Publications

Ralph, PJ, Hill, R, Doblin, MA & Davy, SK 2015, 'Theory and Application of Pulse Amplitude Modulated Chlorophyll Fluorometry in Coral Health Assessment' in Woodley, CM, Downs, CA, Bruckner, AW, Porter, JW & Galloway, SB (eds), Diseases of Coral, Wiley, Hoboken, New Jersey, pp. 506-523.
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© 2016 John Wiley & Sons, Inc. Scleractinian corals exist in symbiosis with dinoflagellate alga (genus Symbiodinium), which provides access to nutrients by the host but also makes it makes the holobiont vulnerable to photosynthetic stress, providing an opportunity for rapid health assessment using chlorophyll a (chl-a) fluorescence techniques. Common photosynthetic stressors of corals are high irradiance, ultraviolet light, temperature extremes, chemical pollution and low salinity, which are further compounded by other major anthropogenic pressures on coral reefs. Coral Symbiodinium cells contain chlorophyll (chl) a, c2 and a range of accessory pigments. The chl-a within the pigment complex absorbs light maximally in the blue (peak at 440 nm) and red (peak at 678 nm) regions of the spectrum and re-emits light energy in the form of fluorescence, maximally in the red bandwidth (630 to 770 m with a peak at 680 nm). In vivo chl-a has a variable fluorescence yield that is dependent upon the wavelength of excitation irradiance and varies over time as a result of the complex interaction of the photosynthetic pathways (Kautsky effect). When a chloroplast captures a photon of energy, the chl a molecule is excited from its ground state to an excited state. There are three competing and complementary energy dissipation processes for that excited molecule: (i) driving photosynthesis via the electron transport chain leading to carbon fixation, (ii) heat dissipation, or (iii) returning to the ground state and re-emitting some of the energy as fluorescence. This is why chl a fluorescence can be used as a proxy for photochemistry (and energy dissipation). During periods of high incident irradiance, if the amount of absorbed light exceeds the maximum rate of electron transport, then the excess energy must be dissipated, or photodamage can occur. Pulse-amplitude modulated (PAM) fluorometry provides a versatile technique for monitoring and assessing zooxanthellae health. It measure...

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 Published by Elsevier Ltd. 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 Published by Elsevier Ltd. 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.

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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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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© 2014 New Phytologist Trust. Seagrass is constantly challenged with transporting sufficient O2 from above- to belowground tissue via aerenchyma in order to maintain aerobic metabolism and provide protection against phytotoxins. Electrochemical microsensors were used in combination with a custom-made experimental chamber to analyse the belowground biogeochemical microenvironment of Zostera muelleri under changing environmental conditions. Measurements revealed high radial O2 release of up to 500 nmol O2 cm-2 h-1 from the base of the leaf sheath, maintaining a c. 300-μm-wide plant-mediated oxic microzone and thus protecting the vital meristematic regions of the rhizome from reduced phytotoxic metabolites such as hydrogen sulphide (H2S). H2S intrusion was prevented through passive diffusion of O2 to belowground tissue from leaf photosynthesis in light, as well as from the surrounding water column into the flow-exposed plant parts during darkness. Under water column hypoxia, high belowground H2S concentrations at the tissue surface correlated with the inability to sustain the protecting oxic microshield around the meristematic regions of the rhizome. We also found increased pH levels in the immediate rhizosphere of Z. muelleri, which may contribute to further detoxification of H2S through shifts in the chemical speciation of sulphide. Zostera muelleri can modify the geochemical conditions in its immediate rhizosphere, thereby reducing its exposure to H2S.

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, M, Zavřel, T & Los, D 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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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, JGY, Tyne, AS, Pang, A, McLachlan, AJ, Perera, V, Chan, JCY, Britton, WJ, Chan, HK, Duke, CC, Young, PM & Traini, D 2015, 'Murine pharmacokinetics of rifapentine delivered as an inhalable dry powder', International Journal of Antimicrobial Agents, vol. 45, no. 3, pp. 319-323.
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Chan, Y, 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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SummaryAcaryochloris marina is a symbiotic species of cyanobacteria that is capable of utilizing far‐red light. We report the characterization of the phages A‐HIS1 and A‐HIS2, capable of infecting Acaryochloris. Morphological characterization of these phages places them in the family Siphoviridae. However, molecular characterization reveals that they do not show genetic similarity with any known siphoviruses. While the phages do show synteny between each other, the nucleotide identity between the phages is low at 45–67%, suggesting they diverged from each other some time ago. The greatest number of genes shared with another phage (a myovirus infecting marine Synechococcus) was four. Unlike most other cyanophages and in common with the Siphoviridae infecting Synechococcus, no photosynthesis‐related genes were found in the genome. CRISPR (clustered regularly interspaced short palindromic repeats) spacers from the host

Chejara, DR, Kondaveeti, S & Siddhanta, AK 2015, 'Facile synthesis of new sodium alginate–anthracene based photosensitizers', Polymer Bulletin, vol. 72, no. 1, pp. 35-48.
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Chen, S, Sun, B, Xie, X, Mondal, AK, Huang, X & Wang, G 2015, 'Multi-chambered micro/mesoporous carbon nanocubes as new polysulfides reserviors for lithium-sulfur batteries with long cycle life', NANO ENERGY, vol. 16, pp. 268-280.
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© 2015 Elsevier Ltd. Achieving rechargeable batteries with high-energy density, long cycle life and excellent rate capability is of significant importance for a vast energy-consuming society. Lithium sulfur (Li-S) batteries, attracting extensive attentions, are regarded as one of the most promising energy storage system. However, Li-S batteries are facing big challenges, owing to the fast capacity degradation, low Coulombic efficiency and poor rate capabilities. By adopting a dual confinement strategy, we successfully synthesized homogenous poly(3,4-ethylenedioxythiophene) (PEDOT) coated multi-chambered micro/mesoporous carbon nanocube encapsulated sulfur (P@CNC-S) composites. Sulfur is impregnated in individual interconnected multi-chambered micro/mesoporous carbon nanocubes, which act as the physical confinement and multilayered reservoirs for soluble lithium polysulfides. The PEDOT conductive polymer provides chemical bondings to soluble lithium polysulfides. When applied as cathodes in Li-S batteries, the P@CNC-S composites exhibited superior performances, including high specific capacities, long cycle life and outstanding high rate capabilities. Ex-situ TEM analysis confirmed the successful confinement of the dissolution of lithium polysulfides and volume expansion of the discharged product (Li2S), which could contribute to the high Coulombic efficiency and excellent cyclabilities.

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', The ISME Journal, vol. 9, no. 10, pp. 2261-2274.
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Abstract 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.

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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© 2015 Elsevier Ltd. Determining the magnitude of primary production (PP) in a changing ocean is a major research challenge. Thousands of estimates of marine PP exist globally, but there remain significant gaps in data availability, particularly in the Southern Hemisphere. In situ PP estimates are generally single-point measurements and therefore we rely on satellite models of PP in order to scale up over time and space. To reduce the uncertainty around the model output, these models need to be assessed against in situ measurements before use. This study examined the vertically-integrated productivity in four water-masses associated with the East Australian Current (EAC), the major western boundary current (WBC) of the South Pacific. We calculated vertically integrated PP from shipboard ¹⁴C PP estimates and then compared them to estimates from four commonly used satellite models (ESQRT, VGPM, VGPM-Eppley, VGPM-Kameda) to assess their utility for this region. Vertical profiles of the water-column show each water-mass had distinct temperature-salinity signatures. The depth of the fluorescence-maximum (fmax) increased from onshore (river plume) to offshore (EAC) as light penetration increased. Depth integrated PP was highest in river plumes (792±181mgCm^-2d^-1) followed by the EAC (534±116mgCm^-2d^-1), continental shelf (140±47mgCm^-2d^-1) and cyclonic eddy waters (121±4mgCm^-2d^-1). Surface carbon assimilation efficiency was greatest in the EAC (301±145mgC (mgChl-a)^-1d^-1) compared to other water masses. All satellite primary production models tested underestimated EAC PP and overestimated continental shelf PP. The ESQRT model had the highest skill and lowest bias of the tested models, providing the best first-order estimates of PP on the continental shelf, including at a coastal time-series station, Port Hacking, which showed conside...

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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AbstractBiogenic 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 forBVOCs 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 ofBVOCs on the planet. Here, we synthesize our existing understanding ofBVOCemissions to produce a novel conceptual framework of the tropical marine coast as a continuum fromDMS‐dominated reef producers to isoprene‐dominated mangroves. We use existing and previously unpublished data to consider how current environmental conditions shapeBVOCproduction across the tropical coastal continuum, and in turn howBVOCs 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 coastalBVOCemissions, and the roles they play, are effectively restricted to present day ‘baseline’ trends ofBVOCproductio...

Fristedt, R, Herdean, A, Blaby-Haas, CE, Mamedov, F, Merchant, SS, Last, RL & Lundin, B 2015, 'PHOTOSYSTEM II PROTEIN33, a Protein Conserved in the Plastid Lineage, Is Associated with the Chloroplast Thylakoid Membrane and Provides Stability to Photosystem II Supercomplexes in Arabidopsis', Plant Physiology, vol. 167, no. 2, pp. 481-492.
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Frommlet, JC, Sousa, ML, Alves, A, Vieira, SI, Suggett, DJ & Serôdio, J 2015, 'Coral symbiotic algae calcify ex hospite in partnership with bacteria', Proceedings of the National Academy of Sciences, vol. 112, no. 19, pp. 6158-6163.
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Significance The dinoflagellate genus Symbiodinium is best known for harboring important endosymbiotic algae of marine invertebrates, notably reef-building corals. However, these dinoflagellates also live freely within coral reef waters and sediments and provide an important environmental pool for the colonization of new coral recruits. Although Symbiodinium facilitate coral calcification indirectly when in hospite , we show that they also can calcify in partnership with bacteria when free living. This discovery offers entirely new perspectives on fundamental questions regarding the life cycle and ecology of these dinoflagellates and could help explain how changes in ocean chemistry created a selective pressure that ultimately led Symbiodinium to establish an endosymbiotic life style. To our knowledge, our findings document the first identified dinoflagellate–bacterial calcifying community.

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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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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© 2014 Elsevier B.V. Growth limitation of marine algae due to lack of iron occurs in up to 40% of the global ocean. Despite important advances on the impact of organic compounds on iron biogeochemistry, their roles in controlling iron availability to prokaryotic and eukaryotic phytoplankton remain unclear. Whether algal and bacterial exopolymeric substances (EPS) include organic ligands which may help iron-limited phytoplankton growth remains an unknown. If so, then EPS could relieve phytoplankton iron limitation with implications for the biological carbon pump and hence the regulation of atmospheric CO2. Here we compared the biological impact of algal, bacterial and in situ EPS with model compounds, a siderophore and two saccharides on biological parameters including, iron bioavailability, phytoplankton growth, photo-physiology and community structure. Laboratory and field experiments demonstrated that EPS produced by marine microorganisms are efficient in sustaining biological iron uptake as well as algal growth, and can affect natural phytoplankton community structure. Our data suggest that natural phytoplankton growth enhancement in the presence of EPS was not solely due to highly bioavailable iron forms, but also because EPS contains other micronutrients. Stronger ligands were detected following iron-siderophore enrichments (log KFe'L=12.0) and weaker ligands were measured in the presence of EPS (log KFe'L=10.4-11.0). The trend of the conditional stability constants of organic ligands did not seem to be affected as a result of biological activity and photo-chemistry during our four day incubations. The shift in the phytoplankton community observed during our field experiments was not uniformly observed between different sites rendering it difficult to extrapolate which functional group(s) would benefit the most from iron bound to EPS.

Henschke, N, Everett, JD, Suthers, KM, 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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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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© 2015 CSIRO. Sydney Harbour is a global hotspot for marine and estuarine diversity. Despite its social, economic and biological value, the available knowledge has not previously been reviewed or synthesised. We systematically reviewed the published literature and consulted experts to establish our current understanding of the Harbour's natural systems, identify knowledge gaps, and compare Sydney Harbour to other major estuaries worldwide. Of the 110 studies in our review, 81 focussed on ecology or biology, six on the chemistry, 10 on geology and 11 on oceanography. Subtidal rocky reef habitats were the most studied, with a focus on habitat forming macroalgae. In total 586 fish species have been recorded from the Harbour, which is high relative to other major estuaries worldwide. There has been a lack of process studies, and an almost complete absence of substantial time series that constrains our capacity to identify trends, environmental thresholds or major drivers of biotic interactions. We also highlight a lack of knowledge on the ecological functioning of Sydney Harbour, including studies on microbial communities. A sound understanding of the complexity, connectivity and dynamics underlying ecosystem functioning will allow further advances in management for the Harbour and for similarly modified estuaries around the world.

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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Karlsson, PM, Herdean, A, Adolfsson, L, Beebo, A, Nziengui, H, Irigoyen, S, Ünnep, R, Zsiros, O, Nagy, G, Garab, G, Aronsson, H, Versaw, WK & Spetea, C 2015, 'The Arabidopsis thylakoid transporter PHT4;1 influences phosphate availability for ATP synthesis and plant growth', The Plant Journal, vol. 84, no. 1, pp. 99-110.
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SummaryThe Arabidopsis phosphate transporter PHT4;1 was previously localized to the chloroplast thylakoid membrane. Here we investigated the physiological consequences of the absence of PHT4;1 for photosynthesis and plant growth. In standard growth conditions, two independent Arabidopsis knockout mutant lines displayed significantly reduced leaf size and biomass but normal phosphorus content. When mutants were grown in high‐phosphate conditions, the leaf phosphorus levels increased and the growth phenotype was suppressed. Photosynthetic measurements indicated that in the absence of PHT4;1 stromal phosphate was reduced to levels that limited ATP synthase activity. This resulted in reduced CO2 fixation and accumulation of soluble sugars, limiting plant growth. The mutants also displayed faster induction of non‐photochemical quenching than the wild type, in line with the increased contribution of ΔpH to the proton‐motive force across thylakoids. Small‐angle neutron scattering showed a smaller lamellar repeat distance, whereas circular dichroism spectroscopy indicated a perturbed long‐range order of photosystem II (PSII) complexes in the mutant thylakoids. The absence of PHT4;1 did not alter the PSII repair cycle, as indicated by wild‐type levels of phosphorylation of PSII proteins, inactivation ...

Kondaveeti, S, Chudasama, NA, Chaudhary, JP, Meena, R & Siddhanta, AK 2015, 'Functional modification of agarose: Synthesis of nanosize half-esters of succinic, phthalic and maleic acids', Indian Journal of Chemistry - Section A Inorganic, Physical, Theoretical and Analytical Chemistry, vol. 54A, no. 6, pp. 734-743.
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A facile synthetic method for preparing new half-esters of agarose (Ag) with succinic (SA), phthalic (PA) and maleic (MA) acids has been described. The half-esters (Ag-SA, Ag-PA and Ag-MA) wherein the acid moieties are attached to the backbone of the agarose are characterized. Dynamic light scattering measurements show that nano-sized polymeric vesicles (32-124 nm) are formed in aqueous solution. A series of Ag-SA, Ag-PA and Ag-MA derivatives have been prepared with degrees of substitution ranging from 0.36 to 0.89 using varying molar ratios of Ag/SA, Ag/PA and Ag/MA (1:1-1:5). The highest degrees of substitution are found to be 0.89, 0.69 and 0.39 for Ag-SA (1:4), Ag-PA (1:3) and Ag-MA (1:2) respectively. The aqueous solution of sodium salts of these esters exhibit enhanced electrical conductivity (ca. 17.5 mS/cm at 40 °C) as compared to those of the parent half-esters (ca. 0.3 mS/cm at 40 °C). These new agarose based nanosized materials may have potential applications in electrochemical devices, sensors and as drug carriers.

Kondaveeti, S, Chudasama, NA, Chaudhary, JP, Meena, R & Siddhanta, AK 2015, 'Functional modification of agarose: Synthesis of nanosize half-esters of succinic, phthalic and maleic acids', INDIAN JOURNAL OF CHEMISTRY SECTION A-INORGANIC BIO-INORGANIC PHYSICAL THEORETICAL & ANALYTICAL CHEMISTRY, vol. 54, no. 6, pp. 734-743.

Kumar, M, Reddy, CRK & Ralph, PJ 2015, 'Polyamines in morphogenesis and development: a promising research area in seaweeds', Frontiers in Plant Science, vol. 6, no. FEB, 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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© The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2015. Manipulations of urine samples by urine substitution, urine dilution, and urine adulteration with highly oxidative chemicals to escape detection in doping control analysis have been reported in the past. Adulteration of urine with oxidising chemicals such as potassium permanganate, cerium ammonium nitrate, pyridinium chlorochromate etc. can lead to considerable changes in the endogenous steroidal profile parameters and thus mask the abnormality in the steroidal profile following steroid abuse. In this study we have identified the formation of two stable oxidation products upon reaction of potassium permanganate with testosterone, an important endogenous urinary steroid. Isolation and characterisation of these oxidation products were performed using chromatography and spectroscopy and the products were elucidated as 4α,5α-dihydroxytestosterone and 4β,5β-dihydroxytestosterone. Formation of these two molecules in human urine after adulteration with potassium permanganate has been demonstrated by liquid chromatography-mass spectrometry (LC-MS) analysis. The products 4α,5α-dihydroxytestosterone and 4β,5β-dihydroxytestosterone have not been previously reported in urine and hence have the potential to be included in the routine drug testing program for monitoring possible testosterone abuse and permanganate adulteration of urine.

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, pp. 2283-2295.
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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, J-B, Motti, CA, Miller, DJ & van Oppen, MJH 2015, 'Host Coenzyme Q Redox State Is an Early Biomarker of Thermal Stress in the Coral Acropora millepora', PLOS ONE, vol. 10, no. 10, pp. e0139290-e0139290.
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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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© 2014 Elsevier Ltd. The objective of this work is to establish whether algal bio-crude production is environmentally, economically and socially sustainable. To this end, an economic multi-regional input-output model of Australia was complemented with engineering process data on algal bio-crude production. This model was used to undertake hybrid life-cycle assessment for measuring the direct, as well as indirect impacts of producing bio-crude. Overall, the supply chain of bio-crude is more sustainable than that of conventional crude oil. The results indicate that producing 1. million tonnes of bio-crude will generate almost 13,000 new jobs and 4. billion dollars' worth of economic stimulus. Furthermore, bio-crude production will offer carbon sequestration opportunities as the production process is net carbon-negative.

Matthews, JL, Sproles, AE, Oakley, CA, Grossman, AR, Weis, VM & Davy, SK 2015, 'Menthol-induced bleaching rapidly and effectively provides experimental aposymbiotic sea anemones (Aiptasiasp.) for symbiosis investigations', Journal of Experimental Biology, vol. 219, no. Pt 3, pp. 306-310.
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Experimental manipulation of the symbiosis between cnidarians and photosynthetic dinoflagellates (Symbiodinium spp.) is critical to advance understanding of the cellular mechanisms involved in host–symbiont interactions, and overall coral reef ecology. The anemone Aiptasia sp. is a model for the cnidarian-dinoflagellate symbiosis, and notably it can be rendered aposymbiotic (i.e. dinoflagellate-free) and re-infected with a range of Symbiodinium types. Various methods exist for generating aposymbiotic hosts, however they can be hugely time-consuming and not wholly effective. Here, we optimise a method using menthol for production of aposymbiotic Aiptasia. The menthol treatment produced aposymbiotic hosts within just four weeks (97–100% symbiont loss), which was maintained long after treatment when anemones were held under a standard light/dark cycle. The ability of Aiptasia to form a stable symbiosis appeared unaffected by menthol exposure, as demonstrated by successful symbiosis re-establishment when experimentally re-infected. Furthermore, there was no significant impact on photosynthetic or respiratory performance of re-infected anemones.

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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© 2015 CSIRO. Sydney Harbour is a hotspot for diversity. However, as with estuaries worldwide, its diversity and functioning faces increasing threats from urbanisation. This is the first synthesis of threats and impacts in Sydney Harbour. In total 200 studies were reviewed: 109 focussed on contamination, 58 on habitat modification, 11 addressed non-indigenous species (NIS) and eight investigated fisheries. Metal concentrations in sediments and seaweeds are among the highest recorded worldwide and organic contamination can also be high. Contamination is associated with increased abundances of opportunistic species, and changes in benthic community structure. The Harbour is also heavily invaded, but invaders' ecological and economic impacts are poorly quantified. Communities within Sydney Harbour are significantly affected by extensive physical modification, with artificial structures supporting more NIS and lower diversity than their natural equivalents. We know little about the effects of fishing on the Harbour's ecology, and although ocean warming along Sydney is among the fastest in the world, we know little about how the ecosystem will respond to warming. The interactive and cumulative effects of stressors on ecosystem functioning and services in the Harbour are largely unknown. Sustainable management of this iconic natural system requires that knowledge gaps are addressed and translated into coherent environmental plans.

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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Mondal, AK, Chen, S, Su, D, Kretschmer, K, Liu, H & Wang, G 2015, 'Microwave synthesis of alpha-Fe2O3 nanoparticles and their lithium storage properties: A comparative study', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 648, pp. 732-739.
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© 2015 Elsevier B.V. All rights reserved. This work introduces a simple microwave method for the preparation of α-Fe2O3 nanoparticles with two different sizes. Both the materials were characterized by X-ray powder diffraction, scanning electron microscopy, transmission electron microscopy and Brunauer-Emmett-Teller methods. The lithium storage properties were evaluated and compared in terms of their reversible capacity, rate capability and cycling performance. Interestingly, the electrode made of large particles (200-300 nm) show the reversible capacity of 1012 mA h g-1, better rate capability and excellent cycling stability than those of the small particles (20-30 nm). The poor electrochemical performances of small particles can be ascribed to their agglomeration during repeated charging and discharge process. The agglomeration of small particles may substantially decrease the surface area, which results in the lack of sufficient electro active sites for electrochemical reaction.

Najafpour, MM, Ghobadi, MZ, Larkum, AW, Shen, J-R & Allakhverdiev, 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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Pernice, M, Dunn, SR, Tonk, L, Dove, S, Domart‐Coulon, I, Hoppe, P, Schintlmeister, A, Wagner, M & Meibom, A 2015, 'A nanoscale secondary ion mass spectrometry study of dinoflagellate functional diversity in reef‐building corals', Environmental Microbiology, vol. 17, no. 10, pp. 3570-3580.
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SummaryNutritional 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 coral–dinoflagellate 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 S

Pulpitel, T, Pernice, M, Simpson, S & 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.

Raven, JA & Ralph, PJ 2015, 'Enhanced biofuel production using optimality, pathway modification and waste minimization', JOURNAL OF APPLIED PHYCOLOGY, vol. 27, no. 1, 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.

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 algae does not affect rates of recruitment in coral larvae', CORAL REEFS, vol. 34, no. 4, 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, Komárek, O, Lawrenz, E, Prášil, O, Röttgers, R, Šicner, 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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AbstractThis study presents a methods evaluation and intercalibration of active fluorescence‐based measurements of the quantum yield () and absorption coefficient () of photosystem II (PSII) photochemistry. Measurements of , , and irradiance (E) can be scaled to derive photosynthetic electron transport rates (), the process that fuels phytoplankton carbon fixation and growth. Bio‐optical estimates of and were evaluated using 10 phytoplankton cultures across different pigment groups with varying bio‐optical absorption characteristics on six different fast‐repetition rate fluorometers that span two different manufacturers and four differe...

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.

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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© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. This study presents the first in-depth analysis of CO2 limitation on the biomass productivity of the biofuel candidate marine microalga Nannochloropsis oculata. Net photosynthesis decreased by 60 from 125 to 50 μmolO2L^-1h^-1 over a 12 h light cycle as a direct result of carbon limitation. Continuous dissolved O2 and pH measurements were used to develop a detailed diurnal mechanism for the interaction between photosynthesis, gas exchange and carbonate chemistry in the photo-bioreactor. Gas exchange determined the degree of carbon limitation experienced by the algae. Carbon limitation was confirmed by delivering more CO2, which increased net photosynthesis back to its steady-state maximum. This study highlights the importance of maintaining replete carbon concentrations in photo-bioreactors and other culturing facilities, either by constant pH operation or preferably by designing a feedback loop based on the dissolved O2 concentration. Just grow it: We present the first in-depth analysis of CO2 limitation on biomass productivity of the marine microalga Nannochloropsis oculata. Net photosynthesis decreases by 60 over a 12 h light cycle as a direct result of carbon limitation. Continuous dissolved O2 and pH measurements are used to develop a detailed diurnal mechanism for the interaction between photosynthesis, gas exchange and carbonate chemistry in the photo-bioreactor.

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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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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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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© 2015 International Society for Microbial Ecology. All rights reserved. Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral-microbe associations, which may ultimately infl...

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 damicomis', 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.

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.

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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Wang, R, Zhong, Y, Gu, X, Yuan, J, Saeed, AF & Wang, S 2015, 'Corrigendum: The pathogenesis, detection, and prevention of Vibrio parahaemolyticus.', Front Microbiol, vol. 6, pp. 437-437.
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[This corrects the article on p. 144 in vol. 6, PMID: 25798132.].

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', ANZIAM JOURNAL, vol. 56, no. 4, pp. 373-380.
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© Australian Mathematical Society 2015. Because of its central role in the global carbon cycle, quantifying the biomass of photosynthetic microalgae in the oceans is crucial to our ability to estimate the oceans' carbon drawdown. Many traditional methods of primary production assessment have proven to be extremely time consuming and, consequently, have handled only very small sample sizes. The recent advent of in situ bio-optical sensors, such as the water quality monitor (WQM), is now providing lower cost and higher throughput data on these crucial biological communities. These WQMs, however, only quantify the total fluorescence of all individual cells within their optical sample windows, irrespective of size. In this paper, we further develop an established model, based on Pareto random variables, of the size structure of the microalgae community to understand the effect of the WQMs' sampling and data pooling on their estimates of algal biomass. Unfortunately, evaluating sums of Pareto variables is a notoriously difficult problem. Here, we utilize an approximation for the right-tail of the resulting distribution to derive parameter estimates for the underlying size structure of the microalgae community.

Xie, X, Su, D, Zhang, J, Chen, S, Mondal, AK & Wang, G 2015, 'A comparative investigation on the effects of nitrogen-doping into graphene on enhancing the electrochemical performance of SnO₂/graphene for sodium-ion batteries', Nanoscale, vol. 7, no. 7, pp. 3164-3172.
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Enhanced electron transfer efficiency plays a dominant role for improving the performance of SnO₂/N-doped graphene for sodium-ion batteries.

Zavřel, T, Sinetova, MA, Búzová, D, Literáková, P & Červený, 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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We characterized the photoautotrophic growth of glucose‐tolerant Synechocystis sp. PCC 6803 in a flat‐panel photobioreactor running on a semicontinuous regime under various lights, temperatures, and influx carbon dioxide concentrations. The maximum reached growth rate was 0.135 h−1, which corresponds to a doubling time of 5.13 h—a growth speed never reported for Synechocystis before. Saturating red light intensity for the strain was 220–360 μmol(photons) m−2 s−1, and we did not observe any photoinhibition up to 660 μmol(photons) m−2 s−1. Synechocystis was able to grow under red light only; however, photons of wavelengths 405–585 and 670–700 nm further improved its growth. Optimal growth temperature was 35°C. Below 32°C, the growth rates decreased linearly with temperature coefficient (Q10) 1.70. Semicontinuous cultivation is known to be efficient for growth characterization and optimization. However, the assumption of correct growth rates calculation—culture exponential growth—is often not fulfilled. The semicontinuous setup in this study was operated as a turbidostat. Accurate online OD measurements with high time‐resolution allowed fast and reliable growth rates determination. Repeating diluting frequencies (up to 18 dilutions per day) were essential for rapid growth stability evaluation. The presented setup provides improvement to previously published semicontinuous characterization strategies by decreasing experimental time requirements and maintaining the culture in exponential growth phase throughout the entire characterization procedure.

Minh Phan, T, Duy Nguyen, HA & Pacas, M 1970, 'Active Lifetime Extension for a 3L-NPC inverter with Direct Torque Control', 2015 Intl Aegean Conference on Electrical Machines & Power Electronics (ACEMP), 2015 Intl Conference on Optimization of Electrical & Electronic Equipment (OPTIM) & 2015 Intl Symposium on Advanced Electromechanical Motion Systems (ELECTROMOTION), 2015 Intl Aegean Conference on Electrical Machines & Power Electronics (ACEMP), 2015 Intl Conference on Optimization of Electrical & Electronic Equipment (OPTIM) & 2015 Intl Symposium on Advanced Electromechanical Motion Systems (ELECTROMOTION), IEEE, pp. 468-475.
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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.

Roberts, C, Nicastro, A, Pernice, M & Blount, C 2015, Coral Monitoring Post-Dredging Report − Ichthys Nearshore Environmental Monitoring Program, pp. 1-249, Sydney.

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', pp. 166-166.

Fujise, L, Suggett, DJ, Frommlet, JC, Serodio, J & Ralph, PJ 2015, 'TURNING UP THE HEAT ON SYMBIODINIUM CELL CYCLE ANALYSIS', pp. 58-59.

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', pp. 35-35.

Radford, D, Szabo, M, Raven, J & Ralph, PJ 2015, 'SATISFYING THE NUTRIENT TANK OF NANNOCHLOROPSIS OCULATA; CO-LIMITATION REDUCES FILLING EFFICIENCY', TAYLOR & FRANCIS LTD, pp. 138-139.