of 32 BVOCs were detected (from 12 in D. trenchii to 27 in S. linucheae) with halogenated hydrocarbons, alkanes and esters the most common chemical functional groups. A thermal stress experiment on thermally-sensitive Cladocopium goreaui and thermally-tolerant D. trenchii significantly affected the volatilomes of both species. More BVOCs were detected in D. trenchii following thermal stress (32 °C), while fewer BVOCs were recorded in stressed C. goreaui. The onset of stress caused dramatic increases of dimethyl-disulfide (98.52%) in C. goreaui and nonanoic acid (99.85%) in D. trenchii. This first volatilome analysis of Symbiodiniaceae reveals that both species-specificity and environmental factors govern the composition of BVOC emissions among the Sym...

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.
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© 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.
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AbstractThe continuous development of integrated electronics such as maintenance‐free biosensors, remote and mobile environmental sensors, wearable personal electronics, nanorobotics etc. and their continued miniaturization has led to an increasing demand for miniaturized energy storage units. Microsupercapacitors with graphene electrodes hold great promise as miniaturized, integrated power sources thanks to their fast charge/discharge rates, superior power performance, and long cycling stability. In addition, planar interdigitated electrodes also have the capability to reduce ion diffusion distances leading to a greatly improved electrochemical performance. Either as standalone power sources or complementing energy harvesting units, it is expected that graphene‐based microsupercapacitors will play a key role as miniaturized power sources in electronic microsystems. This review highlights the recent development, challenges, and perspectives in this area, with an emphasis on the link between material and geometry design of planar graphene‐based electrodes and their electrochemical performance and integrability.

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.
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Corals continuously adjust to short term variation in light availability on shallow reefs. Long-term light alterations can also occur due to natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short term photophysiological responses are relatively well-understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species (Acropora muricata). High (HL) and low light (LL) acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ. Rapid light curves using Pulse Amplitude Modulation (PAM) fluorometry revealed photophysiological acclimation of LL to HL and HL to LL shifted corals within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL treated corals than their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL shifted corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability.

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.
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© 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.
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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.
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Abstract Experimentation at sea provides insight into which traits of ocean microbes are linked to performance in situ. Here we show distinct patterns in thermal tolerance of microbial phototrophs from adjacent water masses sampled in the south-west Pacific Ocean, determined using a fluorescent marker for reactive oxygen species (ROS). ROS content of pico-eukaryotes was assessed after 1, 5 and 25 h of incubation along a temperature gradient (15.6–32.1 °C). Pico-eukaryotes from the East Australian Current (EAC) had relatively constant ROS and showed greatest mortality after 25 h at 7 °C below ambient, whereas those from the Tasman Sea had elevated ROS in both warm and cool temperature extremes and greatest mortality at temperatures 6–10 °C above ambient, interpreted as the outcome of thermal stress. Tracking of water masses within an oceanographic circulation model showed populations had distinct thermal histories, with EAC pico-eukaryotes experiencing higher average temperatures for at least 1 week prior to sampling. While acclimatization and community assembly could both influence biological responses, this study clearly demonstrates that phenotypic divergence occurs along planktonic drift trajectories.

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.
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Abstract Coral reefs are threatened by global warming, which disrupts the symbiosis between corals and their photosynthetic symbionts (Symbiodiniaceae), leading to mass coral bleaching. Planktonic diazotrophs or dinitrogen (N2)-fixing prokaryotes are abundant in coral lagoon waters and could be an alternative nutrient source for corals. Here we incubated untreated and bleached coral colonies of Stylophora pistillata with a 15N2-pre-labelled natural plankton assemblage containing diazotrophs. 15N2 assimilation rates in Symbiodiniaceae cells and tissues of bleached corals were 5- and 30-fold higher, respectively, than those measured in untreated corals, demonstrating that corals incorporate more nitrogen derived from planktonic diazotrophs under bleaching conditions. Bleached corals also preferentially fed on Synechococcus, nitrogen-rich picophytoplanktonic cells, instead of Prochlorococcus and picoeukaryotes, which have a lower cellular nitrogen content. By providing an alternative source of bioavailable nitrogen, both the incorporation of nitrogen derived from planktonic diazotrophs and the ingestion of Synechococcus may have profound consequences for coral bleaching recovery, especially for the many coral reef ecosystems characterized by high abundance and activity of planktonic diazotrophs.

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.
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© 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.
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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.
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AbstractPhotosynthetic organisms developed various strategies to mitigate high light stress. For instance, aquatic organisms are able to spend excessive energy by exchanging dissolved CO2 (dCO2) and bicarbonate () with the environment. Simultaneous uptake and excretion of the two carbon species is referred to as inorganic carbon cycling. Often, inorganic carbon cycling is indicated by displacements of the extracellular dCO2 signal from the equilibrium value after changing the light conditions. In this work, we additionally use (i) the extracellular pH signal, which requires non‐ or weakly‐buffered medium, and (ii) a dynamic model of carbonate chemistry in the aquatic environment to detect and quantitatively describe inorganic carbon cycling. Based on simulations and experiments in precisely controlled photobioreactors, we show that the magnitude of the observed dCO2 displacement crucially depends on extracellular pH level and buffer concentration. Moreover, we find that the dCO2 displacement can also be caused by simultaneous uptake of both dCO2 and (no inorganic carbon cycling). In a next step, the dynamic model of carbonate chemistry allows for a quantitative assessment of cellular dCO2, , and H+ exchange rates from the measur...

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.
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© 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.
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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.
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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.
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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.
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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.
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© 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.
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© 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.
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AbstractMarine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca. Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca. Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca. Poseidoniales to occupy a variety...

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.
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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.
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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.
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© 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.
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AbstractPolicies aiming to preserve vegetated coastal ecosystems (VCE; tidal marshes, mangroves and seagrasses) to mitigate greenhouse gas emissions require national assessments of blue carbon resources. Here, we present organic carbon (C) storage in VCE across Australian climate regions and estimate potential annual CO2 emission benefits of VCE conservation and restoration. Australia contributes 5–11% of the C stored in VCE globally (70–185 Tg C in aboveground biomass, and 1,055–1,540 Tg C in the upper 1 m of soils). Potential CO2 emissions from current VCE losses are estimated at 2.1–3.1 Tg CO2-e yr-1, increasing annual CO2 emissions from land use change in Australia by 12–21%. This assessment, the most comprehensive for any nation to-date, demonstrates the potential of conservation and restoration of VCE to underpin national policy development for reducing greenhouse gas emissions.

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.
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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.
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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.

Songsomboon, K, Crawford, R, Crawford, J, Hansen, J, Cummings, J, Mattson, N, Bergstrom, G & Viands, D 2019, 'Recurrent phenotypic selection for resistance to diseases caused by Bipolaris oryzae in switchgrass (Panicum virgatum L.)', Biomass and Bioenergy, vol. 125, pp. 105-113.
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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.
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AbstractThe acquisition of thermally tolerant algal symbionts by corals has been proposed as a natural or assisted mechanism of increasing coral reef resilience to anthropogenic climate change, but the cell-level processes determining the performance of new symbiotic associations are poorly understood. We used liquid chromatography–mass spectrometry to investigate the effects of an experimentally induced symbiosis on the host proteome of the model sea anemone Exaiptasia pallida. Aposymbiotic specimens were colonised by either the homologous dinoflagellate symbiont (Breviolum minutum) or a thermally tolerant, ecologically invasive heterologous symbiont (Durusdinium trenchii). Anemones containing D. trenchii exhibited minimal expression of Niemann-Pick C2 proteins, which have predicted biochemical roles in sterol transport and cell recognition, and glutamine synthetases, which are thought to be involved in nitrogen assimilation and recycling between partners. D. trenchii-colonised anemones had higher expression of methionine-synthesising betaine–homocysteine S-methyltransferases and proteins with predicted oxidative stress response functions. Multiple lysosome-associated proteins were less abundant in both symbiotic treatments compared with the aposymbiotic treatment. The differentially abundant proteins are predicted to represent pathways that may be involved in nutrient transport or resource allocation between partners. These results provide targets for specific experiments to elucidate the mechanisms underpinning compensatory physiology in the coral–dinoflagellate symbiosis.

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.
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Coral nursery and outplanting practices have grown in popularity worldwide for targeted restoration of degraded “high value” reef sites, and recovery of threatened taxa. Success of these practices is commonly gauged from coral propagule growth and survival, which fundamentally determines the return‐on‐effort (RRE) critical to the cost‐effectiveness and viability of restoration programs. In many cases, RRE has been optimized from past successes and failures, which therefore presents a major challenge for locations such as the Great Barrier Reef (GBR) where no local history of restoration exists to guide best practice. In establishing the first multi‐taxa coral nursery on the GBR (Opal Reef, February 2018), we constructed a novel scoring criterion from concurrent measurements of growth and survivorship to guide our relative RRE, including nursery propagule numbers (stock density). We initially retrieved RRE scores from a database of global restoration efforts to date (n = 246; 52 studies) to evaluate whether and how success commonly varied among coral taxa. We then retrieved RRE scores for Opal Reef using initial growth and survivorship data for six key coral taxa, to demonstrate that RRE scores were high for all taxa predominantly via high survivorship over winter. Repeated RRE scoring in summer is therefore needed to capture the full dynamic range of success where seasonal factors regulating growth versus survivorship differ. We discuss how RRE scoring can be easily adopted across restoration practices globally to standardize and benchmark success, but also as a tool to aid decision‐making in optimizing future propagation (and outplanting) efforts.

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.
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© 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.
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© 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.
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AbstractSeagrass ecosystems are highly productive, and are sites of significant carbon sequestration. Sediment‐held carbon stocks can be many thousands of years old, and persist largely due to sediment anoxia and because microbial activity is decreasing with depth. However, the carbon sequestered in seagrass ecosystems may be susceptible to remineralization via the activity of bioturbating fauna. Microbial priming is a process whereby remineralization of sediment carbon (recalcitrant organic matter) is stimulated by disturbance, i.e., burial of a labile source of organic matter (seagrass). We investigated the hypothesis that bioturbation could mediate remineralization of sediment carbon stocks through burial of seagrass leaf detritus. We carried out a 2‐month laboratory study to compare the remineralization (measured as CO2 release) of buried seagrass leaves (Zostera muelleri) to the total rate of sediment organic matter remineralization in sediment with and without the common Australian bioturbating shrimp Trypaea australiensis (Decapoda: Axiidea). In control sediment containing seagrass but no bioturbators, we observed a negative microbial priming effect, whereby seagrass remineralization was favored over sediment remineralization (and thus preserving sediment stocks). Bioturbation treatments led to a two‐ to five‐fold increase in total CO2 release compared to controls. The estimated bioturbator‐stimulated microbial priming effect was equivalent to 15% of the total daily sediment‐derived CO2 releases. We propose that these results indicate that bioturbation is a potential mechanism that converts these sediments from carbon sinks to sources through stimulation of priming‐enhanced sediment carbon remineralization. We further hypothesized that significant changes to seagrass faunal communities may influence...

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.
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© 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.
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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.
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SummaryIn marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth. Their ecological success may be related to their production of complex toxic polyketide compounds. Ostreopsis species produce potent palytoxin‐like compounds (PLTX), which are associated with human skin and eye irritations, and illnesses through the consumption of contaminated seafood. To investigate the genetic basis of PLTX‐like compounds, we sequenced and annotated transcriptomes from two PLTX‐producing Ostreopsis species; O. cf. ovata, O. cf. siamensis, one non‐PLTX producing species, O. rhodesae and compared them to a close phylogenetic relative and non‐PLTX producer, Coolia malayensis. We found no clear differences in the presence or diversity of ketosynthase and ketoreductase transcripts between PLTX producing and non‐producing Ostreopsis and Coolia species, as both groups contained >90 and > 10 phylogenetically diverse ketosynthase and ketoreductase transcripts, respectively. We report for the first‐time type I single‐, multi‐domain polyketide synthases (PKSs) and hybrid non‐ribosomal peptide synthase/PKS transcripts from all species. The long multi‐modular PKSs were insufficient by themselves to synthesize the large complex polyether backbone of PLTX‐like compounds. This implies that numerous PKS domains, including both single and multi‐, work together on the biosynthesis of PLTX‐like and other related polyketide compounds.

Vo, HNP, Bui, X-T, Nguyen, H-H, Tran, T-D, Lee, K-J, Nguyen, T-T-T, Dang, B-T, Bui, M-H, Nguyen, DD & Ngo, T-T-M 2019, 'Effects of dissolved oxygen concentration on the performance of sponge membrane bioreactor treating hospital wastewater', Desalination and Water Treatment, vol. 151, pp. 128-137.
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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.
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© 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.
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© 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.
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© 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, Larkum, AWD, Ferrier-Pagès, C, Salih, A, Warner, ME, Dubinsky, Z & Kühl, M 2019, 'Editorial: Optics and Ecophysiology of Coral Reef Organisms', Frontiers in Marine Science, vol. 6.
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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.
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© 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.

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.
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Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.

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.
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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, 'CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases', Methods in Ecology and Evolution, vol. 10, no. 5, pp. 744-751.
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AbstractSpecies occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo‐referencing or dating, can diminish their usefulness. Manual cleaning is time‐consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records.Here, we present CoordinateCleaner, an r‐package to scan datasets of species occurrence records for geo‐referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo‐referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio‐temporal tests for fossils.We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90 million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%...

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.

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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Sutherland, D, Buxton, L & Ralph, P 1970, 'Algae and waste in a circular economy. Oral Presentation', Organix19, Sydney, Australia.

Baird, ME, Wild-Allen, KA, Parslow, J, Mongin, M, Robson, B, Skerratt, J, Rizwi, F, Soja-Woznaik, M, Jones, E, Herzfeld, M, Margvelashvili, N, Andrewartha, J, Langlais, C, Adams, MP, Cherukuru, N, Gustafsson, M, Hadley, S, Ralph, PJ, Rosebrock, U, Schroeder, T, Laiolo, L, Harrison, D & Steven, ADL 2019, 'CSIRO Environmental Modelling Suite (EMS): Scientific description of the optical and biogeochemical models (vB3p0)', Copernicus GmbH.
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Abstract. Since the mid 1990s, Australia's Commonwealth Science Industry and Research Organisation (CSIRO) has developed a biogeochemical (BGC) model for coupling with a hydrodynamic and sediment model for application in estuaries, coastal waters and shelf seas. The suite of coupled models is referred to as the CSIRO Environmental Modelling Suite (EMS) and has been applied at tens of locations around the Australian continent. At a mature point in the BGC model's development, this paper presents a full mathematical description, as well as links to the freely available code and User Guide. The mathematical description is structured into processes so that the details of new parameterisations can be easily identified, along with their derivation. The EMS BGC model cycles carbon, nitrogen, phosphorous and oxygen through multiple phytoplankton, zooplankton, detritus and dissolved organic and inorganic forms in multiple water column and sediment layers. The underwater light field is simulated by a spectrally-resolved optical model that includes the calculation of water-leaving reflectance for validation with remote sensing. The water column is dynamically coupled to the sediment to resolve deposition, resuspension and benthic-pelagic biogeochemical fluxes. With a focus on shallow waters, the model also includes particularly-detailed representations of benthic plants such as seagrass, macroalgae and coral polyps. A second focus has been on, where possible, the use of geometric derivations of physical limits to constrain ecological rates, which generally requires population-based rates to be derived from initially considering the size and shape of individuals. For example, zooplankton grazing considers encounter rates of one predator on a prey field based on summing relative motion of the predator with the prey individuals and the search area, chlorophyll synthesis includes a geometrically-derived self-shading term, and the bottom coverage of benthic plants is gen...

Nguyen, VK, King, WL, Siboni, N, Mahbub, KR, Dove, M, O’connor, W, Seymour, J & Labbate, M 2019, 'The sydney rock oyster microbiome is influenced by local environmental parameters and QX disease resistance', Elsevier BV, pp. 438-438.
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