Publications

Hildebrand, M, Davis, A, Abbriano Burke, R, Pugsley, HR, Traller, JC, Smith, SR, Shrestha, RP, Cook, O, Sánchez-Alvarez, EL, Manandhar-Shrestha, K & Alderete, B 2015, 'Applications of Imaging Flow Cytometry for Microalgae' in Imaging Flow Cytometry Methods and Protocols, Humana Press.
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This detailed volume for the first time explores techniques and protocols involving quantitative imaging flow cytometry (IFC), which has revolutionized our ability to analyze cells, cellular clusters, and populations in a remarkable fashion ...

Kohli, GS, Farrell, H & Murray, SA 2015, 'Gambierdiscus, the cause of ciguatera fish poisoning: a review of progress in ecology and toxicology' in Luis Botana, Natalia.Vilarino (ed), Climate change and marine and freshwater toxins, Walter de Gruyter, Germany, pp. 273-312.

Murray, SA, Uwe, J & Kremp, A 2015, 'Alexandrium spp.: genetic and ecological factors influencing saxitoxin production and proliferation' in Botana, LM, Louzao, MC & Vilarino, N (eds), Climate Change and Marine and Freshwater Toxins, Walter de Gruyter, Germany, pp. 125-154.
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Ajani, PA 2015, 'Photo Credit, corrected after print 16 April 2015. Editorial 'Ocean wanderers' the image did not show marine phytoplankton.', Nature Climate Change, vol. 5, pp. 1-1.
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Ament, SA, Szelinger, S, Glusman, G, Ashworth, J, Hou, L, Akula, N, Shekhtman, T, Badner, JA, Brunkow, ME, Mauldin, DE, Stittrich, A-B, Rouleau, K, Detera-Wadleigh, SD, Nurnberger, JI, Edenberg, HJ, Gershon, ES, Schork, N, Price, ND, Gelinas, R, Hood, L, Craig, D, McMahon, FJ, Kelsoe, JR & Roach, JC 2015, 'Rare variants in neuronal excitability genes influence risk for bipolar disorder', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 112, no. 11, pp. 3576-3581.
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Ampuero, D, Miranda, CE, Delgado, LE, Goyen, S & Weaver, S 2015, 'Empathy and critical thinking: primary students solving local environmental problems through outdoor learning', JOURNAL OF ADVENTURE EDUCATION AND OUTDOOR LEARNING, vol. 15, no. 1, pp. 64-78.
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Ampuero, DA, Miranda, C & Goyen, S 2015, 'Positive psychology in education for sustainable development at a primary-education institution', LOCAL ENVIRONMENT, vol. 20, no. 7, pp. 745-763.
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Arotsker, L, Kramarsky-Winter, E, Ben-Dov, E, Siboni, N & Kushmaro, A 2015, 'Changes in the bacterial community associated with black band disease in a Red Sea coral, Favia sp., in relation to disease phases', Diseases of Aquatic Organisms, vol. 116, no. 1, pp. 47-58.
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Changes of the black band disease (BBD)-associated microbial consortium on the surface of a Favia sp. coral colony were assessed in relation to the different disease phases. A number of highly active bacterial groups changed in numbers as the BBD disease signs changed. These included Gamma- and Epsilonproteobacteria, Bacteroidetes and Firmicutes groups. One cyanobacterium strain, BGP10_4ST (FJ210722), was constantly present in the disease interface and adjacent tissues of the affected corals, regardless of disease phase. The dynamics of the operational taxonomic units (OTUs) of this BBD-specific strain provide a marker regarding the disease phase. The disease's active phase is characterized by a wide dark band progressing along the tissue-skeleton interface and by numerous bacterial OTUs. Cyanobacterial OTUs decreased in numbers as the disease signs waned, perhaps opening a niche for additional microorganisms. Even when black band signs disappeared there was a consistent though low abundance of the BBD-specific cyanobacteria (BGP10_4ST), and the microbial community of the disease-skeleton interface remained surprisingly similar to the original band community. These results provide an indication that the persistence of even low numbers of this BBD-specific cyanobacterium in coral tissues during the non-active (or subclinical) state could facilitate reinitiation of BBD signs during the following summer. This may indicate that this bacterium is major constituent of the disease and that its persistence and ability to infiltrate the coral tissues may act to facilitate the assembly of the other BBD-specific groups of bacteria.

Barnes, MK, Tilstone, GH, Smyth, TJ, Widdicombe, CE, Gloël, J, Robinson, C, Kaiser, J & Suggett, DJ 2015, 'Drivers and effects of Karenia mikimotoi blooms in the western English Channel', Progress in Oceanography, vol. 137, no. B, pp. 456-469.
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© 2015. Naturally occurring red tides and harmful algal blooms (HABs) are of increasing importance in the coastal environment and can have dramatic effects on coastal benthic and epipelagic communities worldwide. Such blooms are often unpredictable, irregular or of short duration, and thus determining the underlying driving factors is problematic. The dinoflagellate Karenia mikimotoi is an HAB, commonly found in the western English Channel and thought to be responsible for occasional mass finfish and benthic mortalities. We analysed a 19-year coastal time series of phytoplankton biomass to examine the seasonality and interannual variability of K. mikimotoi in the western English Channel and determine both the primary environmental drivers of these blooms as well as the effects on phytoplankton productivity and oxygen conditions. We observed high variability in timing and magnitude of K. mikimotoi blooms, with abundances reaching >1000cellsmL^-1 at 10m depth, inducing up to a 12-fold increase in the phytoplankton carbon content of the water column. No long-term trends in the timing or magnitude of K. mikimotoi abundance were evident from the data. Key driving factors were identified as persistent summertime rainfall and the resultant input of low-salinity high-nutrient river water. The largest bloom in 2009 was associated with highest annual primary production and led to considerable oxygen depletion at depth, most likely as a result of enhanced biological breakdown of bloom material; however, this oxygen depletion may not affect zooplankton. Our data suggests that K. mikimotoi blooms are not only a key and consistent feature of western English Channel productivity, but importantly can potentially be predicted from knowledge of rainfall or river discharge.

Barnes, MK, Tilstone, GH, Suggett, DJ, Widdicombe, CE, Bruun, J, Martinez-Vicente, V & Smyth, TJ 2015, 'Temporal variability in total, micro- and nano-phytoplankton primary production at a coastal site in the Western English Channel', Progress in Oceanography, vol. 137, no. B, pp. 470-483.
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© 2015. Primary productivity and subsequent carbon cycling in the coastal zone have a significant impact on the global carbon budget. It is currently unclear how anthropogenic activity could alter these budgets but long term coastal time series of hydrological, biogeochemical and biological measurements represent a key means to better understand past drivers, and hence to predicting future seasonal and inter-annual variability in carbon fixation in coastal ecosystems. An 8-year time series of primary production from 2003 to 2010, estimated using a recently developed absorption-based algorithm, was used to determine the nature and extent of change in primary production at a coastal station (L4) in the Western English Channel (WEC). Analysis of the seasonal and inter-annual variability in production demonstrated that on average, nano- and pico-phytoplankton account for 48% of the total carbon fixation and micro-phytoplankton for 52%. A recent decline in the primary production of nano- and pico-phytoplankton from 2005 to 2010 was observed, corresponding with a decrease in winter nutrient concentrations and a decrease in the biomass of Phaeocystis sp. Micro-phytoplankton primary production (PPM) remained relatively constant over the time series and was enhanced in summer during periods of high precipitation. Increases in sea surface temperature, and decreases in wind speeds and salinity were associated with later spring maxima in PPM. Together these trends indicate that predicted increases in temperature and decrease in wind speeds in future would drive later spring production whilst predicted increases in precipitation would also continue these blooms throughout the summer at this site.

Becraft, ED, Wood, JM, Rusch, DB, Kuehl, M, Jensen, SI, Bryant, DA, Roberts, DW, Cohan, FM & Ward, DM 2015, 'The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park', FRONTIERS IN MICROBIOLOGY, vol. 6.
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Behrendt, L, Brejnrod, A, Schliep, M, Sorensen, SJ, Larkum, AWD & Kuhl, M 2015, 'Chlorophyll f-driven photosynthesis in a cavernous cyanobacterium', ISME JOURNAL, vol. 9, no. 9, pp. 2108-2111.
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Bramucci, AR, Labeeuw, L, Mayers, TJ, Saby, JA & Case, RJ 2015, 'A Small Volume Bioassay to Assess Bacterial/Phytoplankton Co-culture Using WATER-Pulse-Amplitude-Modulated (WATER-PAM) Fluorometry', JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, no. 97.
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Brodersen, KE, Lichtenberg, M, Paz, LC & Kühl, M 2015, 'Epiphyte-cover on seagrass (Zostera marina L.) leaves impedes plant performance and radial O2 loss from the below-ground tissue', Frontiers in Marine Science, vol. 2, no. AUG.
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© 2015 Brodersen, Lichtenberg, Paz and Kühl. The O 2 budget of seagrasses is regulated by a complex interaction between several sources and sinks, which is strongly regulated by light availability and mass transfer over the diffusive boundary layer (DBL) surrounding the plant. Epiphyte growth on leaves may thus strongly affect the O 2 availability of the seagrass plant and its capability to aerate its rhizosphere as a defense against plant toxins. We used electrochemical and fiber-optic microsensors to quantify the O 2 flux, DBL, and light microclimate around leaves with and without filamentous algal epiphytes. We also quantified the below-ground radial O 2 loss (ROL) from roots (~1 mm from the root-apex) to elucidate how this below-ground oxic microzone was affected by the presence of epiphytes. Epiphyte-cover on seagrass leaves (~21% areal cover) resulted in reduced light quality and quantity for photosynthesis, thus leading to reduced plant fitness. A ~4 times thicker DBL around leaves with epiphyte-cover impeded gas (and nutrient) exchange with the surrounding water-column and thus the amount of O 2 passively diffusing down to the below-ground tissue through the aerenchyma in darkness. During light exposure of the leaves, radial oxygen loss from the below-ground tissue was ~2 times higher from plants without epiphyte-cover. In contrast, no O 2 was detectable at the surface of the root-cap tissue of plants with epiphyte-cover during darkness, leaving the plants more susceptible to sulfide intrusion. Epiphyte growth on seagrass leaves thus has a negative effect on the light climate during daytime and O 2 supply in darkness, hampering the plants performance and thereby reducing the oxidation capability of its below-ground tissue.

Brodersen, KE, Nielsen, DA, Ralph, PJ & Kuhl, M 2015, 'Oxic microshield and local pH enhancement protects Zostera muelleri from sediment derived hydrogen sulphide', NEW PHYTOLOGIST, vol. 205, no. 3, pp. 1264-1276.
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Camp, EF, Krause, SL, Santos, LMF, Naumann, MS, Kikuchi, RKP, Smith, DJ, Wild, C & Suggett, DJ 2015, 'The “Flexi-Chamber”: A Novel Cost-Effective In Situ Respirometry Chamber for Coral Physiological Measurements', PLoS One, vol. 10, no. 10, pp. 1-21.
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Carney, RL, Mitrovic, SM, Jeffries, T, Westhorpe, D, Curlevski, N & Seymour, JR 2015, 'River bacterioplankton community responses to a high inflow event', Aquatic Microbial Ecology, vol. 75, no. 3, pp. 187-205.
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© Inter-Research 2015. Microbes drive chemical cycling and productivity within river ecosystems, but their influence may shift when intense allochthonous inputs accompany high freshwater inflow (flood) events. Investigating how floods influence microbial processes is fundamentally important for our understanding of river ecology, but is generally overlooked. We analysed bacterioplankton community composition (BCC) and abundance over 4 mo following an enormous flood event in the Hunter River, Australia, that resulted in a major fish kill. Concentrations of dissolved organic carbon (DOC) and inorganic nutrients (N and P) were up to 3 times higher during the flood event compared to prior and subsequent months. Bacterial cell abundances were up to 10 times higher at impacted sites during the flood event. Using Automated Ribosomal Intergenic Spacer Analysis we found significant shifts in BCC between the flood impacted month and subsequent months (p < 0.05). Distance linear modelling indicated that DOC and dissolved N and P correlated most strongly with BCC patterns during the high inflow, whereas community dynamics correlated most strongly with nitrogen oxides and ammonium during the river's recovery phase. 16S rRNA amplicon pyrosequencing revealed that common soil-associated and facultative anaerobic genera of Proteobacteria were most dominant during the flood period, suggesting that a proportion of the bacterial community observed during this event were potentially inactive soil microbes transported into the river via terrestrial runoff. During the recovery period, Cyanobacteria and freshwater- associated genera of Actinobacteria and Proteobacteria became dominant in 16S rRNA pyrosequencing profiles. These observations indicate that allochthonous nutrients delivered via floods can significantly stimulate bacterial growth, underpinning substrate-controlled succession of bacterial communities and ultimately shaping the ecology within river ecosystems.

Červený, J, Sinetova, MA, Zavřel, T & Los, DA 2015, 'Mechanisms of high temperature resistance of Synechocystis sp. PCC 6803: An Impact of histidine kinase 34', Life, vol. 5, no. 1, pp. 676-699.
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© 2015 by the authors; licensee MDPI, Basel, Switzerland. Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying responses and acclimation to different abiotic stresses. Changes in transcriptome, proteome, lipidome, and photosynthesis in response to short term heat stress are well studied in this organism, and histidine kinase 34 (Hik34) is shown to play an important role in mediating such response. Corresponding data on long term responses, however, are fragmentary and vary depending on parameters of experiments and methods of data collection, and thus are hard to compare. In order to elucidate how the early stress responses help cells to sustain long-term heat stress, as well as the role of Hik34 in prolonged acclimation, we examined the resistance to long-term heat stress of wild-type and ΔHik34 mutant of Synechocystis. In this work, we were able to precisely control the long term experimental conditions by cultivating Synechocystis in automated photobioreactors, measuring selected physiological parameters within a time range of minutes. In addition, morphological and ultrastructural changes in cells were analyzed and western blotting of individual proteins was used to study the heat stress-affected protein expression. We have shown that the majority of wild type cell population was able to recover after 24 h of cultivation at 44 °C. In contrast, while ΔHik34 mutant cells were resistant to heat stress within its first hours, they could not recover after 24 h long high temperature treatment. We demonstrated that the early induction of HspA expression and maintenance of high amount of other HSPs throughout the heat incubation is critical for successful adaptation to long-term stress. In addition, it appears that histidine kinase Hik34 is an essential component for the long term high temperature resistance.

Chan, Y-W, Millard, AD, Wheatley, PJ, Holmes, AB, Mohr, R, Whitworth, AL, Mann, NH, Larkum, AWD, Hess, WR, Scanlan, DJ & Clokie, MRJ 2015, 'Genomic and proteomic characterization of two novel siphovirus infecting the sedentary facultative epibiont cyanobacterium Acaryochloris marina', ENVIRONMENTAL MICROBIOLOGY, vol. 17, no. 11, pp. 4239-4252.
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Commault, AS, Barrière, F, Lapinsonnière, L, Lear, G, Bouvier, S & Weld, RJ 2015, 'Influence of inoculum and anode surface properties on the selection of Geobacter-dominated biofilms', Bioresource Technology, vol. 195, pp. 265-272.
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This study evaluated the impact of inoculum source and anode surface modification (carboxylate –COO− and sulfonamide –SO2NH2 groups) on the microbial composition of anode-respiring biofilms. These two factors have not previously been considered in detail. Three different inoculum sources were investigated, a dry aerobic soil, brackish estuarine mud and freshwater sediment. The biofilms were selected using a poised anode (−0.36 V vs Ag/AgCl) and acetate as the electron donor in a three-electrode configuration microbial fuel cell (MFC). Population profiling and cloning showed that all biofilms selected were dominated by Geobacter sp., although their electrochemical properties varied depending on the source inoculum and electrode surface modification. These findings suggest that Geobacter sp. are widespread in soils, even those that do not provide a continuously anaerobic environment, and are better at growing in the MFC conditions than other bacteria.

Commault, AS, Lear, G & Weld, RJ 2015, 'Maintenance of Geobacter-dominated biofilms in microbial fuel cells treating synthetic wastewater', Bioelectrochemistry, vol. 106, no. Part A, pp. 150-158.
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Geobacter-dominated biofilms can be selected under stringent conditions that limit the growth of competing bacteria. However, in many practical applications, such stringent conditions cannot be maintained and the efficacy and stability of these artificial biofilms may be challenged. In this work, biofilms were selected on low-potential anodes (− 0.36 V vs Ag/AgCl, i.e. − 0.08 V vs SHE) in minimal acetate or ethanol media. Selection conditions were then relaxed by transferring the biofilms to synthetic wastewater supplemented with soil as a source of competing bacteria. We tracked community succession and functional changes in these biofilms. The Geobacter-dominated biofilms showed stability in their community composition and electrochemical properties, with Geobacter sp. being still electrically active after six weeks in synthetic wastewater with power densities of 100 ± 19 mW·m− 2 (against 74 ± 14 mW·m− 2 at week 0) for all treatments. After six weeks, the ethanol-selected biofilms, despite their high taxon richness and their efficiency at removing the chemical oxygen demand (0.8 g·L− 1 removed against the initial 1.3 g·L− 1 injected), were the least stable in terms of community structure. These findings have important implications for environmental microbial fuel cells based on Geobacter-dominated biofilms and suggest that they could be stable in challenging environments.

Craggs, R, Park, J, Sutherland, D & Heubeck, S 2015, 'Economic construction and operation of hectare-scale wastewater treatment enhanced pond systems', JOURNAL OF APPLIED PHYCOLOGY, vol. 27, no. 5, pp. 1913-1922.
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D Ainsworth, T, Krause, L, Bridge, T, Torda, G, Raina, J-B, Zakrzewski, M, Gates, RD, Padilla-Gamiño, JL, Spalding, HL, Smith, C, Woolsey, ES, Bourne, DG, Bongaerts, P, Hoegh-Guldberg, O & Leggat, W 2015, 'The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts', ISME Journal, vol. 9, pp. 2261-2274.
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Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse host-associated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals’ endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes.The ISME Journal advance online publication, 17 April 2015; doi:10.1038/ismej.2015.39.

Ertan, H, Cassel, C, Verma, A, Poljak, A, Charlton, T, Aldrich-Wright, J, Omar, SM, Siddiqui, KS & Cavicchioli, R 2015, 'A new broad specificity alkaline metalloprotease from a Pseudomonas sp isolated from refrigerated milk: Role of calcium in improving enzyme productivity', JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, vol. 113, pp. 1-8.
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Everett, JD & Doblin, MA 2015, 'Characterising primary productivity measurements across a dynamic western boundary current region', DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS, vol. 100, pp. 105-116.
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Exton, DA, McGenity, TJ, Steinke, M, Smith, DJ & Suggett, DJ 2015, 'Uncovering the volatile nature of tropical coastal marine ecosystems in a changing world.', Global change biology, vol. 21, no. 4, pp. 1383-1394.
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Biogenic volatile organic compounds (BVOCs), in particular dimethyl sulphide (DMS) and isoprene, have fundamental ecological, physiological and climatic roles. Our current understanding of these roles is almost exclusively established from terrestrial or oceanic environments but signifies a potentially major, but largely unknown, role for BVOCs in tropical coastal marine ecosystems. The tropical coast is a transition zone between the land and ocean, characterized by highly productive and biodiverse coral reefs, seagrass beds and mangroves, which house primary producers that are amongst the greatest emitters of BVOCs on the planet. Here, we synthesize our existing understanding of BVOC emissions to produce a novel conceptual framework of the tropical marine coast as a continuum from DMS-dominated reef producers to isoprene-dominated mangroves. We use existing and previously unpublished data to consider how current environmental conditions shape BVOC production across the tropical coastal continuum, and in turn how BVOCs can regulate environmental stress tolerance or species interactions via infochemical networks. We use this as a framework to discuss how existing predictions of future tropical coastal BVOC emissions, and the roles they play, are effectively restricted to present day 'baseline' trends of BVOC production across species and environmental conditions; as such, there remains a critical need to focus research efforts on BVOC responses to rapidly accelerating anthropogenic impacts at local and regional scales. We highlight the complete lack of current knowledge required to understand the future ecological functioning of these important systems, and to predict whether feedback mechanisms are likely to regulate or exacerbate current climate change scenarios through environmentally and ecologically mediated changes to BVOC budgets at the ecosystem level.

Farrell, H, Seebacher, F, O'Connor, W, Zammit, A, Harwood, DT & Murray, S 2015, 'Warm temperature acclimation impacts metabolism of paralytic shellfish toxins from Alexandrium minutum in commercial oysters.', Global Change Biology, vol. 21, no. 9, pp. 3402-3413.
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Species of Alexandrium produce potent neurotoxins termed paralytic shellfish toxins and are expanding their ranges worldwide, concurrent with increases in sea surface temperature. The metabolism of molluscs is temperature dependent, and increases in ocean temperature may influence both the abundance and distribution of Alexandrium and the dynamics of toxin uptake and depuration in shellfish. Here, we conducted a large-scale study of the effect of temperature on the uptake and depuration of paralytic shellfish toxins in three commercial oysters (Saccostrea glomerata and diploid and triploid Crassostrea gigas, n = 252 per species/ploidy level). Oysters were acclimated to two constant temperatures, reflecting current and predicted climate scenarios (22 and 27 °C), and fed a diet including the paralytic shellfish toxin-producing species Alexandrium minutum. While the oysters fed on A. minutum in similar quantities, concentrations of the toxin analogue GTX1,4 were significantly lower in warm-acclimated S. glomerata and diploid C. gigas after 12 days. Following exposure to A. minutum, toxicity of triploid C. gigas was not affected by temperature. Generally, detoxification rates were reduced in warm-acclimated oysters. The routine metabolism of the oysters was not affected by the toxins, but a significant effect was found at a cellular level in diploid C. gigas. The increasing incidences of Alexandrium blooms worldwide are a challenge for shellfish food safety regulation. Our findings indicate that rising ocean temperatures may reduce paralytic shellfish toxin accumulation in two of the three oyster types; however, they may persist for longer periods in oyster tissue.

Frommlet, JC, Sousa, ML, Alves, A, Vieira, SI, Suggett, DJ & Serodio, J 2015, 'Coral symbiotic algae calcify ex hospite in partnership with bacteria', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 112, no. 19, pp. 6158-6163.
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Fujise, L, Suggett, DJ, Frommlet, JC, Serodio, J & Ralph, PJ 2015, 'TURNING UP THE HEAT ON SYMBIODINIUM CELL CYCLE ANALYSIS', EUROPEAN JOURNAL OF PHYCOLOGY, vol. 50, pp. 58-59.

Gao, Y, Yu, R-C, Murray, SA, Chen, J-H, Kang, Z-J, Zhang, Q-C, Kong, F-Z & Zhou, M-J 2015, 'High Specificity of a Quantitative PCR Assay Targeting a Saxitoxin Gene for Monitoring Toxic Algae Associated with Paralytic Shellfish Toxins in the Yellow Sea', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 81, no. 20, pp. 6973-6981.
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Gardner, SG, Nielsen, DA, Petrou, K, Larkum, AWD & Ralph, PJ 2015, 'Characterisation of coral explants: a model organism for cnidarian-dinoflagellate studies', CORAL REEFS, vol. 34, no. 1, pp. 133-142.
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Golicz, AA, Schliep, M, Lee, HT, Larkum, AWD, Dolferus, R, Batley, J, Chan, C-KK, Sablok, G, Ralph, PJ & Edwards, D 2015, 'Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network', JOURNAL OF EXPERIMENTAL BOTANY, vol. 66, no. 5, pp. 1489-1498.
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Grob, C, Jardillier, L, Hartmann, M, Ostrowski, M, Zubkov, MV & Scanlan, DJ 2015, 'Cell-specific CO2 fixation rates of two distinct groups of plastidic protists in the Atlantic Ocean remain unchanged after nutrient addition', ENVIRONMENTAL MICROBIOLOGY REPORTS, vol. 7, no. 2, pp. 211-218.
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Hassler, CS, Norman, L, Nichols, CAM, Clementson, LA, Robinson, C, Schoemann, V, Watson, RJ & Doblin, MA 2015, 'Iron associated with exopolymeric substances is highly bioavailable to oceanic phytoplankton', MARINE CHEMISTRY, vol. 173, pp. 136-147.
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Hennon, GMM, Ashworth, J, Groussman, RD, Berthiaume, C, Morales, RL, Baliga, NS, Orellana, MV & Armbrust, EV 2015, 'Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression', NATURE CLIMATE CHANGE, vol. 5, no. 8, pp. 761-U179.
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Henschke, N, Everett, JD, Suthers, IM, Smith, JA, Hunt, BPV, Doblin, MA & Taylor, MD 2015, 'Zooplankton trophic niches respond to different water types of the western Tasman Sea: A stable isotope analysis', DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS, vol. 104, pp. 1-8.
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Hill, R, Bellgrove, A, Macreadie, PI, Petrou, K, Beardall, J, Steven, A & Ralph, PJ 2015, 'Can macroalgae contribute to blue carbon? An Australian perspective', LIMNOLOGY AND OCEANOGRAPHY, vol. 60, no. 5, pp. 1689-1706.
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Hoeksema, BW & Matthews, JL 2015, 'Partial bleaching in an assemblage of small apozooxanthellate corals of the genera Heteropsammia and Heterocyathus', CORAL REEFS, vol. 34, no. 4, pp. 1227-1227.
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Hong, Y, Burford, MA, Ralph, PJ & Doblin, MA 2015, 'Subtropical zooplankton assemblage promotes the harmful cyanobacterium Cylindrospermopsis raciborskii in a mesocosm experiment', JOURNAL OF PLANKTON RESEARCH, vol. 37, no. 1, pp. 90-101.
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Jeffries, TC, Ostrowski, M, Williams, RB, Xie, C, Jensen, RM, Grzymski, JJ, Senstius, SJ, Givskov, M, Hoeke, R, Philip, GK, Neches, RY, Drautz-Moses, DI, Chénard, C, Paulsen, IT & Lauro, FM 2015, 'Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll', Scientific Reports, vol. 5, pp. 15383-15383.
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Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a ‘citizen oceanography’ approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.

Johnston, EL, Mayer-Pinto, M, Hutchings, PA, Marzinelli, EM, Ahyong, ST, Birch, G, Booth, DJ, Creese, RG, Doblin, MA, Figueira, W, Gribben, PE, Pritchard, T, Roughan, M, Steinberg, PD & Hedge, LH 2015, 'Sydney Harbour: what we do and do not know about a highly diverse estuary', MARINE AND FRESHWATER RESEARCH, vol. 66, no. 12, pp. 1073-1087.
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Jones, EM, Doblin, MA, Matear, R & King, E 2015, 'Assessing and evaluating the ocean-colour footprint of a regional observing system', JOURNAL OF MARINE SYSTEMS, vol. 143, pp. 49-61.
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Kaźmierczak, J, Fenchel, T, Kühl, M, Kempe, S, Kremer, B, Łącka, B & Małkowski, K 2015, 'Caco3 precipitation in multilayered cyanobacterial mats: Clues to explain the alternation of micrite and sparite layers in calcareous stromatolites', Life, vol. 5, no. 1, pp. 744-769.
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© 2015 by the authors; licensee MDPI, Basel, Switzerland. Marine cyanobacterial mats were cultured on coastal sediments (Nivå Bay, Øresund, Denmark) for over three years in a closed system. Carbonate particles formed in two different modes in the mat: (i) through precipitation of submicrometer-sized grains of Mg calcite within the mucilage near the base of living cyanobacterial layers, and (ii) through precipitation of a variety of mixed Mg calcite/aragonite morphs in layers of degraded cyanobacteria dominated by purple sulfur bacteria. The 13C values were about 2‰ heavier in carbonates from the living cyanobacterial zones as compared to those generated in the purple bacterial zones. Saturation indices calculated with respect to calcite, aragonite, and dolomite inside the mats showed extremely high values across the mat profile. Such high values were caused by high pH and high carbonate alkalinity generated within the mats in conjunction with increased concentrations of calcium and magnesium that were presumably stored in sheaths and extracellular polymer substances (EPS) of the living cyanobacteria and liberated during their post-mortem degradation. The generated CaCO3 morphs were highly similar to morphs reported from heterotrophic bacterial cultures, and from bacterially decomposed cyanobacterial biomass emplaced in Ca-rich media. They are also similar to CaCO3 morphs precipitated from purely inorganic solutions. No metabolically (enzymatically) controlled formation of particular CaCO3 morphs by heterotrophic bacteria was observed in the studied mats. The apparent alternation of in vivo and post-mortem generated calcareous layers in the studied cyanobacterial mats may explain the alternation of fine-grained (micritic) and coarse-grained (sparitic) laminae observed in modern and fossil calcareous cyanobacterial microbialites as the result of a probably similar multilayered mat organization.

Kim, Y-M, Nowack, S, Olsen, MT, Becraft, ED, Wood, JM, Thiel, V, Klapper, I, Kuhl, M, Fredrickson, JK, Bryant, DA, Ward, DM & Metz, TO 2015, 'Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms', FRONTIERS IN MICROBIOLOGY, vol. 6.
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Kohli, GS, John, U, Figueroa, RI, Rhodes, LL, Harwood, DT, Groth, M, Bolch, CJS & Murray, SA 2015, 'Polyketide synthesis genes associated with toxin production in two species of Gambierdiscus (Dinophyceae)', BMC GENOMICS, vol. 16.
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Kolpen, M, Kragh, KN, Bjarnsholt, T, Line, L, Hansen, CR, Dalboge, CS, Hansen, N, Kuhl, M, Hoiby, N & Jensen, PO 2015, 'Denitrification by cystic fibrosis pathogens - Stenotrophomonas maltophilia is dormant in sputum', INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY, vol. 305, no. 1, pp. 1-10.
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Kopf, A, Bicak, M, Kottmann, R, Schnetzer, J, Kostadinov, I, Lehmann, K, Fernandez-Guerra, A, Jeanthon, C, Rahav, E, Ullrich, M, Wichels, A, Gerdts, G, Polymenakou, P, Kotoulas, G, Siam, R, Abdallah, RZ, Sonnenschein, EC, Cariou, T, O'Gara, F, Jackson, S, Orlic, S, Steinke, M, Busch, J, Duarte, B, Cacador, I, Canning-Clode, J, Bobrova, O, Marteinsson, V, Reynisson, E, Loureiro, CM, Luna, GM, Quero, GM, Loescher, CR, Kremp, A, DeLorenzo, ME, Ovreas, L, Tolman, J, LaRoche, J, Penna, A, Frischer, M, Davis, T, Katherine, B, Meyer, CP, Ramos, S, Magalhaes, C, Jude-Lemeilleur, F, Leopoldina Aguirre-Macedo, M, Wang, S, Poulton, N, Jones, S, Collin, R, Fuhrman, JA, Conan, P, Alonso, C, Stambler, N, Goodwin, K, Yakimov, MM, Baltar, F, Bodrossy, L, Van De Kamp, J, Frampton, DMF, Ostrowski, M, Van Ruth, P, Malthouse, P, Claus, S, Deneudt, K, Mortelmans, J, Pitois, S, Wallom, D, Salter, I, Costa, R, Schroeder, DC, Kandil, MM, Amaral, V, Biancalana, F, Santana, R, Pedrotti, ML, Yoshida, T, Ogata, H, Ingleton, T, Munnik, K, Rodriguez-Ezpeleta, N, Berteaux-Lecellier, V, Wecker, P, Cancio, I, Vaulot, D, Bienhold, C, Ghazal, H, Chaouni, B, Essayeh, S, Ettamimi, S, Zaid, EH, Boukhatem, N, Bouali, A, Chahboune, R, Barrijal, S, Timinouni, M, El Otmani, F, Bennani, M, Mea, M, Todorova, N, Karamfilov, V, ten Hoopen, P, Cochrane, G, L'Haridon, S, Bizsel, KC, Vezzi, A, Lauro, FM, Martin, P, Jensen, RM, Hinks, J, Gebbels, S, Rosselli, R, De Pascale, F, Schiavon, R, dos Santos, A, Villar, E, Pesant, S, Cataletto, B, Malfatti, F, Edirisinghe, R, Silveira, JAH, Barbier, M, Turk, V, Tinta, T, Fuller, WJ, Salihoglu, I, Serakinci, N, Ergoren, MC, Bresnan, E, Iriberri, J, Nyhus, PAF, Bente, E, Karlsen, HE, Golyshin, PN, Gasol, JM, Moncheva, S, Dzhembekova, N, Johnson, Z, Sinigalliano, CD, Gidley, ML, Zingone, A, Danovaro, R, Tsiamis, G, Clark, MS, Costa, AC, El Bour, M, Martins, AM, Collins, RE, Ducluzeau, A-L, Martinez, J, Costello, MJ, Amaral-Zettler, LA, Gilbert, JA, Davies, N, Field, D & Gloeckner, FO 2015, 'The ocean sampling day consortium', GIGASCIENCE, vol. 4.
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Koren, K & Kuhl, M 2015, 'A simple laminated paper-based sensor for temperature sensing and imaging', SENSORS AND ACTUATORS B-CHEMICAL, vol. 210, pp. 124-128.
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Koren, K, Brodersen, KE, Jakobsen, SL & Kuehl, M 2015, 'Optical Sensor Nanoparticles in Artificial Sediments-A New Tool To Visualize O-2 Dynamics around the Rhizome and Roots of Seagrasses', ENVIRONMENTAL SCIENCE & TECHNOLOGY, vol. 49, no. 4, pp. 2286-2292.
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Kumar, M, Pandya-Kumar, N, Dam, A, Haor, H, Mayzlish-Gati, E, Belausov, E, Wininger, S, Abu-Abied, M, McErlean, CSP, Bromhead, LJ, Prandi, C, Kapulnik, Y & Koltai, H 2015, 'Arabidopsis response to low-phosphate conditions includes active changes in actin filaments and PIN2 polarization and is dependent on strigolactone signalling', Journal of Experimental Botany, vol. 66, no. 5, pp. 1499-1510.
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Strigolactones (SLs) are plant hormones that regulate the plant response to phosphate (Pi) growth conditions. At least part of SL-signalling execution in roots involves MAX2-dependent effects on PIN2 polar localization in the plasma membrane (PM) and actin bundling and dynamics. We examined PIN2 expression, PIN2 PM localization, endosome trafficking, and actin bundling under low-Pi conditions: a MAX2-dependent reduction in PIN2 trafficking and polarization in the PM, reduced endosome trafficking, and increased actin-filament bundling were detected in root cells. The intracellular protein trafficking that is related to PIN proteins but unassociated with AUX1 PM localization was selectively inhibited. Exogenous supplementation of the synthetic SL GR24 to a SL-deficient mutant (max4) led to depletion of PIN2 from the PM under low-Pi conditions. Accordingly, roots of mutants in MAX2, MAX4, PIN2, TIR3, and ACTIN2 showed a reduced low-Pi response compared with the wild type, which could be restored by auxin (for all mutants) or GR24 (for all mutants except max2-1). Changes in PIN2 polarity, actin bundling, and vesicle trafficking may be involved in the response to low Pi in roots, dependent on SL/MAX2 signalling.

Kumar, M, Pandya-Kumar, N, Kapulnik, Y & Koltai, H 2015, 'Strigolactone signaling in root development and phosphate starvation', Plant Signaling and Behavior, vol. 10, no. 7.
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Strigolactones (SLs), have recently been recognized as phytohormone involve in orchestrating shoot and root architecture. In, roots SLs positively regulate root hair length and density, suppress lateral root formation and promote primary root meristem cell number. The biosynthesis and exudation of SLs increases under low phosphate level to regulate root responses. This hormonal response suggests an adaptation strategy of plant to optimize growth and development under nutrient limitations. However, little is known on signal-transduction pathways associated with SL activities. In this review, we outline the current knowledge on SL biology by describing their role in the regulation of root development. Also, we discuss the recent findings on the non-cell autonomous signaling of SLs, that involve PIN polarization, vesicle trafficking, changes in actin architecture and dynamic in response to phosphate starvation.

Kumar, M, Reddy, CRK & Ralph, PJ 2015, 'Polyamines in morphogenesis and development: a promising research area in seaweeds.', Frontiers in plant science, vol. 6, pp. 27-27.
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Kuzhiumparambil, U, Watanabe, S & Fu, S 2015, 'Oxidation of testosterone by permanganate and its implication in sports drug testing', NEW JOURNAL OF CHEMISTRY, vol. 39, no. 3, pp. 1597-1602.
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Labeeuw, L, Martone, PT, Boucher, Y & Case, RJ 2015, 'Ancient origin of the biosynthesis of lignin precursors', BIOLOGY DIRECT, vol. 10.
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Lichtenberg, M & Kuehl, M 2015, 'Pronounced gradients of light, photosynthesis and O-2 consumption in the tissue of the brown alga Fucus serratus', NEW PHYTOLOGIST, vol. 207, no. 3, pp. 559-569.
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Luong, S, Kuzhiumparambil, U & Fu, S 2015, 'Elucidation of markers for monitoring morphine and its analogs in urine adulterated with pyridinium chlorochromate.', Bioanalysis, vol. 7, no. 18.
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Currently, procedures that identify the drugs 'destroyed' in adulterated urine specimens are very limited. This study aimed to determine the effect of pyridinium chlorochromate (PCC) on routine opiate assays and identify reaction products formed. Results/methodology: Opiate-positive urines adulterated with PCC (20 and 100 mM) were analyzed using CEDIA(®) immunoassay and GC-MS. Urine and water samples spiked with 6-monoacetylmorphine, morphine and its glucuronides (10 µg/ml) and PCC (0.02-100 mM) were monitored with LC-MS, and the products characterized.PCC significantly decreased the abundance of morphine, codeine and IS. Adulterated water and urine samples containing 6-monoacetylmorphine, morphine and morphine-3-glucuronide yielded morphinone-3-glucuronide, 7,14-dihydroxy-6-monoacetylmorphine, 7,8-diketo-6-monoacetylmorphine and 7,8-diketo-morphine (tentative assignment). Reaction pathways may be different in the two matrices.

Lutz, A, Raina, JB, Motti, CA, Miller, DJ & van Oppen, MJH 2015, 'Host Coenzyme Q Redox State Is an EarlyBiomarker of Thermal Stress in the CoralAcropora millepora', PLoS One, vol. 10, no. 10, pp. 1-18.
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Bleaching episodes caused by increasing seawater temperatures may induce mass coral mortality and are regarded as one of the biggest threats to coral reef ecosystems worldwide. The current consensus is that this phenomenon results from enhanced production of harmful reactive oxygen species (ROS) that disrupt the symbiosis between corals and their endosymbiotic dinoflagellates, Symbiodinium. Here, the responses of two important antioxidant defence components, the host coenzyme Q (CoQ) and symbiont plastoquinone (PQ) pools, are investigated for the first time in colonies of the scleractinian coral, Acropora millepora, during experimentally-induced bleaching under ecologically relevant conditions. Liquid chromatography-mass spectrometry (LC-MS) was used to quantify the states of these two pools, together with physiological parameters assessing the general state of the symbiosis (including photosystem II photochemical efficiency, chlorophyll concentration and Symbiodinium cell densities). The results show that the responses of the two antioxidant systems occur on different timescales: (i) the redox state of the Symbiodinium PQ pool remained stable until twelve days into the experiment, after which there was an abrupt oxidative shift; (ii) by contrast, an oxidative shift of approximately 10% had occurred in the host CoQ pool after 6 days of thermal stress, prior to significant changes in any other physiological parameter measured. Host CoQ pool oxidation is thus an early biomarker of thermal stress in corals, and this antioxidant pool is likely to play a key role in quenching thermally-induced ROS in the coral-algal symbiosis. This study adds to a growing body of work that indicates host cellular responses may precede the bleaching process and symbiont dysfunction.

Macreadie, PI, Trevathan-Tackett, SM, Skilbeck, CG, Sanderman, J, Curlevski, N, Jacobsen, G & Seymour, JR 2015, 'Losses and recovery of organic carbon from a seagrass ecosystem following disturbance', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 282, no. 1817.
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Malik, A, Lenzen, M, Ralph, PJ & Tamburic, B 2015, 'Hybrid life-cycle assessment of algal biofuel production', BIORESOURCE TECHNOLOGY, vol. 184, pp. 436-443.
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Mayer-Pinto, M, Johnston, EL, Hutchings, PA, Marzinelli, EM, Ahyong, ST, Birch, G, Booth, DJ, Creese, RG, Doblin, MA, Figueira, W, Gribben, PE, Pritchard, T, Roughan, M, Steinberg, PD & Hedge, LH 2015, 'Sydney Harbour: a review of anthropogenic impacts on the biodiversity and ecosystem function of one of the world's largest natural harbours', MARINE AND FRESHWATER RESEARCH, vol. 66, no. 12, pp. 1088-1105.
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McCauley, JI, Meyer, BJ, Winberg, PC, Ranson, M & Skropeta, D 2015, 'Selecting Australian marine macroalgae based on the fatty acid composition and anti-inflammatory activity', JOURNAL OF APPLIED PHYCOLOGY, vol. 27, no. 5, pp. 2111-2121.
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Messer, LF, Doubell, M, Jeffries, TC, Brown, MV & Seymour, JR 2015, 'Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary', AQUATIC MICROBIAL ECOLOGY, vol. 74, no. 1, pp. 1-15.
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Murray, SA, Diwan, R, Orr, RJS, Kohli, GS & John, U 2015, 'Gene duplication, loss and selection in the evolution of saxitoxin biosynthesis in alveolates', MOLECULAR PHYLOGENETICS AND EVOLUTION, vol. 92, pp. 165-180.
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Murray, SA, Kohli, GS, Farrell, H, Spiers, ZB, Place, AR, Dorantes-Aranda, JJ & Ruszczyk, J 2015, 'A fish kill associated with a bloom of Amphidinium carterae in a coastal lagoon in Sydney, Australia.', Harmful Algae, vol. 49, pp. 19-28.
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We report on a dense bloom (1.80 105 cells mL 1 ) of the marine dinoflagellate species Amphidinium carterae (Genotype 2) in a shallow, small intermittently open coastal lagoon in south eastern Australia. This bloom co-occurred with the deaths of >300 individuals of three different species of fish. The opening of the lagoon to the ocean, as well as localized high nutrient levels, preceded the observations of very high cell numbers. A. carterae is usually benthic and sediment-dwelling, but temporarily became abundant throughout the water column in this shallow (<2 m) sandy habitat. Histopathological results showed that the Anguilla reinhardtii individuals examined had damage to epithelial and gill epithelial cells. An analysis of the bloom water indicated the presence of a compound with a retention time and UV spectra similar to Luteophanol A, a compound known from a strain of Amphidinium. Assays with a fish gill cell line were conducted using a purified compound from cells concentrated from the bloom, and was found to cause a loss of 87% in cell viability in 6 h. The fish deaths were likely due to the low dissolved oxygen levels in the water and/or the presence of Luteophanol A-like compounds released during the bloom.

Najafpour, MM, Ghobadi, MZ, Larkum, AW, Shen, J-R & Alliakhverdiev, SI 2015, 'The biological water-oxidizing complex at the nano-bio interface', TRENDS IN PLANT SCIENCE, vol. 20, no. 9, pp. 559-568.
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Nielsen, DA, Pernice, M, Schliep, M, Sablok, G, Jeffries, TC, Kuehl, M, Wangpraseurt, D, Ralph, PJ & Larkum, AWD 2015, 'Microenvironment and phylogenetic diversity of Prochloron inhabiting the surface of crustose didemnid ascidians', ENVIRONMENTAL MICROBIOLOGY, vol. 17, no. 10, pp. 4121-4132.
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Nielsen, M, Revsbech, NP & Kuehl, M 2015, 'Microsensor measurements of hydrogen gas dynamics in cyanobacterial microbial mats', FRONTIERS IN MICROBIOLOGY, vol. 6.
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Perdig ao, N, Heinrich, J, Stolte, C, Sabir, KS, Buckley, MJ, Tabor, B, Signal, B, Gloss, BS, Hammang, CJ, Rost, B & others 2015, 'Unexpected features of the dark proteome', Proceedings of the National Academy of Sciences, vol. 112, pp. 15898-15903.

Pernice, M, Dunn, SR, Tonk, L, Dove, SG, Domart-Coulon, I, Hoppe, P, Schintlmeister, A, Wagner, M & Meibom, A 2015, 'A nanoscale secondary ion mass spectrometry study of dinoagellate functional diversity in reef-building corals', Environmental Microbiology, vol. 17, no. 10, pp. 3570-3580.
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Nutritional interactions between corals and symbiotic dinoflagellate algae lie at the heart of the structural foundation of coral reefs. Whilst the genetic diversity of Symbiodinium has attracted particular interest because of its contribution to the sensitivity of corals to environmental changes and bleaching (i.e. disruption of coraldinoflagellate symbiosis), very little is known about the in hospite metabolic capabilities of different Symbiodinium types. Using a combination of stable isotopic labelling and nanoscale secondary ion mass spectrometry (NanoSIMS), we investigated the ability of the intact symbiosis between the reef-building coral Isopora palifera, and Symbiodinium C or D types, to assimilate dissolved inorganic carbon (via photosynthesis) and nitrogen (as ammonium). Our results indicate that Symbiodinium types from two clades naturally associated with I.?palifera possess different metabolic capabilities. The Symbiodinium C type fixed and passed significantly more carbon and nitrogen to its coral host than the D type. This study provides further insights into the metabolic plasticity among different Symbiodinium types in hospite and strengthens the evidence that the more temperature-tolerant Symbiodinium D type may be less metabolically beneficial for its coral host under non-stressful conditions.

Pulpitel, T, Pernice, M, Simpson, SJ & Ponton, F 2015, 'Tissue-Specific Immune Gene Expression in the Migratory Locust, Locusta Migratoria.', Insects, vol. 6, no. 2, pp. 368-380.
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The ability of hosts to respond to infection involves several complex immune recognition pathways. Broadly conserved pathogen-associated molecular patterns (PAMPs) allow individuals to target a range of invading microbes. Recently, studies on insect innate immunity have found evidence that a single pathogen can activate different immune pathways across species. In this study, expression changes in immune genes encoding peptidoglycan-recognition protein SA (PGRP-SA), gram-negative binding protein 1 (GNBP1) and prophenoloxidase (ProPO) were investigated in Locusta migratoria, following an immune challenge using injected lipopolysaccharide (LPS) solution from Escherichia coli. Since immune activation might also be tissue-specific, gene expression levels were followed across a range of tissue types. For PGRP-SA, expression increased in response to LPS within all seven of the tissue-types assayed and differed significantly between tissues. Expression of GNBP1 similarly varied across tissue types, yet showed no clear expression difference between LPS-injected and uninfected locusts. Increases in ProPO expression in response to LPS, however, could only be detected in the gut sections. This study has revealed tissue-specific immune response to add a new level of complexity to insect immune studies. In addition to variation in recognition pathways identified in previous works, tissue-specificity should be carefully considered in similar works.

Radford, D, Szabo, M, Raven, J & Ralph, PJ 2015, 'SATISFYING THE NUTRIENT TANK OF NANNOCHLOROPSIS OCULATA; CO-LIMITATION REDUCES FILLING EFFICIENCY', EUROPEAN JOURNAL OF PHYCOLOGY, vol. 50, pp. 138-139.

Raven, J & Ralph, PJ 2015, 'Enhanced biofuel production using optimality, pathway modification and waste minimization', Journal of Applied Phycology, vol. 27, pp. 1-31.
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In response to their environment, algae in the wild may use an approximation to optimality of resource allocation in cellular structures, photosynthetic pigments, enzymes, transporters in membranes and RNAs and in their genetic material. However, under controlled conditions, when algae are grown for biofuel (lipid) production for example, some of these processes can be altered to increase the efficiency of photosynthesis and therefore, lipid yield. This suggests that there is scope for selecting mutations and for genetic engineering at various levels in the photosynthetic apparatus with the aim of increasing efficiency of photon use and the rate of transformation of resources per unit biomass to improve biofuel yields. More specifically, the wavelength range covered by photosynthetic pigments and photochemical reaction centres could be increased, the number of protons transported from the thylakoid lumen to the stroma per unit ATP synthesised by the ATP synthetase could be decreased, the fluctuating light effect could be utilised and photosynthetic pathways changed, e.g. replacing part or all of the current machinery for autotrophic fixation of inorganic carbon. There are also possibilities for decreasing carbon loss by decreasing `wasteful aspects of dark respiration and of dissolved organic carbon loss. Provided that the environmental fluctuations to which algal growth conditions are constrained, there are possibilities for decreasing the resource costs of protection from ROS, and by down-regulating photoprotective mechanisms, as well as limiting the capacity to repair processes related to photoinhibition. Decreased protein turnover is also a potential energetic saving. These interventions apply to individual processes; however, this may not be immediately incorporated into the optimal allocation of resources by the alga, and further intervention using a system biology approach may be required.

Rickelt, LF, Ottosen, LDM & Kuhl, M 2015, 'Etching of multimode optical glass fibers: A new method for shaping the measuring tip and immobilization of indicator dyes in recessed fiber-optic microprobes', SENSORS AND ACTUATORS B-CHEMICAL, vol. 211, pp. 462-468.
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Sablok, G, Raju, GVP, Mudunuri, SB, Prabha, R, Singh, DP, Baev, V, Yahubyan, G, Ralph, PJ & La Porta, N 2015, 'ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection', DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
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Sablok, G, Srivastva, AK, Suprasanna, P, Baev, V & Ralph, PJ 2015, 'isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology.', Frontiers in plant science, vol. 6, pp. 949-949.
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Schliep, M, Pernice, M, Sinutok, S, Bryant, CV, York, PH, Rasheed, MA & Ralph, PJ 2015, 'Evaluation of Reference Genes for RT-qPCR Studies in the Seagrass Zostera muelleri Exposed to Light Limitation', SCIENTIFIC REPORTS, vol. 5.
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Siboni, N, Abrego, D, Evenhuis, C, Logan, M & Motti, CA 2015, 'Adaptation to local thermal regimes by crustose coralline algaedoes not affect rates of recruitment in coral larvae', Coral Reefs, vol. 34, pp. 1243-1253.
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Crustose coralline algae (CCA) are well known for their ability to induce settlement in coral larvae. While their wide distribution spans reefs that differ substantially in temperature regimes, the extent of local adaptation to these regimes and the impact they have on CCA inductive ability are unknown. CCA Porolithon onkodes from Heron (southern) and Lizard (northern) islands on Australia’s Great Barrier Reef (separated by 1181 km) were experimentally exposed to acute or prolonged thermal stress events and their thermal tolerance and recruitment capacity determined. A sudden onset bleaching model was developed to determine the health status of CCA based on the rate of change in the CCA live surface area (LSA). The interaction between location and temperature was significant (F (2,119) = 6.74, p = 0.0017), indicating that thermally driven local adaptation had occurred. The southern population remained healthy after prolonged exposure to 28 °C and exhibited growth compared to the northern population (p = 0.022), with its optimum temperature determined to be slightly below 28 °C. As expected, at the higher temperatures (30 and 32 °C) the Lizard Island population performed better that those from Heron Island, with an optimum temperature of 30 °C. Lizard Island CCA displayed the lowest bleaching rates at 30 °C, while levels consistently increased with temperature in their southern counterparts. The ability of those CCA deemed thermally tolerant (based on LSA) to induce Acropora millepora larval settlement was then assessed. While spatial differences influenced the health and bleaching levels of P. onkodes during prolonged and acute thermal exposure, thermally tolerant fragments, regardless of location, induced similar rates of coral larval settlement. This confirmed that recent thermal history does not influence the ability of CCA to induce settlement of A. millepora larvae.

Silsbe, GM, Oxborough, K, Suggett, DJ, Forster, RM, Ihnken, S, Komarek, O, Lawrenz, E, Prasil, O, Rottgers, R, Sicner, M, Simis, SGH, Van Dijk, MA & Kromkamp, JC 2015, 'Toward autonomous measurements of photosynthetic electron transport rates: An evaluation of active fluorescence-based measurements of photochemistry', Limnology and Oceanography: Methods, vol. 13, no. 3, pp. 138-155.
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Suggett, DJ, Goyen, S, Evenhuis, C, Szabo, M, Pettay, DT, Warner, ME & Ralph, PJ 2015, 'Functional diversity of photobiological traits within the genus Symbiodinium appears to be governed by the interaction of cell size with cladal designation', New Phytologist, vol. 208, no. 2, pp. 370-381.
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© 2015 New Phytologist Trust. Dinoflagellates of the genus Symbiodinium express broad diversity in both genetic identity (phylogeny) and photosynthetic function to presumably optimize ecological success across extreme light environments; however, whether differences in the primary photobiological characteristics that govern photosynthetic optimization are ultimately a function of phylogeny is entirely unresolved. We applied a novel fast repetition rate fluorometry approach to screen genetically distinct Symbiodinium types (n = 18) spanning five clades (A-D, F) for potential phylogenetic trends in factors modulating light absorption (effective cross-section, reaction center content) and utilization (photochemical vs dynamic nonphotochemical quenching; [1 - C] vs [1 - Q]) by photosystem II (PSII). The variability of PSII light absorption was independent of phylogenetic designation, but closely correlated with cell size across types, whereas PSII light utilization intriguingly followed one of three characteristic patterns: (1) similar reliance on [1 - C] and [1 - Q] or (2) preferential reliance on [1 - C] (mostly A, B types) vs (3) preferential reliance on [1 - Q] (mostly C, D, F types), and thus generally consistent with cladal designation. Our functional trait-based approach shows, for the first time, how Symbiodinium photosynthetic function is governed by the interplay between phylogenetically dependent and independent traits, and is potentially a means to reconcile complex biogeographic patterns of Symbiodinium phylogenetic diversity in nature.

Sutherland, DL, Howard-Williams, C, Turnbull, MH, Broady, PA & Craggs, RJ 2015, 'Enhancing microalgal photosynthesis and productivity in wastewater treatment high rate algal ponds for biofuel production', BIORESOURCE TECHNOLOGY, vol. 184, pp. 222-229.
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Sutherland, DL, Howard-Williams, C, Turnbull, MH, Broady, PA & Craggs, RJ 2015, 'Frequency of CO2 supply affects wastewater microalgal photosynthesis, productivity and nutrient removal efficiency in mesocosms: implications for full-scale high rate algal ponds', JOURNAL OF APPLIED PHYCOLOGY, vol. 27, no. 5, pp. 1901-1911.
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Sutherland, DL, Howard-Williams, C, Turnbull, MH, Broady, PA & Craggs, RJ 2015, 'The effects of CO2 addition along a pH gradient on wastewater microalgal photo-physiology, biomass production and nutrient removal', WATER RESEARCH, vol. 70, pp. 9-26.
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Sutherland, DL, Montemezzani, V, Howard-Williams, C, Turnbull, MH, Broady, PA & Craggs, RJ 2015, 'Modifying the high rate algal pond light environment and its effects on light absorption and photosynthesis', WATER RESEARCH, vol. 70, pp. 86-96.
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Tamburic, B, Evenhuis, CR, Suggett, DJ, Larkum, AWD, Raven, JA & Ralph, PJ 2015, 'Gas Transfer Controls Carbon Limitation During Biomass Production by Marine Microalgae', CHEMSUSCHEM, vol. 8, no. 16, pp. 2727-2736.
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Taylor, DL, Thevarajah, JJ, Narayan, DK, Murphy, P, Mangala, MM, Lim, S, Wuhrer, R, Lefay, C, O'Connor, MD, Gaborieau, M & Castignolles, P 2015, 'Real-time monitoring of peptide grafting onto chitosan films using capillary electrophoresis', ANALYTICAL AND BIOANALYTICAL CHEMISTRY, vol. 407, no. 9, pp. 2543-2555.
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Tebben, J, Motti, CA, Siboni, N, Tapiolas, DM, Negri, AP, Schupp, PJ, Kitamura, M, Hatta, M, Steinberg, PD & Harder, T 2015, 'Chemical mediation of coral larval settlement by crustose coralline algae', SCIENTIFIC REPORTS, vol. 5.
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Thode, SK, Kahlke, T, Robertsen, EM, Hansen, H & Haugen, P 2015, 'The immediate global responses of Aliivibrio salmonicida to iron limitations', BMC MICROBIOLOGY, vol. 15.
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Thompson, PA, Bonham, P, Thomson, P, Rochester, W, Doblin, MA, Waite, AM, Richardson, A & Rousseaux, CS 2015, 'Climate variability drives plankton community composition changes: the 2010-2011 El Nino to La Nina transition around Australia', JOURNAL OF PLANKTON RESEARCH, vol. 37, no. 5, pp. 966-984.
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Thomson, AC, York, PH, Smith, TM, Sherman, CD, Booth, DJ, Keough, MJ, Ross, DJ & Macreadie, PI 2015, 'Seagrass Viviparous Propagules as a Potential Long-Distance Dispersal Mechanism', Estuaries and Coasts, vol. 38, no. 3, pp. 927-940.
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Resilience of seagrass meadows relies on the ability of seagrass to successfully recolonise denuded areas or disperse to new areas. While seed germination and rhizome extension have been explored as modes of recovery and expansion, the contribution of seagrass viviparous propagules to meadow population dynamics has received little attention. Here, we investigated the potential of seagrass viviparous propagules to act as dispersal vectors. We performed a series of density surveys, and in situ and mesocosm-based experiments in Port Phillip Bay, VIC, Australia, using Zostera nigricaulis, a species known to produce viviparous propagules. Production of viviparous propagules was higher at sites with high wind and current exposure, compared to more sheltered environments. A number of propagules remained buoyant and healthy for more than 85 days, suggesting the capacity for relatively long-distance dispersal. Transplanted propagules were found to have improved survivorship within seagrass habitats compared to bare sediment over the short term (4 weeks); however, all propagules suffered longer-term (<100 days) mortality in field experiments. Conditions outside of meadows, including sediment scouring, reduced the likelihood of successful colonisation in bare sediment. Furthermore, sediment characteristics within meadows, such as a smaller grain size and high organic content, positively influenced propagule establishment. This research provides preliminary evidence that propagules have the potential to act as an important long-distance dispersal vector, a process that has previously gone unrecognised. Even though successful establishment of propagules may be rare, viviparous propagules show great potential for seagrass populations given they are facing global decline.

Thomson, ACG, York, PH, Smith, TM, Sherman, CDH, Booth, DJ, Keough, MJ, Ross, DJ & Macreadie, PI 2015, 'Response to "Comment on 'Seagrass Viviparous Propagules as a Potential Long-Distance Dispersal Mechanism' by A. C. G. Thomson et al"', ESTUARIES AND COASTS, vol. 39, no. 3, pp. 875-876.
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Tian, C, Pei, H, Hu, W, Hao, D, Doblin, MA, Ren, Y, Wei, J & Feng, Y 2015, 'Variation of phytoplankton functional groups modulated by hydraulic controls in Hongze Lake, China', ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH, vol. 22, no. 22, pp. 18163-18175.
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Tout, J, Jeffries, TC, Petrou, K, Tyson, GW, Webster, NS, Garren, M, Stocker, R, Ralph, PJ & Seymour, JR 2015, 'Chemotaxis by natural populations of coral reef bacteria', ISME JOURNAL, vol. 9, no. 8, pp. 1764-1777.
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Tout, J, Siboni, N, Messer, LF, Garren, M, Stocker, R, Webster, NS, Ralph, PJ & Seymour, JR 2015, 'Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis', Frontiers in Microbiology, vol. 6, pp. 1-12.
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Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2–3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2–3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.

Tout, J, Siboni, N, Messer, LF, Garren, M, Stocker, R, Webster, NS, Ralph, PJ & Seymour, JR 2015, 'Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis.', Frontiers in Microbiology, vol. 6, pp. 432-432.
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Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2-3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2-3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.

Trampe, E, Hansen, PJ & Kuhl, M 2015, 'A comparison of photosynthesis measurements by O-2 evolution, C-14 assimilation, and variable chlorophyll fluorescence during light acclimatization of the diatom Coscinodiscus granii', ALGAE, vol. 30, no. 2, pp. 103-119.
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Trevathan-Tackett, SM, Kelleway, J, Macreadie, PI, Beardall, J, Ralph, P & Bellgrove, A 2015, 'Comparison of marine macrophytes for their contributions to blue carbon sequestration', ECOLOGY, vol. 96, no. 11, pp. 3043-3057.
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Tschitschko, B, Williams, TJ, Allen, MA, Paez-Espino, D, Kyrpides, N, Zhong, L, Raftery, MJ & Cavicchioli, R 2015, 'Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation', ISME JOURNAL, vol. 9, no. 9, pp. 2094-2107.
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Wilkinson, AD, Collier, CJ, Flores, F, Mercurio, P, O'Brien, J, Ralph, PJ & Negri, AP 2015, 'A Miniature Bioassay for Testing the Acute Phytotoxicity of Photosystem II Herbicides on Seagrass', PLOS ONE, vol. 10, no. 2.
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Woodcock, S, Manojlovic, B, Baird, ME & Ralph, PJ 2015, 'A Poisson-Pareto Model of chlorophyll-A Fluorescence Signals in Marine Environments', Australia and New Zealand Industrial and Applied Mathematics (ANZIAM) Journal, vol. 56, no. 4, pp. 373-370.
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Zavafer, A, Cheah, MH, Hillier, W, Chow, WS & Takahashi, S 2015, 'Photodamage to the oxygen evolving complex of photosystem II by visible light', SCIENTIFIC REPORTS, vol. 5.
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Zavafer, A, Chow, WS & Cheah, MH 2015, 'The action spectrum of Photosystem II photoinactivation in visible light', JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, vol. 152, pp. 247-260.
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Zavrel, T, Sinetova, MA, Buzova, D, Literakova, P & Cerveny, J 2015, 'Characterization of a model cyanobacterium Synechocystis sp PCC 6803 autotrophic growth in a flat-panel photobioreactor', ENGINEERING IN LIFE SCIENCES, vol. 15, no. 1, pp. 122-132.
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Ajani, P, Hallegraeff, GM, Kohli, G & Murray, S 2015, 'Population structure of ecologically significant diatoms in south eastern Australia using microsatellite markers', Molecular Life of Diatoms Conference, Washington, USA.

Craggs, RJ, Park, J, Sutherland, DL & Heubeck, S 2015, 'Enhancements of wastewater treatment High Rate Algal Ponds', Japanese Algae Workshop, Hamilton, New Zealand.

Craggs, RJ, Park, J, Sutherland, DL & Heubeck, S 2015, 'Hectare-scale wastewater treatment and resource recovery high rate algal ponds', Green and Life Innovations by Algae Biomass Symposium, Japan.

Craggs, RJ, Park, J, Sutherland, DL & Heubeck, S 2015, 'Initial performance of the Cambridge enhanced pond system', Waipa District Council Wastewater Project Advisory Group Meeting 20th April, Cambridge, Cambridge, NZ.

Fedorko, J, Buzova, D & Cerveny, J 2015, 'Development of methods for breeding high-lipid-content algal strain Chlamydomonas reinhardtii using fluorescence-activated cell sorting', GLOBAL CHANGE: A COMPLEX CHALLENGE, 4th Annual Global Change - A Complex Challenge, GLOBAL CHANGE RESEARCH CENTRE CAS, Brno, CZECH REPUBLIC, pp. 150-153.

Huete, A, Xie, Z, Restrepo-Coupe, N, Devadas, R, Davies, K & Waston, C 2015, 'Terrestrial Total Water Storage Dynamics Of Australia's Recent Dry And Wet Events', Proceedings of the 2015 IEEE International Geoscience and Remote Sensing Symposium (IGARSS), 2015 IEEE International Geoscience and Remote Sensing Symposium (IGARSS), IEEE, Milan, pp. 992-995.
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Australia recently experienced a long-term continental drought (“big dry”, 2001-2009) followed by an anomalous wet two-year period (“big wet”, 2010-2011). Despite the significance of the two extreme events, continental-wide information regarding the effects of the high and low precipitation conditions on the hydrological components, stress and recovery is not available. In this paper, we use terrestrial total water storage changes (ATWS) from the Gravity Recovery and Climate Experiment (GRACE) and precipitation data from the Tropical Rainfall Measuring Mission (TRMM) spanning from 2002 to 2013, where ATWS represents the main source of water available for human consumption, agriculture and natural ecosystems. We rely on a combination of temporal trend analysis and spatial statistics methods in order to evaluate the terrestrial total water storage (TWS) dynamics and the relationship between TWS and rainfall during the “big dry” and “big wet” events. Here we report the occurrence of hydrological cycle intensification during the study period in Australia which exhibited strong spatial variations: the wet areas (the northern and northeast regions) got wetter while the dry areas (the west and interior of the continent) became drier. By contrast, in southeastern Australia TWS changes over time showed sudden extreme responses to both events. Our results constitute a step beyond quantifying droughts/anomalous wet years that rely solely on precipitation data. This work demonstrates the ability of TWS observations as a significant indicator of hydrological system performance during hydroclimatic events and also an important tool for understanding continental-wide and regional spatial and temporal patterns of water availability.

Tanner, C, Sukias, J, de Winton, M, Larned, S, Sutherland, DL & Hughs, AA 1970, 'Te Waihora wetland assessment', Whakaora Te Waihora and Te Waihora Zone Committee.

Zavrel, T, Ocenasova, P, Sinetova, M & Cerveny, J 2015, 'Comparative growth characterization of frequently used substrains of the model cyanobacterium Synechocystis sp PCC 6803 under varying culture conditions', GLOBAL CHANGE: A COMPLEX CHALLENGE, 4th Annual Global Change - A Complex Challenge, GLOBAL CHANGE RESEARCH CENTRE CAS, Brno, CZECH REPUBLIC, pp. 154-157.

Pernice, M, Schliep, M, Szabo, M, Rasheed, M, Bryant, C, York, P, Chartrand, K & Petrou, K 2015, Development of a molecular biology tool kit to monitor dredging-related light stress in the seagrass Zostera muelleri ssp. capricorniin Port Curtis - final report, no. 15/08, Cairns.
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Roberts, C, Nicastro, A, Pernice, M & Blount, C 2015, Coral Monitoring Post-Dredging Report − Ichthys Nearshore Environmental Monitoring Program, pp. 1-249, Sydney.
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Ruvindy, R, Ajani, P & Murray, S 2015, Microalgal Community Composition Assessment in Warringah Lagoons 2014-2015.

Sigel, B, Plew, D, Hamilton, D, Sutherland, D & Howard-Williams, C 2015, Updated model assessment of the effects of increased nutrient loads into Lake Benmore, Christchurch.

Sutherland, D 2015, Ecological impact of the salmon farms in the Upper Waitaki hydro-canals, Christchurch.

Sutherland, D & Burton, T 2015, Assessment of the ecological condition of six Canterbury lakes using LakeSPI and weed surveillance in sixteen lakes, Christchurch.

Sutherland, D, Inder, F, Molineux, M & Wells, R 2015, Monitoring the potential effects of MTAD on the Waiau Arm water quality and macrophytes: year three, Christchurch.

Sutherland, DL 2015, Assessment of Ulva / Graciliaria growth dynamics in the Avon-Heathcote Estuary, Christchurch, NZ.

Sutherland, DL 2015, Water quality in the Wainono Lagoon and potential impacts of proposed flow augmentation on water clarity. Evidence prepared for the Proposed Plan Change 3 (SCCS Area) to the Operative Canterbury Land and Water Regional Plan, Christchurch, NZ.

Sutherland, DL & Craggs, RJ 2015, Alofi wastewater management project. Project design document., Christchurch, NZ.

Baker, KG, Doblin, MA & Robinson, C 2015, 'THERMAL PERFORMANCE CURVES REVEAL ALTERNATIVE ENERGY PATHWAYS AT STRESSFUL TEMPERATURES: A MULTI-TRAIT ANALYSIS OF PHENOTYPIC PLASTICITY IN THALASSIOSIRA PSEUDONANA'.

Hughes, DJ, Doblin, MA, Ralph, PJ, van Dongen-Vogels, V, Ingleton, T & Suggett, DJ 2015, 'NITROGEN AVAILABILITY DRIVES VARIABILITY OF THE ELECTRON REQUIREMENT FOR CARBON FIXATION IN COASTAL PHYTOPLANKTON COMMUNITIES'.