Publications

Ajani, PA, Eriksen, R & Rissik, D 2019, 'Coastal and marine phytoplankton: diversity and ecology' in Suthers, I & Rissik, D (eds), Plankton, A Guide to Their Ecology and Monitoring for Water Quality, 2nd Edition, CSIRO Publishing.

Murray, SA & Hallegraeff, G 2019, 'Harmful Algae Introductions: Vectors of Transfer, Mitigation, and Management' in Shumway, S, Burkholder, JA & Morton, S (eds), Harmful Algal Blooms A Compendium Desk Reference, John Wiley & Sons, pp. 493-506.
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Chapters in this volume will provide readers with information on causes of HAB, successful management and monitoring programs, control, prevention, and mitigation strategies, economic consequences of HAB, associated risks to human health, ...

Rissik, D, Ajani, P, Bowling, L, gibbs, M, Kobayashi, T, Pitt, K, Richardson, A & Suthers, I 2019, 'Use of Plankton for Management' in Plankton A Guide to Their Ecology and Monitoring for Water Quality, CSIRO PUBLISHING.
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This Second Edition of Plankton is a fully updated introduction to the biology, ecology and identification of plankton and their use in monitoring water quality.

Rissik, D, van Senden, D, Doherty, M, Ingleton, I, Ajani, P, Bowling, L, Gibbs, M, Gladstone, M, Kobayashi, T, Suthers, I & Froneman, W 2019, 'Plankton-related water quality issues' in Suthers, I, Richardson, A & Rissik, D (eds), Plankton, A Guide to Their Ecology and Monitoring for Water Quality, 2nd Edition, CSIRO Publishing.

Wilkinson, S, Ralph, P & Biloria, NM 2019, 'Algae Building: Is This the New Smart Sustainable Technology' in Biloria, N (ed), Data-Driven Multivalence in the Built Environment, Springer Nature, Switzerland, pp. 245-268.
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Building energy use contributes around 40% of total greenhouse gas (GHG) emissions (UNEP 2009) and reducing building-related GHG emissions could mitigate global warming significantly. With a three degree increase in global temperature by 2100 predicted by the United Nations Intergovernmental Panel on Climate Change we need to explore ways to mitigate these impacts. An option for the built environment is to build and retrofit using innovative technologies to adopt onsite energy generation and reduce energy use (UNEP 2015). Increasing energy efficiency and using renewable energy are ways to reduce GHG emissions. Technological innovations change over time, and innovations that start as expensive and inefficient can become economic and highly productive, solar energy is an example. In the mid 1800s the photovoltaic (PV) effect was discovered but it took a century to invent a suitable storage device, after which rapid innovation in efficiency and costs followed. Could the same happen for bio-energy? Global biomass energy production reached 88 GW in 2014 (Rosillo et al, 2016); and bio-energy is no longer a transition energy source. In 2013, a residential building in Hamburg Germany adopted algae, as a renewable energy source. Several questions arise; how does algae produce energy for buildings? And how much energy is produced? How does it compare to other renewable energy sources? Furthermore, which building types are suited to adoption of algae as an energy source? This chapter explores the feasibility of algae building technology explaining the technology and how it works; the strengths and weaknesses. Then the chapter sets out the drivers and barriers to adopting Algae Building Technology, and; to assesses opportunities across a range of building types.

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. Biological sciences, vol. 286, no. 1916.
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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 15N- and 13C-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, JB, 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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© 2019 The Author(s). Background: Coral reefs can experience salinity fluctuations due to rainfall and runoff; these events can have major impacts on the corals and lead to bleaching and mortality. On the Great Barrier Reef (GBR), low salinity events, which occur during summer seasons and can involve salinity dropping ~ 10 PSU correlate with declines in coral cover, and these events are predicted to increase in frequency and severity under future climate change scenarios. In other marine invertebrates, exposure to low salinity causes increased expression of genes involved in proteolysis, responses to oxidative stress, and membrane transport, but the effects that changes in salinity have on corals have so far received only limited attention. To better understand the coral response to hypo-osmotic stress, here we investigated the transcriptomic response of the coral Acropora millepora in both adult and juvenile life stages to acute (1 h) and more prolonged (24 h) exposure to low salinity. Results: Differential gene expression analysis revealed the involvement of both common and specific response mechanisms in Acropora. The general response to environmental stressors included up-regulation of genes involved in the mitigation of macromolecular and oxidative damage, while up-regulation of genes involved in amino acid metabolism and transport represent specific responses to salinity stress. Conclusions: This study is the first comprehensive transcriptomic analysis of the coral response to low salinity stress and provides important insights into the likely consequences of heavy rainfall and runoff events on coral reefs.

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.

Andersson, AJ, Venn, AA, Pendleton, L, Brathwaite, A, Camp, EF, Cooley, S, Gledhill, D, Koch, M, Maliki, S & Manfrino, C 2019, 'Ecological and socioeconomic strategies to sustain Caribbean coral reefs in a high-CO2 world', Regional Studies in Marine Science, vol. 29.
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© 2019 The Authors The Caribbean and Western Atlantic region hosts one of the world's most diverse geopolitical regions and a unique marine biota distinct from tropical seas in the Pacific and Indian Oceans. While this region varies in human population density, GDP and wealth, coral reefs, and their associated ecosystem services, are central to people's livelihoods. Unfortunately, the region's reefs have experienced extensive degradation over the last several decades. This degradation has been attributed to a combination of disease, overfishing, and multiple pressures from other human activities. Furthermore, the Caribbean region has experienced rapid ocean warming and acidification as a result of climate change that will continue and accelerate throughout the 21st century. It is evident that these changes will pose increasing threats to Caribbean reefs unless imminent actions are taken at the local, regional and global scale. Active management is required to sustain Caribbean reefs and increase their resilience to recover from acute stress events. Here, we propose local and regional solutions to halt and reverse Caribbean coral reef degradation under ongoing ocean warming and acidification. Because the Caribbean has already experienced high coral reef degradation, we suggest that this region may be suitable for more aggressive interventions that might not be suitable for other regions. Solutions with direct ecological benefits highlighted here build on existing knowledge of factors that can contribute to reef restoration and increased resilience in the Caribbean: (1)management of water quality, (2)reduction of unsustainable fishing practices, (3)application of ecological engineering, and (4)implementing marine spatial planning. Complementary socioeconomic and governance solutions include: (1)increasing communication and leveraging resources through the establishment of a regional reef secretariat, (2)incorporating reef health and sustainability goals into the bl...

Andrews, M, Condron, LM, Kemp, PD, Topping, JF, Lindsey, K, Hodge, S & Raven, JA 2019, 'Elevated CO2 effects on nitrogen assimilation and growth of C3 vascular plants are similar regardless of N-form assimilated.', Journal of experimental botany, vol. 70, no. 2, pp. 683-690.
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Atmospheric carbon dioxide concentration ([CO2]) increased from around 280 ppm in 1750 to 400 ppm in 2016 and is likely to continue to increase throughout this century. It has been argued that wheat, Arabidopsis, and C3 plants in general respond more positively to elevated atmospheric [CO2] under ammonium (NH4+) nutrition than under nitrate (NO3-) nutrition because elevated CO2 inhibits their photoreduction of NO3- and hence reduces their total plant nitrogen (N) assimilation and ultimately growth. Here, it is argued that the weight of evidence in the literature indicates that elevated atmospheric [CO2] does not inhibit NO3- assimilation and growth of C3 vascular plants. New data for common bean and wheat support this view and indicate that the effects of elevated atmospheric [CO2] on N assimilation and growth of C3 vascular plants will be similar regardless of the form of N assimilated.

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.
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Badis, Y, Klochkova, TA, Brakel, J, Arce, P, Ostrowski, M, Tringe, SG, Kim, GH & Gachon, CMM 2019, 'Hidden diversity in the oomycete genus Olpidiopsis is a potential hazard to red algal cultivation and conservation worldwide', EUROPEAN JOURNAL OF PHYCOLOGY.
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Bai, J, Shi, H, Yu, Q, Xie, Z, Li, L, Luo, G, Jin, N & Li, J 2019, 'Satellite-observed vegetation stability in response to changes in climate and total water storage in Central Asia.', The Science of the total environment, vol. 659, pp. 862-871.
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Ecosystems in arid and semi-arid regions are vulnerable to climatic and anthropogenic disturbances. However, our understanding of vegetation stability (including resistance and resilience, which are the abilities of ecosystems to resist perturbations and return to pre-disturbance structure or function, respectively) in response to environmental changes in dryland ecosystems remains insufficient, particularly in the absence of large-scale observations of water availability. Here we introduced GRACE monthly total water storage anomaly (TWSA) data into an autoregressive model with remote sensed EVI, air temperature and precipitation to investigate the short-term vegetation stability and its influencing factors in Central Asia (CA) during 2003-2015. The results showed that the grid-level vegetation resilience in CA increased logarithmically as mean annual precipitation (R2 = 0.33, P < 0.05) but decreased linearly with increasing mean annual temperature (R2 = 0.41, P < 0.05). Vegetation resilience was not correlated with TWSA, due to the decoupling of TWSA with precipitation both spatially and temporally in the majority of CA. At the biome level, vegetation resilience also increased as a logarithmical function of aridity index (R2 = 0.80, P < 0.05). Vegetation resistance to TWSA showed minor difference across biomes, while vegetation resistance to precipitation functioned as a parabolic curve along the aridity gradient (R2 = 0.59, P < 0.05). Our results suggest that accounting for the effects of total water column instead of precipitation only is critical in understanding vegetation-water relationships in drylands. The steep decrease in vegetation resilience in areas with high temperature and low water availability implies a high risk of collapse for these water-limited ecosystems if there are severe droughts. Furthermore, reduction in total water storage, induced by, e.g., large-scale extraction of surface runoff or shallow-layer groundwater for irrigation, can resul...

Bates, H, Zavafer, A, Szabo, 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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Behrendt, L, Trampe, EL, Nord, NB, Nguyen, J, Kuhl, M, Lonco, D, Nyarko, A, Dhinojwala, A, Hershey, OS & Barton, H 2019, 'Life in the dark: far-red absorbing cyanobacteria extend photic zones deep into terrestrial caves', ENVIRONMENTAL MICROBIOLOGY.
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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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Ionic 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 Bronsted and Lewis Acidity', CHEMSUSCHEM, vol. 12, no. 14, pp. 3263-3270.
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Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'A Systematic Study of Metal Triflates in Catalytic Transformations of Glucose in Water and Methanol: Identifying the Interplay of Brønsted and Lewis Acidity', ChemSusChem, vol. 12, pp. 3208-3208.
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© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Invited 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, '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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© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Acid-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, 'Catalytic Valorization of Native Biomass in a Deep Eutectic Solvent: A Systematic Approach toward High-Yielding Reactions of Polysaccharides', ACS Sustainable Chemistry and Engineering.
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© 2019 American Chemical Society. This work investigates catalytic reactions of raw, bulk, native biomass (poly)carbohydrates in the choline chloride/oxalic acid deep eutectic solvent. In particular, we systematically explore the reactivity of native glucans, fructans, and xylans in model transformations of refined substrates and unrefined cellulosic materials in the catalyst-solvent. We show that α-linked glucose polymers, fructans, and xylans are all amenable to hydrolytic processing, and only the linear polysaccharide cellulose remains rather intractable under our conditions. Improved fundamental understanding of the chemistry permits tuning the reaction parameters toward high yielding conversion of undervalued terrestrial and marine biomass into significantly value-added glucose (yield up to 68 wt %), fructose (yield up to 60 wt %), xylose (yield up to 73 wt %), 5-(hydroxymethyl)furfural (yield up to 14 mol %), or furfural (yield up to 72 mol %). Under these optimized conditions, cellulose remains as an unreacted portion, which could be recovered and very effectively beneficiated, delivering additional useful chemicals in high yields from the biomass and optimizing toward total use of the biomass. We realize efficient conversions of polysaccharides of the biomass into high yields of useful small molecules.

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.
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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·: N H2O on its catalyst activity: A systematic study of zinc chloride hydrates in the catalytic valorisation of cellulosic biomass', Catalysis Science and Technology, vol. 9, no. 17, pp. 4693-4701.
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© The Royal Society of Chemistry 2019. We demonstrate the efficient and direct transformation of a range of low value substrates, such as lignocellulose and algal biomass, into significantly higher value chemicals, including low molecular weight reducing saccharides, 5-(hydroxymethyl)furfural, furyl hydroxymethyl ketone and furfural. This is based on a systematic study of ZnCl2·nH2O (n = 2.5-4.5), in particular the role of the molecular formula (the amount of H2O) on its activity in the catalytic transformation of cellulosic materials into value added small molecules. The study includes various model transformations based on refined saccharides and applies the new insights to the highly selective transformation of raw biomass.

Bramucci, AR & Case, RJ 2019, 'Phaeobacter inhibens induces apoptosis-like programmed cell death in calcifying Emiliania huxleyi.', Scientific reports, vol. 9, no. 1.
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The model coccolithophore, Emiliania huxleyi, forms expansive blooms dominated by the calcifying cell type, which produce calcite scales called coccoliths. Blooms last several weeks, after which the calcified algal cells rapidly die, descending into the deep ocean. E. huxleyi bloom collapse is attributed to E. huxleyi viruses (EhVs) that infect and kill calcifying cells, while other E. huxleyi pathogens, such as bacteria belonging to the roseobacter clade, are overlooked. EhVs kill calcifying E. huxleyi by inducing production of bioactive viral-glycosphingolipids (vGSLs), which trigger algal programmed cell death (PCD). The roseobacter Phaeobacter inhibens was recently shown to interact with and kill the calcifying cell type of E. huxleyi, but the mechanism of algal death remains unelucidated. Here we demonstrate that P. inhibens kills calcifying E. huxleyi by inducing a highly specific type of PCD called apoptosis-like-PCD (AL-PCD). Host death can successfully be abolished in the presence of a pan-caspase inhibitor, which prevents the activation of caspase-like molecules. This finding differentiates P. inhibens and EhV pathogenesis of E. huxleyi, by demonstrating that bacterial-induced AL-PCD requires active caspase-like molecules, while the viral pathogen does not. This is the first demonstration of a bacterium inducing AL-PCD in an algal host as a killing mechanism.

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 pCO 2', Limnology and Oceanography, vol. 64, no. 3, pp. 1284-1296.
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© 2019 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography. The 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 pCO 2 with the light : dark (L : D) cycle. We confirmed a general regulatory effect of photoperiod on the pCO 2 response, whereby growth and particulate inorganic carbon and particulate organic carbon (PIC : POC) ratios were reduced with elevated pCO 2 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 pCO 2 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 the variance in reported pCO 2 -induced reductions to growth but not PIC : POC. Our study thus highlights a critical role for day length in moderating the effect of ocean acidification on coccolithophore growth and consequently how this response may play out across latitudes and seasons in future oceans.

Brodersen, KE, Koren, K, Revsbech, NP & Kuehl, M 2019, 'Strong leaf surface basification and CO2 limitation of seagrass induced by epiphytic biofilm microenvironments', PLANT CELL AND ENVIRONMENT, vol. 43, no. 1, pp. 174-187.
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Brown, P, RELISH Consortium & Zhou, Y 2019, 'Large expert-curated database for benchmarking document similarity in biomedical literature search', Database: the journal of biological databases and curation.
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Buapet, P, Mohammadi, NS, Pernice, M, Kumar, M, Kuzhiumparambil, U & Ralph, PJ 2019, 'Excess copper promotes photoinhibition and modulates the expression of antioxidant-related genes in Zostera muelleri', AQUATIC TOXICOLOGY, vol. 207, pp. 91-100.
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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.

Canonico, G, Buttigieg, PL, Montes, E, Muller-Karger, FE, Stepien, C, Wright, D, Benson, A, Helmuth, B, Costello, M, Sousa-Pinto, I, Saeedi, H, Newton, J, Appeltans, W, Bednaršek, N, Bodrossy, L, Best, BD, Brandt, A, Goodwin, KD, Iken, K, Marques, AC, Miloslavich, P, Ostrowski, M, Turner, W, Achterberg, EP, Barry, T, Defeo, O, Bigatti, G, Henry, LA, Ramiro-Sánchez, B, Durán, P, Morato, T, Murray Roberts, J, García-Alegre, A, Cuadrado, MS & Murton, B 2019, 'Global observational needs and resources for marine biodiversity', Frontiers in Marine Science, vol. 6, no. JUL.
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© 2019 Canonico, Buttigieg, Montes, Muller-Karger, Stepien, Wright, Benson, Helmuth, Costello, Sousa-Pinto, Saeedi, Newton, Appeltans, Bednaršek, Bodrossy, Best, Brandt, Goodwin, Iken, Marques, Miloslavich, Ostrowski, Turner, Achterberg, Barry, Defeo, Bigatti, Henry, Ramiro-Sánchez, Durán, Morato, Roberts, García-Alegre, Cuadrado and Murton. The diversity of life in the sea is critical to the health of ocean ecosystems that support living resources and therefore essential to the economic, nutritional, recreational, and health needs of billions of people. Yet there is evidence that the biodiversity of many marine habitats is being altered in response to a changing climate and human activity. Understanding this change, and forecasting where changes are likely to occur, requires monitoring of organism diversity, distribution, abundance, and health. It requires a minimum of measurements including productivity and ecosystem function, species composition, allelic diversity, and genetic expression. These observations need to be complemented with metrics of environmental change and socio-economic drivers. However, existing global ocean observing infrastructure and programs often do not explicitly consider observations of marine biodiversity and associated processes. Much effort has focused on physical, chemical and some biogeochemical measurements. Broad partnerships, shared approaches, and best practices are now being organized to implement an integrated observing system that serves information to resource managers and decision-makers, scientists and educators, from local to global scales. This integrated observing system of ocean life is now possible due to recent developments among satellite, airborne, and in situ sensors in conjunction with increases in information system capability and capacity, along with an improved understanding of marine processes represented in new physical, biogeochemical, and biological models.

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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Photosystem 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.
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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.

Chen, L, Xiang, W, Wu, H, Ouyang, S, Lei, P, Hu, Y, Ge, T, Ye, J & Kuzyakov, Y 2019, 'Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests.', Applied microbiology and biotechnology, vol. 103, no. 13, pp. 5421-5433.
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Subtropical broadleaved forests play a crucial role in supporting terrestrial ecosystem functions, but little is known about their belowground soil fungal communities despite that they have central functions in C, N, and P cycles. This study investigated the structures and identified the drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests, using high-throughput sequencing and FUNGuild for fungal identification and assignment to the trophic guild. Fungal richness was much higher in the deciduous than in the evergreen forest. Both forests were dominated by Ascomycota and Basidiomycota phyla, but saprophytic fungi were more abundant in the deciduous forest and ectomycorrhizal fungi predominated in the evergreen forest. Fungal communities had strong links to plant and soil properties. Specifically, plant diversity and litter biomass were the main aboveground drivers of fungal diversity and composition in the deciduous forest, while host effects were prominent in the evergreen forest. The belowground factors, i.e., soil pH, water content, and nutrients especially available P, were identified as the primary drivers of soil fungal communities in the broadleaved forests. Co-occurrence network analysis revealed assembly of fungal composition in broadleaved forest soils was non-random. The smaller modularity of the network in the deciduous forest reflects lower resistance to environment changes. Concluding, these results showed that plant community attributes, soil properties, and potential interactions among fungal functional guilds operate jointly on the divergence of soil fungal community assembly in the two broadleaved forest types.

Clifton, J, Osman, EO, Suggett, DJ & Smith, DJ 2019, 'Resolving conservation and development tensions in a small island state: A governance analysis of Curieuse Marine National Park, Seychelles', Marine Policy.
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© 2019 Elsevier Ltd The management and conservation of marine resources in Seychelles, a small island developing state (SIDS) in the western Indian Ocean, is fundamental to maintaining the flow of international visitors which forms the mainstay of the nation's economy. There is an increasing trend towards empowering non-governmental organisations and parastatal entities with protected area management responsibilities, which partly reflects the chronic underfunding of the state protected area management institution. This paper explores these and related issues through a governance analysis of Curieuse Marine National Park, which is the most popular state-owned marine national park in terms of recorded visitor numbers. This demonstrates that the inability to implement economic incentives through not fully capitalising on the use and non-use values of the park has deleterious consequences for managing the combined impacts of tourism and fisheries on the ecological assets of the park. Furthermore, the capacity of the state management institution is being eroded through a focus on the development of an extensive network of new marine protected areas under the direction of an international non-governmental organisation. Suggestions are made that could strengthen economic, participative and interpretative incentives to provide a more sustainable basis for marine national park management.

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. 977-985.
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© CSIRO 2018. 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.

Collins, S, Boyd, PW & Doblin, MA 2019, 'Evolution, Microbes, and Changing Ocean Conditions.', Annual review of marine science.
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Experimental evolution and the associated theory are underutilized in marine microbial studies; the two fields have developed largely in isolation. Here, we review evolutionary tools for addressing four key areas of ocean global change biology: linking plastic and evolutionary trait changes, the contribution of environmental variability to determining trait values, the role of multiple environmental drivers in trait change, and the fate of populations near their tolerance limits. Wherever possible, we highlight which data from marine studies could use evolutionary approaches and where marine model systems can advance our understanding of evolution. Finally, we discuss the emerging field of marine microbial experimental evolution. We propose a framework linking changes in environmental quality (defined as the cumulative effect on population growth rate) with population traits affecting evolutionary potential, in order to understand which evolutionary processes are likely to be most important across a range of locations for different types of marine microbes. Expected final online publication date for the Annual Review of Marine Science, Volume 12 is January 3, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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.
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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.

De Lima Ribeiro, A, Artlett, C, Ajani, P, Derkenne, C & Pask, H 2019, 'Impact of fluorescence on Raman remote sensing of temperature in natural water samples', Optics Express, vol. 27, no. 16, pp. 22339-22351.
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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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Duke, NC, Field, C, Mackenzie, JR, Meynecke, JO & Wood, AL 2019, 'Rainfall and its possible hysteresis effect on the proportional cover of tropical tidal-wetland mangroves and saltmarsh-saltpans', Marine and Freshwater Research, vol. 70, no. 8, pp. 1047-1055.
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© 2019 CSIRO. Mangrove-saltmarsh tidal wetlands are highly dynamic ecosystems, responding and adapting to climate and physical conditions at all spatial and temporal scales. Knowledge of the large-scale ecosystem processes involved and how they might be influenced by climate variables is highly relevant today. For tidal-wetland sites well within the latitudinal range of the mostly tropical mangrove communities, we confirm that average annual rainfall influences vegetative cover, as well as species composition and biomass of tidal wetlands. On the basis of 205 largely unmodified, tropical and subtropical estuaries of northern Australia, a sigmoidal relationship, with a centroid inflection point ∼1368 mm, was derived between rainfall and the relative amounts of high-biomass mangroves and low-biomass saltmarsh-saltpan vegetation. The presence and probability of observed combinations of these community types were quantified using the wetland cover index, which is the ratio of total mangrove area to that of mangroves plus intertidal saltmarsh and saltpans. Accordingly, periodic changes in rainfall trends are likely manifest as either encroachment or dieback of mangroves along the ecotones separating them from tidal saltmarsh-saltpans. Presented is a new conceptual framework and model that describes how such ecosystem-scale processes take place in tropical and subtropical tidal wetlands.

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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Filippini, G, Bugnot, AB, Johnston, EL, Ruszczyk, J, Potts, J, Scanes, P, Ferguson, A, Ostrowski, M, Varkey, D & Dafforn, KA 2019, 'Sediment bacterial communities associated with environmental factors in Intermittently Closed and Open Lakes and Lagoons (ICOLLs).', The Science of the total environment, vol. 693.
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Intermittently Closed and Open Lakes and Lagoons (ICOLLS) are important coastal systems that are periodically separated from the ocean by a sand barrier or a berm. In urban ICOLLs, continuous inputs of organic material and nutrients into coastal lagoons are contributing to eutrophic conditions that, together with natural environmental factors have implications for the resident sediment bacterial communities. We used molecular tools to investigate the ecological communities of four ICOLLs; Narrabeen, Dee Why, Curl Curl and Manly in Sydney, Australia, which have been subjected to increasing pressure from anthropogenic activities over the last century. We used targeted gene sequencing of the prokaryotic 16S ribosomal RNA gene to describe the bacterial diversity and community structure and discuss differences with respect to environmental factors at the ICOLL scale (e.g. size, shape, normalised N loading) and site scale (e.g. water and sediment quality) within each lagoon. Due to differences in hydrological patterns, we expected that sediment bacterial communities would be more heterogenous in displacement-dominated lagoons (Curl Curl and Manly) than the mixing-dominated lagoons (Narrabeen and Dee Why). Interestingly, we did not find strong relationships between the main bacterial groups and distance from the lagoon entrance (used as a proxy for salinity and silt) in the displacement-dominated lagoons. Moreover, we found that α diversity was highest in Narrabeen and Manly lagoons despite differences in lagoon size and shape. Furthermore, while bacterial community structure was similar in Curl Curl and Dee Why, communities in Manly and Narrabeen differed along temperature/TOC and salinity/silt gradients respectively. In Manly lagoon, we found relatively more anaerobic bacteria such as Epsilonbactereota which is involved in the oxidation and reduction of sulfur compounds. Moreover, we identified several bacterial taxa (including sulfur metabolising Chlorobiaceae) relat...

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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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.

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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Repeat 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 community profiles. These profiles were conserved across bleached and unbleached colonies of all coral species. As this pattern could also reflect a parallel response of the microbiome to environmental changes, the detailed functional associations will need to be determined in future studies. Further understanding such microbiome-environmental interactions is likely critical to target more effective manag...

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.

Goessling, JW, Su, Y, Maibohm, C, Ellegaard, M & Kuhl, M 2019, 'Differences in the optical properties of valve and girdle band in a centric diatom', INTERFACE FOCUS, vol. 9, no. 1.
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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. 4, pp. 366-+.
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Gómez-Consarnau, L, Raven, JA, Levine, NM, Cutter, LS, Wang, D, Seegers, B, Arístegui, J, Fuhrman, JA, Gasol, JM & Sañudo-Wilhelmy, SA 2019, 'Microbial rhodopsins are major contributors to the solar energy captured in the sea.', Science advances, vol. 5, no. 8.
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All known phototrophic metabolisms on Earth rely on one of three categories of energy-converting pigments: chlorophyll-a (rarely -d), bacteriochlorophyll-a (rarely -b), and retinal, which is the chromophore in rhodopsins. While the significance of chlorophylls in solar energy capture has been studied for decades, the contribution of retinal-based phototrophy to this process remains largely unexplored. We report the first vertical distributions of the three energy-converting pigments measured along a contrasting nutrient gradient through the Mediterranean Sea and the Atlantic Ocean. The highest rhodopsin concentrations were observed above the deep chlorophyll-a maxima, and their geographical distribution tended to be inversely related to that of chlorophyll-a. We further show that proton-pumping proteorhodopsins potentially absorb as much light energy as chlorophyll-a-based phototrophy and that this energy is sufficient to sustain bacterial basal metabolism. This suggests that proteorhodopsins are a major energy-transducing mechanism to harvest solar energy in the surface ocean.

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, 'Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015-2016 heatwave (vol 38, pg 815, 2019)', 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, pp. 855-866.
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© 2019 John Wiley & Sons, Ltd. Hypolimnial 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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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.

Haro, S, Brodersen, KE, Bohórquez, J, Papaspyrou, S, Corzo, A & Kühl, M 2019, 'Radiative Energy Budgets in a Microbial Mat Under Different Irradiance and Tidal Conditions.', Microbial ecology, vol. 77, no. 4, pp. 852-865.
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Irradiance and temperature variations during tidal cycles modulate microphytobenthic primary production potentially by changing the radiative energy balance of photosynthetic mats between immersion and emersion and thus sediment daily net metabolism. To test the effect of tidal stages on the radiative energy budget, we used microsensor measurements of oxygen, temperature, and scalar irradiance to estimate the radiative energy budget in a coastal photosynthetic microbial mat during immersion (constant water column of 2 cm) and emersion under increasing irradiance. Total absorbed light energy was higher in immersion than emersion, due to a lower reflectance of the microbial mat, while most (> 97%) of the absorbed light energy was dissipated as heat irrespective of tidal conditions. During immersion, the upward heat flux was higher than the downward one, whereas the opposite occurred during emersion. At highest photon irradiance (800 μmol photon m-2 s-1), the sediment temperature increased ~ 2.5 °C after changing the conditions from immersion to emersion. The radiative energy balance showed that less than 1% of the incident light energy (PAR, 400-700 nm) was conserved by photosynthesis under both tidal conditions. At low to moderate incident irradiances, the light use efficiency was similar during the tidal stages. In contrast, we found an ~ 30% reduction in the light use efficiency during emersion as compared to immersion under the highest irradiance likely due to the rapid warming of the sediment during emersion and increased non-photochemical quenching. These changes in the photosynthetic efficiency and radiative energy budget could affect both primary producers and temperature-dependent bacterial activity and consequently daily net metabolism rates having important ecological consequences.

Hewson, I, Sullivan, B, Jackson, EW, Xu, Q, Long, H, Lin, C, Carde, EMQ, 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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Hoppenrath, M, Kretzschmar, AL, Kaufmann, MJ & Murray, SA 2019, 'Morphological and molecular phylogenetic identification and record verification of Gambierdiscus excentricus (Dinophyceae) from Madeira Island (NE Atlantic Ocean)', Marine Biodiversity Records, vol. 12, no. 1.
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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.
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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 microenvironment, across geographically discrete sampling...

Jacques, SL, Wangpraseurt, D & Kühl, M 2019, 'Optical properties of living corals determined with diffuse reflectance spectroscopy', Frontiers in Marine Science, vol. 6, no. JUL.
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© 2019 Jacques, Wangpraseurt and Kühl. The internal light field and thus light exposure of the photosymbiotic microalgae (Symbiodinium sp.) in corals is strongly modulated by the optical properties of coral tissue and skeleton. While there are numerous studies documenting the light microenvironment in corals, there are only few measurements of the inherent optical properties of corals in the literature, and this has hampered a more quantitative understanding of coral optics. Here we present a study of the optical properties of 26 live coral samples, representative of 11 coral species and spanning a variety of morphotypes. We employed well-established fiber-optic reflectance spectroscopy techniques from biomedical optics using two methods: (1) A source and a detection fiber separated by a variable distance measured the lateral spread of light in corals, dominated by the skeleton; (2) A fiber-optic field radiance probe measured the diffuse reflectance from the coral surface, dominated by the living coral tissue. Analysis based on diffusion theory and Monte Carlo simulation yielded estimates of the bulk scattering and absorption coefficients of the coral tissue and skeleton, in the 750-1030 nm wavelength range. Extrapolating into the spectral region of photosynthetically active radiation (PAR, 400-700 nm) allowed estimation of the optical depth of absorption by the main Symbiodinium photopigment chlorophyll a. Coral tissue scattering was on average ~1.9x stronger than the scattering of the skeleton, consistent with the model that corals trap photons by high scattering to enhance absorption by algal pigments, while the lower scattering of the skeleton allows spread of light to otherwise shaded coral tissue areas.

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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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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1. Identification 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. 2. 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. 3. 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. 4. 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, JH, Kim, H, Kang, D, Lim, YK, Ajani, P, Jung, SW & Baek, SH 2019, 'Field application and validity of a red-tide acoustic sensing system (RASS) for monitoring and alerting of harmful algal blooms (HABs) in Korean coastal waters', Journal of Applied Phycology.
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Kim, M, Pernice, M, Watson-Lazowski, A, Guagliardo, P, Kilburn, MR, Larkum, AWD, Raven, JA & Ralph, PJ 2019, 'Effect of reduced irradiance on 13C uptake, gene expression and protein activity of the seagrass Zostera muelleri.', Marine environmental research, vol. 149, pp. 80-89.
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Photosynthesis in the seagrass Zostera muelleri remains poorly understood. We investigated the effect of reduced irradiance on the incorporation of 13C, gene expression of photosynthetic, photorespiratory and intermediates recycling genes as well as the enzymatic content and activity of Rubisco and PEPC within Z. muelleri. Following 48 h of reduced irradiance, we found that i) there was a ∼7 fold reduction in 13C incorporation in above ground tissue, ii) a significant down regulation of photosynthetic, photorespiratory and intermediates recycling genes and iii) no significant difference in enzyme activity and content. We propose that Z. muelleri is able to alter its physiology in order to reduce the amount of C lost through photorespiration to compensate for the reduced carbon assimilation as a result of reduced irradiance. In addition, the first estimated rate constant (Kcat) and maximum rates of carboxylation (Vcmax) of Rubisco is reported for the first time for Z. muelleri.

King, WL, Jenkins, C, Go, J, Siboni, N, Seymour, JR & Labbate, M 2019, 'Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event.', Microbial Ecology, vol. 77, pp. 502-512.
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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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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, 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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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 detrimental role in OsHV-1 μvar disease outbreaks.

Koren, K, Moßhammer, M, Scholz, VV, Borisov, SM, Holst, G & Kühl, M 2019, 'Luminescence Lifetime Imaging of Chemical Sensors-A Comparison between Time-Domain and Frequency-Domain Based Camera Systems.', Analytical chemistry, vol. 91, no. 5, pp. 3233-3238.
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Luminescence lifetime based imaging is still the most reliable method for generating chemical images using chemical sensor technology. However, only few commercial systems are available that enable imaging lifetimes within the relevant nanosecond to microsecond range. In this technical note we compare the performance of an older time-domain (TD) based camera system with a frequency-domain (FD) based camera system regarding their measuring characteristics and applicability for O2 and pH imaging in environmental samples and with different indicator dye systems emitting in the visible and near-infrared part of the spectrum. We conclude that the newly introduced FD imaging system delivers comparable if not better results than its predecessor, now enabling robust and simple chemical imaging based on FD luminescence lifetime measurements.

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.
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Kretzschmar, AL, Verma, A, Kohli, G & Murray, S 2019, 'Development of a quantitative PCR assay for the detection and enumeration of a potentially ciguatoxin-producing dinoflagellate, Gambierdiscus lapillus (Gonyaulacales, Dinophyceae)'.
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Ciguatera fish poisoning is an illness contracted through the ingestion of seafood containing ciguatoxins. It is prevalent in tropical regions worldwide, including in Australia. Ciguatoxins are produced by some species of Gambierdiscus. Therefore, screening of Gambierdiscus species identification through quantitative PCR (qPCR), along with the determination of species toxicity, can be useful in monitoring potential ciguatera risk in these regions. In Australia, the identity, distribution and abundance of ciguatoxin producing Gambierdiscus spp. is largely unknown. In this study we developed a rapid qPCR assay to quantify the presence and abundance of Gambierdiscus lapillus, a likely ciguatoxic species. We assessed the specificity and efficiency of the qPCR assay. The assay was tested on 25 environmental samples from the Heron Island reef in the southern Great Barrier Reef, a ciguatera endemic region, in triplicate to determine the presence and patchiness of these species across samples from Chnoospora sp., Padina sp. and Sargassum macroalgal hosts.

Kretzschmar, AL, Verma, A, Kohli, G & Murray, S 2019, 'Development of a quantitative PCR assay for the detection and enumeration of a potentially ciguatoxin-producing dinoflagellate, Gambierdiscus lapillus (Gonyaulacales, Dinophyceae).', PloS one, vol. 14, no. 11.
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Ciguatera fish poisoning (CFP) is an illness contracted through the ingestion of seafood containing ciguatoxins. It is prevalent in tropical regions worldwide, including in Australia. Ciguatoxins are produced by some species of Gambierdiscus. Therefore, screening of Gambierdiscus species identification through quantitative PCR (qPCR), along with the determination of species toxicity, can be useful in monitoring potential ciguatera risk in these regions. In Australia, CFP is prevalent in tropical Queensland and increasingly in sub-tropical regions of Australia, but has a report rate of approximately 10%. Yet the identity, distribution and abundance of ciguatoxin producing Gambierdiscus spp. is largely unknown. In this study, we developed a rapid qPCR assay to quantify the presence and abundance of Gambierdiscus lapillus, a likely ciguatoxic species first described from Australia. We assessed the specificity and efficiency of the qPCR assay. The assay was tested on 25 environmental samples from the Heron Island reef in the southern Great Barrier Reef, a ciguatera endemic region, to determine the presence and patchiness of this species across samples from Chnoospora sp., Padina sp. and Sargassum sp. macroalgal hosts.

Kretzschmar, AL, Verma, A, Murray, S, Kahlke, T, Fourment, M & Darling, A 2019, 'Trial by phylogenetics - Evaluating the Multi-Species Coalescent for phylogenetic inference on taxa with high levels of paralogy (Gonyaulacales, Dinophyceae)'.
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ABSTRACT From publicly available next-gen sequencing datasets of non-model organisms, such as marine protists, arise opportunities to explore their evolutionary relationships. In this study we explored the effects that dataset and model selection have on the phylogenetic inference of the Gonyaulacales, single celled marine algae of the phylum Dinoflagellata with genomes that show extensive paralogy. We developed a method for identifying and extracting single copy genes from RNA-seq libraries and compared phylogenies inferred from these single copy genes with those inferred from commonly used genetic markers and phylogenetic methods. Comparison of two datasets and three different phylogenetic models showed that exclusive use of ribosomal DNA sequences, maximum likelihood and gene concatenation showed very different results to that obtained with the multi-species coalescent. The multi-species coalescent has recently been recognized as being robust to the inclusion of paralogs, including hidden paralogs present in single copy gene sets (pseudoorthologs). Comparisons of model fit strongly favored the multi-species coalescent for these data, over a concatenated alignment (single tree) model. Our findings suggest that the multi-species coalescent (inferred either via Maximum Likelihood or Bayesian Inference) should be considered for future phylogenetic studies of organisms where accurate selection of orthologs is difficult.

Larsson, ME, Harwood, TD, Lewis, RJ, Himaya, SWA & 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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© 2018 Japanese Society of Phycology Dinoflagellates 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 Coolia and provides important information to help define species distributions and inform risk management.

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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Biogenic 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 Symbiodiniaceae, which potentially have, as yet unexplored, physiological and ecological importance in shaping coral reef community functioning.

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 : CB, vol. 29, no. 16, pp. 2723-2730.
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Severe marine heatwaves have recently become a common feature of global ocean conditions due to a rapidly changing climate [1, 2]. These increasingly severe thermal conditions are causing an unprecedented increase in the frequency and severity of mortality events in marine ecosystems, including on coral reefs [3]. The degradation of coral reefs will result in the collapse of ecosystem services that sustain over half a billion people globally [4, 5]. Here, we show that marine heatwave events on coral reefs are biologically distinct to how coral bleaching has been understood to date, in that heatwave conditions result in an immediate heat-induced mortality of the coral colony, rapid coral skeletal dissolution, and the loss of the three-dimensional reef structure. During heatwave-induced mortality, the coral skeletons exposed by tissue loss are, within days, encased by a complex biofilm of phototrophic microbes, whose metabolic activity accelerates calcium carbonate dissolution to rates exceeding accretion by healthy corals and far greater than has been documented on reefs under normal seawater conditions. This dissolution reduces the skeletal density and hardness and increases porosity. These results demonstrate that severe-heatwave-induced mortality events should be considered as a distinct biological phenomenon from bleaching events on coral reefs. We also suggest that such heatwave mortality events, and rapid reef decay, will become more frequent as the intensity of marine heatwaves increases and provides further compelling evidence for the need to mitigate climate change and instigate actions to reduce marine heatwaves.

Leles, SG, Mitra, A, Flynn, KJ, Tillmann, U, Stoecker, D, Jeong, HJ, Burkholder, JA, Hansen, PJ, Caron, DA, Glibert, PM, Hallegraeff, G, Raven, JA, Sanders, RW & Zubkov, M 2019, 'Sampling bias misrepresents the biogeographical significance of constitutive mixotrophs across global oceans', Global Ecology and Biogeography, vol. 28, no. 4, pp. 418-428.
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© 2019 John Wiley & Sons Ltd Aim: Most protist plankton are mixotrophic, with potential to engage in photoautotrophy and phagotrophy; however, the ecology of these organisms has been misdiagnosed for over a century. A large proportion of these organisms are constitutive mixotrophs (CMs), with an innate ability to photosynthesize. Here, for the first time, an analysis is presented of the biogeography of CMs across the oceans. Location: Global marine ecosystems. Time period: 1970–2018. Major taxa studied: Marine planktonic protists. Methods: Records for CM species, primarily from the Ocean Biogeographic Information System (OBIS), were grouped by taxonomy and size to evaluate sampling efforts across Longhurst's oceanic provinces. Biases were evaluated through nonparametric tests and multivariate analysis. Biogeographies of CMs from OBIS data were compared with data from studies that specifically targeted these organisms. Results: Constitutive mixotrophs of different taxonomic groups, across all size ranges, are ubiquitous. However, strong database biases were detected with respect to organism size, taxonomic groups and region. A strong bias was seen towards dinophytes. Species < 20 µm, especially non-dinophytes, were least represented, with their recorded distribution limited to coastal regions and to temperate and polar seas. Studies specifically targeting these organisms revealed their distribution to be much wider. Such biases are likely to have occurred owing to a failure to capture and correctly identify these organisms in routine sampling protocols. Main conclusions: Constitutive mixotrophs are dominant members of organisms traditionally termed “phytoplankton”. However, lack of routine protocols for measuring phagotrophy in “phytoplankton” protists has led to widespread misrepresentation of the fundamental nature of marine planktonic primary producers; most express both “animal-like” and “plant-like” nutrition. Our results have implications for studies of th...

Liao, J, Ye, J, Liang, Y, Khalid, M & Huang, D 2019, 'Pakchoi antioxidant improvement and differential rhizobacterial community composition under organic fertilization', Sustainability (Switzerland), vol. 11, no. 8.
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© 2019 by the authors. A high level of antioxidants in organic-produced vegetables has been attributed to soil conditions; however, little is known about the relationships between antioxidants and rhizobacteria under different fertilization treatments. A pot trial for pakchoi (Brassica campestris ssp. chinensis L.) was conducted under greenhouse conditions with: (1) control; (2) chemical fertilizer; and (3) organic fertilizer. The responses of the plant, soil properties, and rhizobacterial community were measured after 45 days of cultivation. Fertilization increased soil nutrient levels and pakchoi productivity and the reshaped rhizobacterial community structure, while no differences in rhizobacterial abundance and total diversity were observed. Generally, most plant antioxidants were negatively correlated with inorganic nitrogen (N) and positively correlated to organic N in soil. The genera of Arthrospira and Acutodesmus contained differential rhizobacteria under chemical fertilizer treatment, which are known as copiotrophs. In addition, the addition of a chemical fertilizer may stimulate organic substance turnover by the enrichment of organic compound degraders (e.g., Microbacterium and Chitinophaga) and the promotion of predicted functional pathways involved in energy metabolism. Several beneficial rhizobacteria were associated with organic fertilizer amended rhizosphere including the genera Bacillus, Mycobacterium, Actinomycetospora, and Frankia. Furthermore, Bacillus spp. were positively correlated with plant biomass and phenolic acid. Moreover, predictive functional profiles of the rhizobacterial community involved in amino acid metabolism and lipid metabolism were significantly increased under organic fertilization, which were positively correlated with plant antioxidant activity. Overall, our study suggests that the short-term application of chemical and organic fertilizers reshapes the rhizobacterial community structure, and such changes might contribute...

Liu, Y, Ge, T, Ye, J, Liu, S, Shibistova, O, Wang, P, Wang, J, Li, Y, Guggenberger, G, Kuzyakov, Y & Wu, J 2019, 'Initial utilization of rhizodeposits with rice growth in paddy soils: Rhizosphere and N fertilization effects', Geoderma, vol. 338, pp. 30-39.
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© 2018 Elsevier B.V. Rhizodeposition represents a readily available C and energy source for soil microorganisms, that plays an important role in the regulation of C and nutrient cycling in ecosystems and exerts a strong influence on C sequestration. The dynamics of rice rhizo-C in soils and its allocation to microorganisms during rice growth, as well as the effects of nitrogen (N-NH 4+ ) fertilization are poorly understood, particularly with respect to the initial uptake of rhizo-C by microorganisms and its utilization during the entire growth period. To assess these two processes, rice plants were grown in pots with or without N fertilization (0 and 225 kg N-NH 4+ ha −1 ), and 13 C incorporation into microbial groups was traced by phospholipid fatty acids (PLFAs) analysis within 6 h after 13 CO 2 pulse labeling. Labeling was performed at five growth stages: tillering, elongation, heading, filling, and maturation. 13 C incorporated into soil microbial biomass C changed rapidly at the beginning of the study period, before elongation, but remained stable thereafter. 13 C incorporation into rhizosphere and bulk soil microbial biomass was higher with than without N addition. This stimulation was likely due to the excessive increase in phytomass formation and root exudates after N fertilization and the increased assimilate C input into the soil. Structural equation modelling suggested that N fertilization strongly affected carbon transfer between rhizosphere and non-rhizosphere. Hence, N-NH 4+ application may not only increase rhizo-C flow into microorganisms but it may also increase the effect of rhizosphere on bulk-soil microorganisms and subsequent processes related to soil C-cycling.

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.', The Journal of experimental biology, vol. 222, no. Pt 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 as a result of 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 light (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 corals to HL and HL corals to LL 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 corals than for 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 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.

Lohr, KE, Khattri, RB, Guingab-Cagmat, J, Camp, EF, Merritt, ME, Garrett, TJ & Patterson, JT 2019, 'Metabolomic profiles differ among unique genotypes of a threatened Caribbean coral.', Scientific reports, vol. 9, no. 1.
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Global threats to reefs require urgent efforts to resolve coral attributes that affect survival in a changing environment. Genetically different individuals of the same coral species are known to exhibit different responses to the same environmental conditions. New information on coral physiology, particularly as it relates to genotype, could aid in unraveling mechanisms that facilitate coral survival in the face of stressors. Metabolomic profiling detects a large subset of metabolites in an organism, and, when linked to metabolic pathways, can provide a snapshot of an organism's physiological state. Identifying metabolites associated with desirable, genotype-specific traits could improve coral selection for restoration and other interventions. A key step toward this goal is determining whether intraspecific variation in coral metabolite profiles can be detected for species of interest, however little information exists to illustrate such differences. To address this gap, we applied untargeted 1H-NMR and LC-MS metabolomic profiling to three genotypes of the threatened coral Acropora cervicornis. Both methods revealed distinct metabolite "fingerprints" for each genotype examined. A number of metabolites driving separation among genotypes were identified or putatively annotated. Pathway analysis suggested differences in protein synthesis among genotypes. For the first time, these data illustrate intraspecific variation in metabolomic profiles for corals in a common garden. Our results contribute to the growing body of work on coral metabolomics and suggest future work could identify specific links between phenotype and metabolite profile in corals.

Lyndby, NH, Holm, JB, Wangpraseurt, D, Ferrier-Pagès, C & Kühl, M 2019, 'Bio-optical properties and radiative energy budgets in fed and unfed scleractinian corals (Pocillopora sp.) during thermal bleaching', Marine Ecology Progress Series, vol. 629, pp. 1-17.
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© 2019 The authors. Corals live in symbiosis with algal dinoflagellates, which can achieve outstanding photo - synthetic energy efficiencies in hospite approaching theo retical limits. However, how such photosynthetic efficiency varies with environmental stress remains poorly known. Using fiber-optic and electrochemical microsensors in combination with variable chlorophyll fluorescence imaging, we investigated the combined effects of thermal stress and active feeding on the radiative energy budget and photosynthetic efficiency of the symbiotic coral Pocillopora sp. At ambient temperature (25°C), the percentage of ab sorbed light energy used for photosynthesis under low irradiance was higher for fed (∼5-6%) compared to unfed corals (4%). Corals from both feeding treatments responded equally to stress from high light ex posure (2400 μmol photons m-2 s-1), exhibiting a de crease in photosynthetic efficiency, down to 0.5-0.6%. Fed corals showed increased resilience to thermal-induced bleaching (loss of symbionts) compared to unfed corals. In addition, while unfed corals decreased their photosynthetic efficiency almost immediately when exposed to thermal stress, fed corals maintained a constant and high photosynthetic efficiency for 5 more days after onset of thermal stress. We conclude that active feeding is beneficial to corals by prolonging coral health and resilience during thermal stress as a result of an overall healthier symbiont population.

Macreadie, PI, Anton, A, Raven, JA, Beaumont, N, Connolly, RM, Friess, DA, Kelleway, JJ, Kennedy, H, Kuwae, T, Lavery, PS, Lovelock, CE, Smale, DA, Apostolaki, ET, Atwood, TB, Baldock, J, Bianchi, TS, Chmura, GL, Eyre, BD, Fourqurean, JW, Hall-Spencer, JM, Huxham, M, Hendriks, IE, Krause-Jensen, D, Laffoley, D, Luisetti, T, Marba, N, Masque, P, McGlathery, KJ, Megonigal, JP, Murdiyarso, D, Russell, BD, Santos, R, Serrano, O, Silliman, BR, Watanabe, K & Duarte, CM 2019, 'The future of Blue Carbon science (vol 10, 3998, 2019)', NATURE COMMUNICATIONS, vol. 10.
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Macreadie, PI, Anton, A, Raven, JA, Beaumont, N, Connolly, RM, Friess, DA, Kelleway, JJ, Kennedy, H, Kuwae, T, Lavery, PS, Lovelock, CE, Smale, DA, Apostolaki, ET, Atwood, TB, Baldock, J, Bianchi, TS, Chmura, GL, Eyre, BD, Fourqurean, JW, Hall-Spencer, JM, Huxham, M, Hendriks, IE, Krause-Jensen, D, Laffoley, D, Luisetti, T, Marbà, N, Masque, P, McGlathery, KJ, Megonigal, JP, Murdiyarso, D, Russell, BD, Santos, R, Serrano, O, Silliman, BR, Watanabe, K & Duarte, CM 2019, 'The future of Blue Carbon science.', Nature communications, vol. 10, no. 1.
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The term Blue Carbon (BC) was first coined a decade ago to describe the disproportionately large contribution of coastal vegetated ecosystems to global carbon sequestration. The role of BC in climate change mitigation and adaptation has now reached international prominence. To help prioritise future research, we assembled leading experts in the field to agree upon the top-ten pending questions in BC science. Understanding how climate change affects carbon accumulation in mature BC ecosystems and during their restoration was a high priority. Controversial questions included the role of carbonate and macroalgae in BC cycling, and the degree to which greenhouse gases are released following disturbance of BC ecosystems. Scientists seek improved precision of the extent of BC ecosystems; techniques to determine BC provenance; understanding of the factors that influence sequestration in BC ecosystems, with the corresponding value of BC; and the management actions that are effective in enhancing this value. Overall this overview provides a comprehensive road map for the coming decades on future research in BC science.

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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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.

McCauley, JI, Winberg, PC, Meyer, BJ & Skropeta, D 2019, 'Corrigendum to “Effects of nutrients and processing on the nutritionally important metabolites of Ulva sp. (Chlorophyta)” (Algal Research (2018) 35 (586–594), (S2211926418305678), (10.1016/j.algal.2018.09.016))', Algal Research, vol. 40.
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© 2019 Elsevier B.V. The authors wish to make the following corrigendum. Venus Shell Systems (VSS) provided the Ulva sp. used in this study. They are listed under the author affiliations, as well as in the Methods Section 2.1 as having provided the samples. To further clarify the involvement of the company we wish to make the following changes to the Conflicts of interest section. The company Venus Shell Systems (VSS), listed in the author affiliations, provided the cultivated Ulva sp. used in this study, obtained using a proprietary culture system. The authors declare that there was no significant financial support that could have influenced the outcome of the project. The research is free of bias and was conducted ethically in accord with the University of Wollongong's policy on external research collaboration. The authors would like to apologise for any inconvenience caused.

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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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 & Houlbreque, F 2019, 'Bleaching forces coral's heterotrophy on diazotrophs and Synechococcus', ISME JOURNAL, vol. 13, no. 11, pp. 2882-2886.
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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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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 analysis identified temperature, nutrient concentrations and water depth as key drivers of the region'...

Moßhammer, M, Brodersen, KE, Kühl, M & Koren, K 2019, 'Nanoparticle- and microparticle-based luminescence imaging of chemical species and temperature in aquatic systems: a review.', Mikrochimica acta, vol. 186, no. 2.
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Most aquatic systems rely on a multitude of biogeochemical processes that are coupled with each other in a complex and dynamic manner. To understand such processes, minimally invasive analytical tools are required that allow continuous, real-time measurements of individual reactions in these complex systems. Optical chemical sensors can be used in the form of fiber-optic sensors, planar sensors, or as micro- and nanoparticles (MPs and NPs). All have their specific merits, but only the latter allow for visualization and quantification of chemical gradients over 3D structures. This review (with 147 references) summarizes recent developments mainly in the field of optical NP sensors relevant for chemical imaging in aquatic science. The review encompasses methods for signal read-out and imaging, preparation of NPs and MPs, and an overview of relevant MP/NP-based sensors. Additionally, examples of MP/NP-based sensors in aquatic systems such as corals, plant tissue, biofilms, sediments and water-sediment interfaces, marine snow and in 3D bioprinting are given. We also address current challenges and future perspectives of NP-based sensing in aquatic systems in a concluding section. Graphical abstract ᅟ.

Moßhammer, M, Scholz, VV, Holst, G, Kühl, M & Koren, K 2019, 'Luminescence Lifetime Imaging of O2 with a Frequency-Domain-Based Camera System.', Journal of visualized experiments : JoVE, no. 154.
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We describe a method to image dissolved oxygen (O2), in 2D at high spatial (< 50-100 µm) and temporal (< 10 s) resolution. The method employs O2 sensitive luminescent sensor foils (planar optodes) in combination with a specialized camera system for imaging luminescence lifetime in the frequency-domain. Planar optodes are prepared by dissolving the O2-sensitive indicator dye in a polymer and spreading the mixture on a solid support in a defined thickness via knife coating. After evaporation of the solvent, the planar optode is placed in close contact with the sample of interest - here demonstrated with the roots of the aquatic plant Littorella uniflora. The O2 concentration-dependent change in the luminescence lifetime of the indicator dye within the planar optode is imaged via the backside of the transparent carrier foil and aquarium wall using a special camera. This camera measures the luminescence lifetime (µs) via a shift in phase angle between a modulated excitation signal and emission signal. This method is superior to luminescence intensity imaging methods, as the signal is independent of the dye concentration or intensity of the excitation source, and solely relies on the luminescence decay time, which is an intrinsically referenced parameter. Consequently, an additional reference dye or other means of referencing are not needed. We demonstrate the use of the system for macroscopic O2 imaging of plant rhizospheres, but the camera system can also easily be coupled to a microscope.

Murray, SA, Ruvindy, R, Kohli, GS, Anderson, DM & Brosnahan, ML 2019, 'Evaluation of sxtA and rDNA qPCR assays through monitoring of an inshore bloom of Alexandrium catenella Group 1.', Scientific reports, vol. 9, no. 1.
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Alexandrium catenella (formerly A. tamarense Group 1, or A. fundyense) is the leading cause of Paralytic Shellfish Poisoning in North and South America, Europe, Africa, Australia and Asia. The quantification of A.catenella via sxtA, a gene involved in Paralytic Shellfish Toxin synthesis, may be a promising approach, but has not been evaluated in situ on blooms of A. catenella, in which cell abundances may vary from not detectable to in the order of 106 cells L-1. In this study, we compared sxtA assay performance to a qPCR assay targeted to a species-specific region of ribosomal DNA (rDNA) and an established fluorescent in situ hybridization (FISH) microscopy method. Passing-Bablok regression analyses revealed the sxtA assay to overestimate abundances when <5 cell equivalents A. catenella DNA were analysed, but otherwise was closer to microscopy estimates than the rDNA assay, which overestimated abundance across the full range of concentrations analysed, indicative of a copy number difference between the bloom population and a culture used for assay calibration a priori. In contrast, the sxtA assay performed more consistently, indicating less copy number variation. The sxtA assay was generally reliable, fast and effective in quantifying A. catenella and was predictive of PST contamination of shellfish.

Nguyen, LN, Commault, AS, Johir, MAH, Bustamante, H, Aurisch, R, Lowrie, R & Nghiem, LD 2019, 'Application of a novel molecular technique to characterise the effect of settling on microbial community composition of activated sludge.', Journal of environmental management, vol. 251.
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Activated sludge (AS) and return activated sludge (RAS) microbial communities from three full-scale municipal wastewater treatment plants (denoted plant A, B and C) were compared to assess the impact of sludge settling (i.e. gravity thickening in the clarifier) and profile microorganisms responsible for nutrient removal and reactor foaming. The results show that all three plants were dominated with microbes in the phyla of Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, Chloroflexi, Firmicutes, Nitrospirae, Spirochaetae, Acidobacteria and Saccharibacteria. AS and RAS shared above 80% similarity in the microbial community composition, indicating that sludge thickening does not significantly alter the microbial composition. Autotrophic and heterotrophic nitrifiers were present in the AS. However, the abundance of autotrophic nitrifiers was significantly lower than that of the heterotrophic nitrifiers. Thus, ammonium removal at these plants was achieved mostly by heterotrophic nitrification. Microbes that can cause foaming were at 3.2% abundance, and this result is well corroborated with occasional aerobic biological reactor foaming. By contrast, these microbes were not abundant (<2.1%) at plant A and C, where aerobic biological reactor foaming has not been reported.

Nguyen, LN, Johir, MAH, Commault, A, Bustamante, H, Aurisch, R, Lowrie, R & Nghiem, LD 2019, 'Impacts of mixing on foaming, methane production, stratification and microbial community in full-scale anaerobic co-digestion process.', Bioresource technology, vol. 281, pp. 226-233.
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This study investigated the impact of mixing on key factors including foaming, substrate stratification, methane production and microbial community in three full scale anaerobic digesters. Digester foaming was observed at one plant that co-digested sewage sludge and food waste, and was operated without mixing. The lack of mixing led to uneven distribution of total chemical oxygen demand (tCOD) and volatile solid (VS) as well as methane production within the digester. 16S rRNA gene-based community analysis clearly differentiated the microbial community from the top and bottom. By contrast, foaming and substrate stratification were not observed at the other two plants with internal circulation mixing. The abundance of methanogens (Methanomicrobia) at the top was about four times higher than at the bottom, correlating to much higher methane production from the top verified by ex-situ biomethane assay, causing foaming. This result is consistent with foaming potential assessment of digestate samples from the digester.

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 and Innovation, vol. 16.
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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.

Ordoñez, A, Wangpraseurt, D, Lyndby, NH, Kühl, M & Diaz-Pulido, G 2019, 'Elevated CO2 leads to enhanced photosynthesis but decreased growth in early life stages of reef building coralline algae', Frontiers in Marine Science, vol. 5, no. JAN.
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© 2019 Ordoñez, Wangpraseurt, Lyndby, Kühl and Diaz-Pulido. Crustose coralline algae (CCA) are key organisms in coral reef ecosystems, where they contribute to reef building and substrate stabilization. While ocean acidification due to increasing CO2can affect the biology, physiology and ecology of fully developed CCA, the impacts of elevated CO2on the early life stages of CCA are much less explored. We assessed the photosynthetic activity and growth of 10-day-old recruits of the reef-building crustose coralline alga Porolithon cf. onkodes exposed to ambient and enhanced CO2seawater concentration causing a downward shift in pH of ~0.3 units. Growth of the CCA was estimated using measurements of crust thickness and marginal expansion, while photosynthetic activity was studied with O2microsensors. We found that elevated seawater CO2enhanced gross photosynthesis and respiration, but significantly reduced vertical and marginal growth of the early life stages of P. cf. onkodes. Elevated CO2stimulated photosynthesis, particularly at high irradiance, likely due to increased availability of CO2, but this increase did not translate into increased algal growth as expected, suggesting a decoupling of these two processes under ocean acidification scenarios. This study confirms the sensitivity of early stages of CCA to elevated CO2and identifies complexities in the physiological processes underlying the decreased growth and abundance in these important coral reef builders upon ocean acidification.

Pernice, M & Hughes, DJ 2019, 'Forecasting global coral bleaching', NATURE CLIMATE CHANGE, vol. 9, no. 11, pp. 803-804.
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Pernice, M, Raina, JB, Rädecker, N, Cárdenas, A, Pogoreutz, C & Voolstra, CR 2019, 'Down to the bone: the role of overlooked endolithic microbiomes in reef coral health', ISME Journal.
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© 2019, The Author(s). Reef-building corals harbour an astonishing diversity of microorganisms, including endosymbiotic microalgae, bacteria, archaea, and fungi. The metabolic interactions within this symbiotic consortium are fundamental to the ecological success of corals and the unique productivity of coral reef ecosystems. Over the last two decades, scientific efforts have been primarily channelled into dissecting the symbioses occurring in coral tissues. Although easily accessible, this compartment is only 2–3 mm thick, whereas the underlying calcium carbonate skeleton occupies the vast internal volume of corals. Far from being devoid of life, the skeleton harbours a wide array of algae, endolithic fungi, heterotrophic bacteria, and other boring eukaryotes, often forming distinct bands visible to the bare eye. Some of the critical functions of these endolithic microorganisms in coral health, such as nutrient cycling and metabolite transfer, which could enable the survival of corals during thermal stress, have long been demonstrated. In addition, some of these microorganisms can dissolve calcium carbonate, weakening the coral skeleton and therefore may play a major role in reef erosion. Yet, experimental data are wanting due to methodological limitations. Recent technological and conceptual advances now allow us to tease apart the complex physical, ecological, and chemical interactions at the heart of coral endolithic microbial communities. These new capabilities have resulted in an excellent body of research and provide an exciting outlook to further address the functional microbial ecology of the “overlooked” coral skeleton.

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, 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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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.
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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.

Raven, JA, Gobler, CS & Hansen, PJ 2019, 'Dynamic CO 2 and pH levels in coastal, estuarine, and inland waters: Theoretical and observed effects on harmful algal blooms', Harmful Algae.
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© 2019 Elsevier B.V. Rising concentrations of atmospheric CO 2 results in higher equilibrium concentrations of dissolved CO 2 in natural waters, with corresponding increases in hydrogen ion and bicarbonate concentrations and decreases in hydroxyl ion and carbonate concentrations. Superimposed on these climate change effects is the dynamic nature of carbon cycling in coastal zones, which can lead to seasonal and diel changes in pH and CO 2 concentrations that can exceed changes expected for open ocean ecosystems by the end of the century. Among harmful algae, i.e. some species and/or strains of Cyanobacteria, Dinophyceae, Prymnesiophyceae, Bacillariophyceae, and Ulvophyceae, the occurrence of a CO 2 concentrating mechanisms (CCMs) is the most frequent mechanism of inorganic carbon acquisition in natural waters in equilibrium with the present atmosphere (400 μmol CO 2 mol −1 total gas), with varying phenotypic modification of the CCM. No data on CCMs are available for Raphidophyceae or the brown tide Pelagophyceae. Several HAB species and/or strains respond to increased CO 2 concentrations with increases in growth rate and/or cellular toxin content, however, others are unaffected. Beyond the effects of altered C concentrations and speciation on HABs, changes in pH in natural waters are likely to have profound effects on algal physiology. This review outlines the implications of changes in inorganic cycling for HABs in coastal zones, and reviews the knowns and unknowns with regard to how HABs can be expected to ocean acidification. We further point to the large regions of uncertainty with regard to this evolving field.

Ricci, F, Rossetto Marcelino, V, Blackall, LL, Kühl, M, Medina, M & Verbruggen, H 2019, 'Beneath the surface: community assembly and functions of the coral skeleton microbiome.', Microbiome, vol. 7, no. 1.
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Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.

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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Marine 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 of ecological niches and to become the most succes...

Sanchez, F, Geffroy, S, Norest, M, Yau, S, Moreau, H & Grimsley, N 2019, 'Simplified Transformation of Ostreococcus tauri Using Polyethylene Glycol.', Genes, vol. 10, no. 5.
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Ostreococcustauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13-22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave >104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20-40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome.

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.
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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.
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Policies 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.
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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.

Simoniello, C, Jencks, J, Lauro, FM, Loftis, JD, Weslawski, JM, Deja, K, Forrest, DR, Gossett, S, Jeffries, TC, Jensen, RM, Kobara, S, Nolan, L, Ostrowski, M, Pounds, D, Roseman, G, Basco, O, Gosselin, S, Reed, A, Wills, P & Wyatt, D 2019, 'Citizen-science for the future: Advisory case studies from around the globe', Frontiers in Marine Science, vol. 6, no. May.
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© 2019 Simoniello, Jencks, Lauro, Loftis, Weslawski, Deja, Forrest, Gossett, Jeffries, Jensen, Kobara, Nolan, Ostrowski, Pounds, Roseman, Basco, Gosselin, Reed, Wills and Wyatt. The democratization of ocean observation has the potential to add millions of observations every day. Though not a solution for all ocean monitoring needs, citizen scientists offer compelling examples showcasing their ability to augment and enhance traditional research and monitoring. Information they are providing is increasing the spatial and temporal frequency and duration of sampling, reducing time and labor costs for academic and government monitoring programs, providing hands-on STEM learning related to real-world issues and increasing public awareness and support for the scientific process. Examples provided here demonstrate the wide range of people who are already dramatically reducing gaps in our global observing network while at the same time providing unique opportunities to meaningfully engage in ocean observing and the research and conservation it supports. While there are still challenges to overcome before widespread inclusion in projects requiring scientific rigor, the growing organization of international citizen science associations is helping to reduce barriers. The case studies described support the idea that citizen scientists should be part of an effective global strategy for a sustained, multidisciplinary and integrated observing system.

Simoniello, C, Jencks, J, Lauro, FM, Loftis, JD, Weslawski, JM, Deja, K, Forrest, DR, Gossetts, S, Jeffries, TC, Jensen, RM, Kobara, S, Nolan, L, Ostrowski, M, Pounds, D, Roseman, G, Basco, O, Gosselin, S, Reed, A, Wills, P & Wyatt, D 2019, 'Citizen-Science for the Future: Advisory Case Studies From Around the Globe', Frontiers in Marine Science, vol. 6.
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Spicer, GLC, Eid, A, Wangpraseurt, D, Swain, TD, Winkelmann, JA, Yi, J, Kühl, M, Marcelino, LA & Backman, V 2019, 'Author Correction: Measuring light scattering and absorption in corals with Inverse Spectroscopic Optical Coherence Tomography (ISOCT): a new tool for non-invasive monitoring.', Scientific reports, vol. 9, no. 1, pp. 18056-18056.
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Spicer, GLC, Eid, A, Wangpraseurt, D, Swain, TD, Winkelmann, JA, Yi, J, Kühl, M, Marcelino, LA & Backman, V 2019, 'Measuring light scattering and absorption in corals with Inverse Spectroscopic Optical Coherence Tomography (ISOCT): a new tool for non-invasive monitoring.', Scientific reports, vol. 9, no. 1.
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The success of reef-building corals for >200 million years has been dependent on the mutualistic interaction between the coral host and its photosynthetic endosymbiont dinoflagellates (family Symbiodiniaceae) that supply the coral host with nutrients and energy for growth and calcification. While multiple light scattering in coral tissue and skeleton significantly enhance the light microenvironment for Symbiodiniaceae, the mechanisms of light propagation in tissue and skeleton remain largely unknown due to a lack of technologies to measure the intrinsic optical properties of both compartments in live corals. Here we introduce ISOCT (inverse spectroscopic optical coherence tomography), a non-invasive approach to measure optical properties and three-dimensional morphology of living corals at micron- and nano-length scales, respectively, which are involved in the control of light propagation. ISOCT enables measurements of optical properties in the visible range and thus allows for characterization of the density of light harvesting pigments in coral. We used ISOCT to characterize the optical scattering coefficient (μs) of the coral skeleton and chlorophyll a concentration of live coral tissue. ISOCT further characterized the overall micro- and nano-morphology of live tissue by measuring differences in the sub-micron spatial mass density distribution (D) that vary throughout the tissue and skeleton and give rise to light scattering, and this enabled estimates of the spatial directionality of light scattering, i.e., the anisotropy coefficient, g. Thus, ISOCT enables imaging of coral nanoscale structures and allows for quantifying light scattering and pigment absorption in live corals. ISOCT could thus be developed into an important tool for rapid, non-invasive monitoring of coral health, growth and photophysiology with unprecedented spatial resolution.

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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The 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 & Smith, DJ 2019, 'Coral bleaching patterns are the outcome of complex biological and environmental networking', GLOBAL CHANGE BIOLOGY, vol. 26, no. 1, pp. 68-79.
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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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© 2018 Society for Ecological Restoration 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.
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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.
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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 coupled with nutrient...

Teoh, F, Shah, B, Ostrowski, M & Paulsen, I 2019, 'Comparative membrane proteomics reveal contrasting adaptation strategies for coastal and oceanic marine Synechococcus cyanobacteria.', Environmental microbiology.
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Marine cyanobacteria genus Synechococcus are among the most abundant and widespread primary producers in the open ocean. Synechococcus strains belonging to different clades have adapted distinct strategies for growth and survival across a range of marine conditions. Clades I and IV are prevalent in colder, mesotrophic, coastal waters, while clades II and III prefer warm, oligotrophic open oceans. To gain insight into the cellular resources these unicellular organisms invest into adaptation strategies we performed shotgun membrane proteomics of four Synechococcus spp. strains namely CC9311 (clade I), CC9605 (clade II), WH8102 (clade III) and CC9902 (clade IV). Comparative membrane proteomes analysis demonstrated that CC9902 and WH8102 showed high resource allocation for phosphate uptake, accounting for 44% and 38% of overall transporter protein expression of the species. WH8102 showed high expression of the iron uptake ABC binding protein FutA, suggesting that high binding affinity for iron is possibly a key adaptation strategy for some strains in oligotrophic ocean environments. One protein annotated as a phosphatase 2c (Sync_2505 and Syncc9902_0387) was highly expressed in the coastal mesotrophic strains CC9311 and CC9902, constituting 14-16% of total membrane protein, indicating a vital, but undefined function, for strains living in temperate mesotrophic environments. This article is protected by copyright. All rights reserved.

Thomson, A, Trevathan-Tackett, S, Ralph, P, Macreadie, P & Maher, D 2019, 'Bioturbator-stimulated loss of seagrass sediment carbon stocks', Limnology and Oceanography, vol. 64, pp. 342-356.
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Seagrass 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 seagrass sediment carbon stocks.

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 and 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.

Verma, A, Barua, A, Ruvindy, R, Savela, H, Ajani, PA & Murray, SA 2019, 'The Genetic Basis of Toxin Biosynthesis in Dinoflagellates.', Microorganisms, vol. 7, no. 8.
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In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.

Verma, A, Kazandjian, A, Sarowar, C, Harwood, DT, Murray, JS, Pargmann, I, Hoppenrath, M & Murray, SA 2019, 'Morphology and Phylogenetics of Benthic Prorocentrum Species (Dinophyceae) from Tropical Northwestern Australia.', Toxins, vol. 11, no. 10.
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Approximately 70 species of Prorocentrum are known, of which around 30 species are associated with benthic habitats. Some produce okadaic acid (OA), dinophysistoxin (DTX) and their derivatives, which are involved in diarrhetic shellfish poisoning. In this study, we isolated and characterized Prorocentrum concavum and P. malayense from Broome in north Western Australia using light and scanning electron microscopy as well as molecular sequences of large subunit regions of ribosomal DNA, marking the first record of these species from Australian waters. The morphology of the motile cells of P. malayense was similar to P. concavum in the light microscopy, but differed by the smooth thecal surface, the pore pattern and the production of mucous stalk-like structures and a hyaline sheath around the non-motile cells. P. malayense could also be differentiated from other closely related species, P. leve and P. foraminosum, despite the similarity in thecal surface and pore pattern, by its platelet formula and morphologies. We tested the production of OA and DTXs from both species, but found that they did not produce detectable levels of these toxins in the given culturing conditions. This study aids in establishing more effective monitoring of potential harmful algal taxa in Australian waters for aquaculture and recreational purposes.

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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Wangpraseurt, D, Jacques, S, Lyndby, N, Holm, JB, Pages, CF & Kuhl, M 2019, 'Microscale light management and inherent optical properties of intact corals studied with optical coherence tomography', JOURNAL OF THE ROYAL SOCIETY INTERFACE, vol. 16, no. 151.
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Wangpraseurt, D, Larkum, AWD, Ferrier-Pages, C, Salih, A, Warner, ME, Dubinsky, Z & Kuhl, 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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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 F 0, Fm , and Fv /Fm in hydrogels with identical light absorption but different degrees of light scattering. Likewise, differences in microalgal density affected variable Chl fluorescence parameters, where higher algal densities led to greater Fv /Fm values and relative electron transport rates. These results have important implications for the use of variable Chl fluorimetry in ecophysiological studies of coral stress and photosynthesis, as well as other optically dense systems such as plant tissue and biofilms.

Wu, S, Gu, W, Huang, A, Li, Y, Kumar, M, Lim, PE, Huan, L, Gao, S & Wang, G 2019, 'Elevated CO2 improves both lipid accumulation and growth rate in the glucose-6-phosphate dehydrogenase engineered Phaeodactylum tricornutum.', Microbial cell factories, vol. 18, no. 1.
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BACKGROUND:Numerous studies have shown that stress induction and genetic engineering can effectively increase lipid accumulation, but lead to a decrease of growth in the majority of microalgae. We previously found that elevated CO2 concentration increased lipid productivity as well as growth in Phaeodactylum tricornutum, along with an enhancement of the oxidative pentose phosphate pathway (OPPP) activity. The purpose of this work directed toward the verification of the critical role of glucose-6-phosphate dehydrogenase (G6PDH), the rate-limiting enzyme in the OPPP, in lipid accumulation in P. tricornutum and its simultaneous rapid growth rate under high-CO2 (0.15%) cultivation. RESULTS:In this study, G6PDH was identified as a target for algal strain improvement, wherein G6PDH gene was successfully overexpressed and antisense knockdown in P. tricornutum, and systematic comparisons of the photosynthesis performance, algal growth, lipid content, fatty acid profiles, NADPH production, G6PDH activity and transcriptional abundance were performed. The results showed that, due to the enhanced G6PDH activity, transcriptional abundance and NAPDH production, overexpression of G6PDH accompanied by high-CO2 cultivation resulted in a much higher of both lipid content and growth in P. tricornutum, while knockdown of G6PDH greatly decreased algal growth as well as lipid accumulation. In addition, the total proportions of saturated and unsaturated fatty acid, especially the polyunsaturated fatty acid eicosapentaenoic acid (EPA; C20:5, n-3), were highly increased in high-CO2 cultivated G6PDH overexpressed strains. CONCLUSIONS:The successful of overexpression and antisense knockdown of G6PDH well demonstrated the positive influence of G6PDH on algal growth and lipid accumulation in P. tricornutum. The improvement of algal growth, lipid content as well as polyunsaturated fatty acids in high-CO2 cultivated G6PDH overexpressed P. tricornutum suggested this G6PDH overexpression-high CO...

Xie, Q, Dash, J, Huete, A, Jiang, A, Yin, G, Ding, Y, Peng, D, Hall, CC, Brown, L, Shi, Y, Ye, H, Dong, Y & Huang, W 2019, 'Retrieval of crop biophysical parameters from Sentinel-2 remote sensing imagery', International Journal of Applied Earth Observation and Geoinformation, vol. 80, pp. 187-195.
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Xie, Z, Huete, A, Cleverly, J, Phinn, S, McDonald-Madden, E, Cao, Y & Qin, F 2019, 'Multi-climate mode interactions drive hydrological and vegetation responses to hydroclimatic extremes in Australia', Remote Sensing of Environment, vol. 231.
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© 2019 Australia has experienced a large frequency of hydroclimatic events since the early 21st century, with multiple large-scale droughts and flooding rains exerting dramatic impacts on water resources and ecosystems. Despite these pronounced consequences, the coupling of ecosystem functioning to extreme climate variability remains elusive due to the lack of complete understanding of hydrological connections. In this study, we investigated the spatiotemporal trends of Australia's hydrological and vegetation responses to three climate modes: El Niño-Southern Oscillation, the Indian Ocean dipole and the Southern Annular Mode, utilizing climate indices, satellite-derived total water storage anomaly (TWSA) from GRACE, precipitation from TRMM and vegetation greenness from MODIS. Using partial cross-correlation and vegetation sensitivity analyses to interpret the interactions among climate modes, water resources and vegetation across Australia, three hydroclimatic extreme events from 2002 to 2017 were analyzed: (i) a prolonged drought (2002–09, colloquially known as the ‘big dry’); (ii) a dramatic wet pulse (2010–11, the ‘big wet’); and (iii) another anomalous El Niño event (2015). Our results showed the entire continent partitioned into three geographic zones with diverse drying and wetting trends in total water storage, precipitation and vegetation greenness, reflecting varying and fundamental influences from the individual climate modes. Ecosystem productivity was found to be better related and more sensitive to TWSA than precipitation across different hydroclimate zones and during both extreme dry and wet conditions. We also observed TWSA increased rapidly during wet extremes, and these gains in water resources persisted for an additional four years (i.e., TWSA remained positive until 2015 following the 2011 ‘big wet’). Lastly, findings from another hydroclimatic event (the 2015 El Niño drought) further confirmed the relationships among climate, water and ecosyst...

You, F, Zhang, L, Ye, J & Huang, L 2019, 'Microbial decomposition of biomass residues mitigated hydrogeochemical dynamics in strongly alkaline bauxite residues.', The Science of the total environment, vol. 663, pp. 216-226.
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Effective neutralization of strongly alkaline conditions in bauxite residues (BR) is the fundamental step to initiate the process of eco-engineering BR into growth substrate (or soil-like medium) for direct phytostabilization with pioneer plant species. The present study aimed to evaluate the effectiveness of microbial decomposition of organic matter (OM) (i.e., biomass residues) in neutralizing the strong alkalinity of residues under saturated conditions, together with the regulatory role of calcium sulfate (CaSO4) addition. Admixing OM (i.e., sugarcane mulch, Lucerne hay) alone in the BR significantly lowered the porewater pH from 11.4 to around 9.0 by Day 7, which persisted until the end of incubation (Day 28). The pH reduction in the porewater of OM-amended BR coincided with the production of acidic organic compounds (mainly acetic acid). Diverse species of organotrophic bacteria (e.g., Enterobacteriales, Pasteurellales, Lactobacillales, and Streptophyta) were found to have colonized in the OM-amended BR, but which were dominated by haloalkaliphilic bacteria (e.g., Halomonas and Bacillaceae). The CaSO4 addition in the OM-amended BR further lowered pH to 8.3 in the porewater. Besides, the bioneutralization effects resulted in dramatic reduction (>90%) of soluble Al in the porewater, which is a prerequisite to lowering Al toxicity in plants. At the same time, the levels of major cations (i.e., K, Ca, Mg) in the porewater were elevated by the OM + CaSO4 amendment, which would facilitate subsequent leaching of these soluble salts to lower the salinity in the BR, and improve the diversity of organotrophic bacterial communities in the amended BR.

Zapata, J, Meynard, A, Anguita, C, Espinoza, C, Alvear, P, Kumar, M & Contreras-Porcia, L 2019, 'Non-Random Distribution and Ecophysiological Differentiation of Pyropia Species (Bangiales, Rhodophyta) Through Environmental Gradients.', Journal of phycology, vol. 55, no. 5, pp. 1140-1153.
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Recently 18 Bangiales seaweed species were reported for the Chilean coast, including Pyropia orbicularis and Pyropia variabilis (large [LM] and green [GM] morphotypes). Porphyra/Pyropia spp. occur mainly in the upper intertidal where desiccation stress is triggered by tidal fluctuations. However, the influence of environmental and ecophysiological variables and seasonal differences on Porphyra/Pyropia (microhabitats) intertidal distributions is unknown. Accordingly, we determined (i) the effect of environmental variables (temperature [T], relative humidity [RH], and photosynthetically active radiation [PAR]) and season on distribution, and (ii) physiological (cellular activity and lipid peroxidation [LPX]) and molecular responses (antioxidant enzymes expression at biochemical and transcript level) to desiccation stress in both Pyropia species and morphotypes (common garden experiment, on flat rocky platforms). Multivariate analyses of coverage and abundance in relation to environmental variables revealed a significant effect of temperature on P. variabilis GM distribution, GM dominating almost exclusively on rocky walls (where lowest PAR and T values but maximum RH were registered). Conversely, Pyropia orbicularis and Pyropia variabilis LM were found in high abundance on flat rocky platforms in summer, LM and GM also dominating flat rocky platforms in winter and spring. LPX and catalase activity did not differed among species in summer, while in winter activity and transcription of cat were higher in P. orbicularis than P. variabilis. Results suggest that tolerance to environmental stresses such as temperature could regulate the occurrence of P. variabilis GM on rocky walls; conversely, abundances of P. variabilis and P. orbicularis on flat rocky platforms would be also regulated by other abiotic and/or biotic factors.

Zavafer, A, Iermak, I, Cheah, MH & Chow, WS 2019, 'Two Quenchers Formed During Photodamage of Phostosystem II and The Role of One Quencher in Preemptive Photoprotection.', Scientific reports, vol. 9, no. 1.
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The quenching of chlorophyll fluorescence caused by photodamage of Photosystem II (qI) is a well recognized phenomenon, where the nature and physiological role of which are still debatable. Paradoxically, photodamage to the reaction centre of Photosystem II is supposed to be alleviated by excitation quenching mechanisms which manifest as fluorescence quenchers. Here we investigated the time course of PSII photodamage in vivo and in vitro and that of picosecond time-resolved chlorophyll fluorescence (quencher formation). Two long-lived fluorescence quenching processes during photodamage were observed and were formed at different speeds. The slow-developing quenching process exhibited a time course similar to that of the accumulation of photodamaged PSII, while the fast-developing process took place faster than the light-induced PSII damage. We attribute the slow process to the accumulation of photodamaged PSII and the fast process to an independent quenching mechanism that precedes PSII photodamage and that alleviates the inactivation of the PSII reaction centre.

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, no. May.
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© 2019 Zhu, Suggett, Liu, He, Lin, Le, Ishizaka, Goes and Hao. Predicting conversion of photosynthetic electron transport to inorganic carbon uptake rates (the so-called electron requirement for carbon fixation, KC) is central to the broad scale deployment of Fast Repetition Rate fluorometry (FRRf) for primary productivity studies. However, reconciling variability of KC over space and time to produce robust algorithms remains challenging, given the large number of factors that influence KC. We have previously shown that light appears to be a proximal driver of Kc in several ocean regions and we therefore examined whether and how light similarly regulated KC variability in the Arctic Ocean, during a summer cruise in 2016. Sampling transited ice-free and ice-covered waters, with temperature, salinity and Chl-a concentrations all higher for the ice-free than ice covered surface waters. Micro- and pico-phytoplankton generally dominated the ice-free and ice-covered waters, respectively. Values of KC, determined from parallel measures of daily integrated electron transport rates and 14C-uptake, were overall lower for the ice-covered vs. ice-free stations. As in our previous studies, KC was strongly linearly correlated to daily PAR (r = 0.68, n = 46, p < 0.001) and this relationship could be further improved (r = 0.84, n = 46, p < 0.001) by separating samples into ice-free (micro-phytoplankton dominated) vs. ice-covered (Nano- and Pico-phytoplankton dominated water. We subsequently contrasted the PAR-KC relationship form the Arctic waters with the previous relationships from the Ariake Bay and East China Sea and revealed that these various PAR-KC relationships can be systematically explained across regions by phytoplankton community size structures. Specifically, the value of the linear slope describing PAR-KC decreases as water bodies have an increasing fraction of larger phytoplankton. We propose that this synoptic trend reflects how phytoplankton community structure ...

Ajani, P, Farrell, H, Hallegraeff, G, Helleren, S, Lamb, P, Turnbull, A, Zammit, A & Murray, S 2019, 'Diarrhetic Shellfish Toxins in Australian Shellfish', Australian Shellfish Quality Assurance Advisory Committee's National Shellfish Symposium, Perth, WA.

Akkineni, AR, Trampe, E, Koren, K, Lode, A, Krujatz, F, Kühl, M & Gelinsky, M 2019, 'In situ quantification of local O2 concentration in 3D bioprinted constructs using luminescent nanoparticles', Transactions of the Annual Meeting of the Society for Biomaterials and the Annual International Biomaterials Symposium, p. 135.
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© 2019 Omnipress - All rights reserved. One major limitation of tissue engineering approaches is the insufficient supply of the cells with oxygen due to a lack of a functional vascular system ex vivo. In complex 3D culture systems, such as bioprinted constructs with clinically relevant dimensions (Kilian D. MRS Bull. 2017; 42: 582-592), the local O2 concentration depends on the macroporosity of the hydrogel scaffold as well as on the permeability of the hydrogel material (bioink) which oxygen has to pass through via diffusion. For better understanding new tools are needed to monitor in real time oxygen distribution dynamics within bioprinted constructs. We propose utilisation of cytocompatible O2 sensitive luminescent nanoparticles (NP) for this purpose.

Awan, Z, Kahlke, T, Ralph, PJ & Kennedy, PJ 2019, 'Chemical named entity recognition with deep contextualized neural embeddings', IC3K 2019 - Proceedings of the 11th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management, 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.

Murray, S, Verma, A, Palanisami, S & Ajani, P 2019, 'The use of eDNA and arrays for precise estuarine water quality assessment', 3rd Australian and New Zealand Marine Biotechnology Society Conference, Sydney, Australia.

Schreiber, I, Muzika, F & Červený, J 2019, 'Reaction Networks, Oscillatory Motifs and Parameter Estimation in Biochemical Systems', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 30-41.
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© 2019, Springer Nature Switzerland AG. We outline an approach to analysis of dynamics of biosystems formulated as reaction networks. In particular, we discuss stability analysis provided that stoichiometric equations are given for each reaction step together with power law rate expressions. Based on stoichiometry alone, the network at stationary state can be decomposed into elementary subnetworks (elementary modes, extreme currents, fluxes). Assuming power law kinetics, the capacity of the elementary subnetworks for displaying dynamical instabilities, such as bistability and oscillations, is evaluated. These subnetworks are then suitably combined to form the entire network satisfying certain stability constraints implied by experiments. Specifically, we assume that an experimentally measured biosystem represented by a reaction network displays an experimentally observed change from a steady state to oscillations. For the assumed reaction mechanism only a limited set kinetic parameters is known. In contrast, input/output parameters are known from the experiment. The set of unknown kinetic parameters may be estimated by finding a suitable linear combination of elementary modes via linear optimization so that the dynamics displayed by the model fits the experimentally observed behavior. Moreover, reaction network theory is useful in identifying subnetworks that are destabilizing the steady state to yield oscillations. Such subnetworks are called oscillatory motifs and possess a characteristic topology. As an example, we analyze a carbon-nitrogen metabolism of cyanobacteria and examine its oscillatory dynamics.

Sutherland, D, Buxton, L & Ralph, P 2019, 'Algae and waste in a circular economy. Oral Presentation', Organix19, Sydney, Australia.

Verma, A, Palanisami, S, Ajani, P & Murray, S 2019, 'Novel molecular ecology tools to predict harmful algal blooms in oyster- producing estuaries', Australian Marine Science Association Conference, Freemantle, Australia.