Publications

Geider, RJ, Moore, CM & Suggett, DJ 2014, 'Ecology of marine phytoplankton' in Monson, RK (ed), Ecology and the Environment, Springer, New York, pp. 483-531.
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Marine phytoplankton account for about 45 % of global net primary production (NPP). In addition, they perform other important biogeochemical functions including nitrogen fixation, calcium carbonate precipitation, and the production of climatically active gases such as dimethyl sulfide. Oceanographers employ a wide variety of platforms for studying marine phytoplankton ecology, including sampling from ships, sampling from autonomous remotely operated vehicles, and collecting observations from Earthorbiting satellites. Marine phytoplankton range in size from <1μm in diameter to about 1 mm in length and include representatives from at least five eukaryotic phyla together with the cyanobacteria. This wide size range and phylogenetic diversity presents challenges for quantifying and characterizing phytoplankton communities. Functional traits that quantify responses of growth rate, photosynthesis and nutrient uptake to temperature, irradiance, and nutrient availability provide a useful basis for understanding phytoplankton ecology. A variety of complementary approaches are used to measure gross and net primary production. These include measuring production of O2 and organic matter in bottle experiments and measuring diel and seasonal changes of O2 in open waters. Information obtained from satellite remote sensing of ocean color is used to calculate NPP on regional and global scales. The physical and chemical variables that drive NPP include temperature, nutrient availability, and solar radiation. These vary in time and space, and our understanding of this variability is largely encapsulated in the concepts of the seasonal production cycle and marine biogeochemical provinces. Nutrient limitation sets an upper limit to NPP over most of the ocean surface, with either inorganic iron or nitrogen being the proximate limiting element in different regions. The upper water column is stably stratified over much of the ocean, and pronounced vertical gradients of light a...

Geider, RJ, Moore, CM & Suggett, DJ 2014, 'Ecology of Marine Phytoplankton' in Ecology and the Environment, Springer New York, pp. 483-531.
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Barnes, MK, Tilstone, GH, Smyth, TJ, Suggett, DJ, Astoreca, R, Lancelot, C & Kromkamp, JC 2014, 'Absorption-based algorithm of primary production for total and size-fractionated phytoplankton in coastal waters', Marine Ecology Progress Series, vol. 504, pp. 73-89.
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Most satellite models of production have been designed and calibrated for use in the open ocean. Coastal waters are optically more complex, and the use of chlorophyll a (chl a) as a first-order predictor of primary production may lead to substantial errors due to significant quantities of coloured dissolved organic matter (CDOM) and total suspended material (TSM) within the first optical depth. We demonstrate the use of phytoplankton absorption as a proxy to estimate primary production in the coastal waters of the North Sea and Western English Channel for both total, micro- and nano+pico-phytoplankton production. The method is implemented to extrapolate the absorption coefficient of phytoplankton and production at the sea surface to depth to give integrated fields of total and micro- and nano+pico-phytoplankton primary production using the peak in absorption coefficient at red wavelengths. The model is accurate to 8% in the Western English Channel and 22% in this region and the North Sea. By comparison, the accuracy of similar chl a based production models was >250%. The applicability of the method to autonomous optical sensors and remotely sensed aircraft data in both coastal and estuarine environments is discussed. © Inter-Research 2014.

Behrendt, L, Nielsen, JL, Sorensen, SJ, Larkum, AWD, Winther, JR & Kuhl, M 2014, 'Rapid TaqMan-Based Quantification of Chlorophyll d-Containing Cyanobacteria in the Genus Acaryochloris', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 80, no. 10, pp. 3244-3249.
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Reports of the chlorophyll (Chl) d-containing cyanobacterium Acaryochloris have accumulated since its initial discovery in 1996. The majority of this evidence is based on amplification of the gene coding for the 16S rRNA, and due to the wide geographical distribution of these sequences, a global distribution of Acaryochloris species was suggested. Here, we present a rapid, reliable, and cost-effective TaqMan-based quantitative PCR (qPCR) assay that was developed for the specific detection of Acaryochloris species in complex environmental samples. The TaqMan probe showed detection limits of ~10 16S rRNA gene copy numbers based on standard curves consisting of plasmid inserts. DNA from five Acaryochloris strains, i.e., MBIC11017, CCMEE5410, HICR111A, CRS, and Awaji-1, exhibited amplification efficiencies of >94% when tested in the TaqMan assay. When used on complex natural communities, the TaqMan assay detected the presence of Acaryochloris species in four out of eight samples of crustose coralline algae (CCA), collected from temperate and tropical regions. In three out of these TaqMan-positive samples, the presence of Chl d was confirmed via high-performance liquid chromatography (HPLC), and corresponding cell estimates of Acaryochloris species amounted to 7.6 × 101 to 3.0 × 103 per mg of CCA. These numbers indicate a substantial contribution of Chl d-containing cyanobacteria to primary productivity in endolithic niches. The new TaqMan assay allows quick and easy screening of environmental samples for the presence of Acaryochloris species and is an important tool to further resolve the global distribution and significance of this unique oxyphototroph.

Brodersen, KE, Nielsen, DA, Ralph, PJ & Kuhl, M 2014, 'A split flow chamber with artificial sediment to examine the below-ground microenvironment of aquatic macrophytes', MARINE BIOLOGY, vol. 161, no. 12, pp. 2921-2930.
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Brodie, J, Williamson, CJ, Smale, DA, Kamenos, NA, Mieszkowska, N, Santos, R, Cunliffe, M, Steinke, M, Yesson, C, Anderson, KM, Asnaghi, V, Brownlee, C, Burdett, HL, Burrows, MT, Collins, S, Donohue, PJC, Harvey, B, Foggo, A, Noisette, F, Nunes, J, Ragazzola, F, Raven, JA, Schmidt, DN, Suggett, D, Teichberg, M & Hall‐Spencer, JM 2014, 'The future of the northeast Atlantic benthic flora in a high CO₂ world', Ecology and Evolution, vol. 4, no. 13, pp. 2787-2798.
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AbstractSeaweed and seagrass communities in the northeast Atlantic have been profoundly impacted by humans, and the rate of change is accelerating rapidly due to runaway CO2 emissions and mounting pressures on coastlines associated with human population growth and increased consumption of finite resources. Here, we predict how rapid warming and acidification are likely to affect benthic flora and coastal ecosystems of the northeast Atlantic in this century, based on global evidence from the literature as interpreted by the collective knowledge of the authorship. We predict that warming will kill off kelp forests in the south and that ocean acidification will remove maerl habitat in the north. Seagrasses will proliferate, and associated epiphytes switch from calcified algae to diatoms and filamentous species. Invasive species will thrive in niches liberated by loss of native species and spread via exponential development of artificial marine structures. Combined impacts of seawater warming, ocean acidification, and increased storminess may replace structurally diverse seaweed canopies, with associated calcified and noncalcified flora, with simple habitats dominated by noncalcified, turf‐forming seaweeds.

Chaudhary, JP, Kondaveeti, S, Gupta, V, Prasad, K & Meena, R 2014, 'Preparation and functional evaluation of agarose derivatives', Journal of Applied Polymer Science, vol. 131, no. 16, pp. n/a-n/a.
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ABSTRACTA facile microwave‐assisted one‐pot synthesis of sodium carboxymethylagarose and calcium carboxymethylagarose from Gracilaria dura agarose (Ag) has been described. The process is user friendly, and the highest degree of substitution was obtained within 15 min compared with the conventional method, which requires more than 3 h. Solubility and gelling behavior of the modified Ag products were found to be dependent on degree of substitution of the products. The characterizations were done by using Fourier transform infrared spectroscopy, 1H‐ and 13C‐nuclear magnetic resonance spectroscopy, thermogravimetric analysis, scanning electron microscopy, Inductively coupled plasma spectrophotometry (ICP), rheology, conductometer analysis, and DNA gel electrophoresis. These agarose derivatives were easily soluble in water and exhibited low thermal hysteresis, improved conductivity, and improved the DNA resolution ability of the parent G. dura Ag hydrogels. These hydrogels may have potential applications in the areas including electrochemical devices, microbiology, biomedical, and pharmaceuticals fields. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40630.

Everett, JD, Baird, ME, Roughan, M, Suthers, IM & Doblin, MA 2014, 'Relative impact of seasonal and oceanographic drivers on surface chlorophyll a along a Western Boundary Current', PROGRESS IN OCEANOGRAPHY, vol. 120, pp. 340-351.
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Strengthening Western Boundary Currents (WBCs) advect warm, low nutrient waters into temperate latitudes, displacing more productive waters. WBCs also influence phytoplankton distribution and growth through current-induced upwelling, mesoscale eddy intrusion and seasonal changes in strength and poleward penetration. Here we examine dynamics of chlorophyll a (Chl. a) in the western Pacific Ocean, a region strongly influenced by the East Australian Current (EAC). We interpreted a spatial and temporal analysis of satellite-derived surface Chl. a, using a hydrodynamic model, a wind-reanalysis product and an altimetry-derived eddy-census. Our analysis revealed regions of persistently elevated surface Chl. a along the continental shelf and showed that different processes have a dominant effect in different locations. In the northern and central zones, upwelling events tend to regulate surface Chl. a patterns, with peaks in phytoplankton biomass corresponding to two known upwelling locations south of Cape Byron (28.5S) and Smoky Cape (31S). Within the central EAC separation zone, positive surface Chl. a anomalies occurred 65% of the time when both wind-stress (sw) and bottom-stress (sB) were upwelling- favourable, and only 17% of the time when both were downwelling-favourable. The interaction of wind and the EAC was a critical driver of surface Chl. a dynamics, with upwelling-favourable sW resulting in a 70% increase in surface Chl. a at some locations, when compared to downwelling-favourable sW. In the southern zone, surface Chl. a was driven by a strong seasonal cycle, with phytoplankton biomass increasing up to 152% annually each spring. The Stockton Bight region (32.2533.25S) contained P20% of the total shelf Chl. a on 27% of occasions due to its location downstream of upwelling locations, wide shelf area and reduced surface velocities. This region is analogous to productive fisheries regions in the Aghulus Current (Natal Bight) and Kuroshio Current (Enshu-nada Sea)...

Flores-Molina, MR, Thomas, D, Lovazzano, C, Núñez, A, Zapata, J, Kumar, M, Correa, JA & Contreras-Porcia, L 2014, 'Desiccation stress in intertidal seaweeds: Effects on morphology, antioxidant responses and photosynthetic performance', Aquatic Botany, vol. 113, pp. 90-99.
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Seaweeds are differentially distributed between the upper and lower limits of the intertidal zone of rocky coasts around the world. Daily changes in tide height cause water loss, triggering desiccation stress as a consequence. How this stress affected some of the morphological characteristics and physiological responses in representative intertidal seaweeds with contrasting vertical distributions was explored in the present work. The selected species were Mazzaella laminarioides (upper-middle distribution), Scytosiphon lomentaria and Ulva compressa (middle distribution), and Lessonia spicata and Gelidium rex (lower distribution). To assess tolerance response to desiccation, cellular and morphological alterations, ROS production, enzymatic activity of catalase (CAT) and ascorbate peroxidase (AP) and photosynthesis performance were measured after a simulated emersion stress experiment. Results show different tolerance responses to desiccation, with seaweeds having higher intertidal distributions displaying greater antioxidant enzymatic activity, suggesting a higher capacity to buffer ROS excess induced during desiccation. Contrarily, this capacity seems to be absent or deficient in low intertidal species (i.e. L. spicata and G. rex), where AP and CAT activities were below detection limits, ROS were higher than normal and caused an over-oxidation of bio-molecules and photosynthetic disarray, explaining from a functional stand point their low distribution in the intertidal zone. © 2013 Elsevier B.V.

Fu, S, Luong, S, Pham, A, Charlton, N & Kuzhiumparambil, U 2014, 'Bioanalysis of urine samples after manipulation by oxidizing chemicals: technical considerations', BIOANALYSIS, vol. 6, no. 11, pp. 1543-1561.
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Garren, M, Son, K, Raina, J-B, Rusconi, R, Menolascina, F, Shapiro, OH, Tout, J, Bourne, DG, Seymour, JR & Stocker, R 2014, 'A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals', ISME JOURNAL, vol. 8, no. 5, pp. 999-1007.
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Diseases are an emerging threat to ocean ecosystems. Coral reefs, in particular, are experiencing a worldwide decline because of disease and bleaching, which have been exacerbated by rising seawater temperatures. Yet, the ecological mechanisms behind most coral diseases remain unidentified. Here, we demonstrate that a coral pathogen, Vibrio coralliilyticus, uses chemotaxis and chemokinesis to target the mucus of its coral host, Pocillopora damicornis. A primary driver of this response is the host metabolite dimethylsulfoniopropionate (DMSP), a key element in the global sulfur cycle and a potent foraging cue throughout the marine food web. Coral mucus is rich in DMSP, and we found that DMSP alone elicits chemotactic responses of comparable intensity to whole mucus. Furthermore, in heat-stressed coral fragments, DMSP concentrations increased fivefold and the pathogen's chemotactic response was correspondingly enhanced. Intriguingly, despite being a rich source of carbon and sulfur, DMSP is not metabolized by the pathogen, suggesting that it is used purely as an infochemical for host location. These results reveal a new role for DMSP in coral disease, demonstrate the importance of chemical signaling and swimming behavior in the recruitment of pathogens to corals and highlight the impact of increased seawater temperatures on disease pathways. © 2014 International Society for Microbial Ecology All rights reserved.

Gustafsson, MSM, Baird, ME & Ralph, PJ 2014, 'Modeling photoinhibition-driven bleaching in Scleractinian coral as a function of light, temperature, and heterotrophy', LIMNOLOGY AND OCEANOGRAPHY, vol. 59, no. 2, pp. 603-622.
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Hassler, CS, Ridgway, KR, Bowie, AR, Butler, ECV, Clementson, LA, Doblin, MA, Davies, DM, Law, C, Ralph, PJ, van der Merwe, P, Watson, R & Ellwood, MJ 2014, 'Primary productivity induced by iron and nitrogen in the Tasman Sea: an overview of the PINTS expedition', MARINE AND FRESHWATER RESEARCH, vol. 65, no. 6, pp. 517-537.
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The Tasman Sea and the adjacent Sub-Antarctic zone (SAZ) are economically important regions, where the parameters controlling the phytoplankton community composition and carbon fixation are not yet fully resolved. Contrasting nutrient distributions as well as phytoplankton biomass, biodiversity and productivity we observed between the North Tasman Sea and the SAZ. In-situ FV/FM, dissolved and particulate nutrients, iron biological uptake, and nitrogen and carbon fixation were used to determine the factor limiting phytoplankton growth and productivity in the North Tasman Sea and the SAZ. Highly productive cyanobacteria dominated the North Tasman Sea. High atmospheric nitrogen fixation and low nitrate dissolved concentrations indicated that non-diazotroph phytoplankton are nitrogen limited. Deck-board incubations also suggested that, at depth, iron could limit eukaryotes, but not cyanobacteria in that region. In the SAZ, the phytoplankton community was dominated by a bloom of haptophytes. The low productivity in the SAZ was mainly explained by light limitation, but nitrogen, silicic acid as well as iron were all depleted to the extent that they could become co-limiting. This study illustrates the challenge associated with identification of the limiting nutrient as it varied between phytoplankton groups, depths and sites.

Henschke, N, Everett, JD, Doblin, MA, Pitt, KA, Richardson, AJ & Suthers, IM 2014, 'Demography and interannual variability of salp swarms (Thalia democratica)', MARINE BIOLOGY, vol. 161, no. 1, pp. 149-163.
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Swarms of the pelagic tunicate, Thalia democratica, form during spring, but the causes of the large interannual variability in the magnitude of salp swarms are unclear. Changes in asexual reproduction (buds per chain) of T. democratica populations in the coastal waters of south-east Australia (32-35°S) were observed in three austral springs (October 2008-2010). T. democratica abundance was significantly higher in 2008 (1,312 individuals m-3) than 2009 and 2010 (210 and 92 individuals m-3, respectively). There was a significant negative relationship (linear regression, r 2 = 0.61, F 1,22 = 33.83, P < 0.001) between abundance and asexual reproduction. Similarly, relative growth rates declined with decreasing abundance. Generalised additive mixed modelling showed that T. democratica abundance was significantly positively related to preferred food >2 μm in size (P < 0.05) and negatively related to the proportion of non-salp zooplankton (P < 0.001). Salp swarm magnitude, growth, and asexual reproduction may depend on the abundance of larger phytoplankton (prymnesiophytes and diatoms) and competition with other zooplankton. © 2013 Springer-Verlag Berlin Heidelberg.

Henschke, N, Everett, JD, Doblin, MA, Pitt, KA, Richardson, AJ & Suthers, IM 2014, 'Demography and interannual variability of salp swarms (Thalia democratica)', Marine Biology, vol. 161, no. 1, pp. 149-163.
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Hill, R, Szabo, M, Rehman, AU, Vass, I, Ralph, PJ & Larkum, AWD 2014, 'Inhibition of photosynthetic CO2 fixation in the coral Pocillopora damicornis and its relationship to thermal bleaching', JOURNAL OF EXPERIMENTAL BIOLOGY, vol. 217, no. 12, pp. 2150-2162.
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© 2014. Published by The Company of Biologists Ltd. Two inhibitors of the Calvin-Benson cycle [glycolaldehyde (GA) and potassium cyanide (KCN)] were used in cultured Symbiodinium cells and in nubbins of the coral Pocillopora damicornis to test the hypothesis that inhibition of the Calvin-Benson cycle triggers coral bleaching. Inhibitor concentration range-finding trials aimed to determine the appropriate concentration to generate inhibition of the Calvin-Benson cycle, but avoid other metabolic impacts to the symbiont and the animal host. Both 3 mmol l-1 GA and 20 uμmol l-1 KCN caused minimal inhibition of host respiration, but did induce photosynthetic impairment, measured by a loss of photosystem II function and oxygen production. GA did not affect the severity of bleaching, nor induce bleaching in the absence of thermal stress, suggesting inhibition of the Calvin-Benson cycle by GA does not initiate bleaching in P. damicornis. In contrast, KCN did activate a bleaching response through symbiont expulsion, which occurred in the presence and absence of thermal stress. While KCN is an inhibitor of the Calvin-Benson cycle, it also promotes reactive oxygen species formation, and it is likely that this was the principal agent in the coral bleaching process. These findings do not support the hypothesis that temperature-induced inhibition of the Calvin-Benson cycle alone induces coral bleaching.

Jeans, J, Szabo, M, Campbell, DA, Larkum, AWD, Ralph, PJ & Hill, R 2014, 'Thermal bleaching induced changes in photosystem II function not reflected by changes in photosystem II protein content of Stylophora pistillata', CORAL REEFS, vol. 33, no. 1, pp. 131-139.
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Scleractinian corals exist in a symbiosis with marine dinoflagellates of the genus Symbiodinium that is easily disrupted by changes in the external environment. Increasing seawater temperatures cause loss of pigments and expulsion of the symbionts from the host in a process known as coral bleaching; though, the exact mechanism and trigger of this process has yet to be elucidated. We exposed nubbins of the coral Stylophora pistillata to bleaching temperatures over a period of 14 daylight hours. Fifty-nine percent of the symbiont population was expelled over the course of this short-term treatment. Maximum quantum yield (F V/F M) of photosystem (PS) II for the in hospite symbiont population did not change significantly over the treatment period, but there was a significant decline in the quantity of PSII core proteins (PsbA and PsbD) at the onset of the experimental increase in temperature. F V/F M from populations of expelled symbionts dropped sharply over the first 6 h of temperature treatment, and then toward the end of the experiment, it increased to an F V/F M value similar to that of the in hospite population. This suggests that the symbionts were likely damaged prior to expulsion from the host, and the most damaged symbionts were expelled earlier in the bleaching. The quantity of PSII core proteins, PsbA and PsbD, per cell was significantly higher in the expelled symbionts than in the remaining in hospite population over 6-10 h of temperature treatment. We attribute this to a buildup of inactive PSII reaction centers, likely caused by a breakdown in the PSII repair cycle. Thus, thermal bleaching of the coral S. pistillata induces changes in PSII content that do not follow the pattern that would be expected based on the results of PSII function. © 2013 Springer-Verlag Berlin Heidelberg.

Kanazawa, A, Blanchard, GJ, Szabo, M, Ralph, PJ & Kramer, DM 2014, 'The site of regulation of light capture in Symbiodinium: Does the peridinin-chlorophyll alpha-protein detach to regulate light capture?', BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, vol. 1837, no. 8, pp. 1227-1234.
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Dinoflagellates from the genus Symbiodinium form symbiotic associations with cnidarians including corals and anemones. The photosynthetic apparatuses of these dinoflagellates possess a unique photosynthetic antenna system incorporating the peridinin-chlorophyll a-protein (PCP). It has been proposed that the appearance of a PCP-specific 77 K fluorescence emission band around 672-675 nm indicates that high light treatment results in PCP dissociation from intrinsic membrane antenna complexes, blocking excitation transfer to the intrinsic membrane-bound antenna complexes, chlorophyll a-chlorophyll c 2-peridinin-protein-complex (acpPC) and associated photosystems (Reynolds et al., 2008 Proc Natl Acad Sci USA 105:13674-13678).We have tested this model using time-resolved fluorescence decay kinetics in conjunction with global fitting to compare the time-evolution of the PCP spectral bands before and after high light exposure. Our results show that no long-lived PCP fluorescence emission components appear either before or after high light treatment, indicating that the efficiency of excitation transfer from PCP to membrane antenna systems remains efficient and rapid even after exposure to high light. The apparent increased relative emission at around 675 nm was, instead, caused by strong preferential exciton quenching of the membrane antenna complexes associated with acpPC and reaction centers. This strong non-photochemical quenching (NPQ) is consistent with the activation of xanthophyll-Associated quenching mechanisms and the generally-observed avoidance in nature of long-lived photoexcited states that can lead to oxidative damage. The acpPC component appears to be the most strongly quenched under high light exposure suggesting that it houses the photoprotective exciton quencher. © 2014 Elsevier B.V.

Kramarsky-Winter, E, Arotsker, L, Rasoulouniriana, D, Siboni, N, Loya, Y & Kushmaro, A 2014, 'The Possible Role of Cyanobacterial Filaments in Coral Black Band Disease Pathology', MICROBIAL ECOLOGY, vol. 67, no. 1, pp. 177-185.
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Black band disease (BBD), characterized by a black mat or line that migrates across a coral colony leaving behind it a bare skeleton, is a persistent disease affecting massive corals worldwide. Previous microscopic and molecular examination of this disease in faviid corals from the Gulf of Eilat revealed a number of possible pathogens with the most prominent being a cyanobacterium identified as Pseudoscillatoria coralii. We examined diseased coral colonies using histopathological and molecular methods in order to further assess the possible role of this cyanobacterium, its mode of entry, and pathological effects on the coral host tissues. Affected areas of colonies with BBD were sampled for examination using both light and transmission electron microscopies. Results showed that this dominant cyanobacterium was found on the coral surface, at the coral-skeletal interface, and invading the polyp tissues and gastrovascular cavity. Although tissues surrounding the invasive cyanobacterial filaments did not show gross morphological alterations, microscopic examination revealed that the coral cells surrounding the lesion were dissociated, necrotic, and highly vacuolated. No amoebocytes were evident in the mesoglea of affected tissues suggesting a possible repression of the coral immune response. Morphological and molecular similarity of the previously isolated BBD-associated cyanobacterium P. coralii to the current samples strengthens the premise that this species is involved in the disease in this coral. These results indicate that the cyanobacteria may play a pivotal role in this disease and that the mode of entry may be via ingestion, penetrating the coral via the gastrodermis, as well as through the skeletal-tissue interface.

Kumar, M, Kumari, P, Reddy, CRK & Jha, B 2014, 'Salinity and Desiccation Induced Oxidative Stress Acclimation in Seaweeds', Advances in Botanical Research, vol. 71, pp. 91-123.
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Marine macroalgae, commonly known as seaweeds, are assemblage of diverse groups of phototrophic marine plants and form the base of the marine trophic pyramid. Rocky intertidal zones are the most dynamic and comprises of highly stressful habitats for marine life including seaweeds. They often experience severe environmental stress as a result of periodic exposure to a wide range of ambient conditions including intense radiation, high temperature, desiccation and salinity with turning tides. The relative abundance, survivability and distribution of seaweeds in such environments are principally determined by their tolerance abilities to diverse environmental stresses. Any adverse effect on seaweeds as a result of fluctuating environmental conditions can directly or indirectly lead to perturbations at higher trophic levels and eventually affect the integrity and sustainability of aquatic ecosystems. The recent proteome, transcriptome, metabolome and other biochemical analysis of seaweeds under oxidative stress have suggested the involvement of mannitol, proline, abscisic acid, polyamines, polyunsaturated fatty acids, oxylipins and fatty acid desaturases among others defending the seaweeds from diverse environmental stress. Both salinity and desiccation stresses are comparable in the context of a reduction of cellular water potential but differ in physiological process of ions uptake and their ratio determines the acclimation potential of seaweeds. In this chapter, we describe various tolerance and adaptive strategies of seaweeds in response to salinity fluctuations and desiccation induced oxidative stress at both biochemical and molecular levels enabling them to endure successfully for extended periods of stresses. Further, the new opportunities that became available from whole genome sequences of the brown alga Ectocarpus siliculosus and the red alga Chondrus crispus, in gaining newer insights into the cellular mechanisms of stress tolerance at molecular l...

Kumari, P, Kumar, M, Reddy, CRK & Jha, B 2014, 'Nitrate and Phosphate Regimes Induced Lipidomic and Biochemical Changes in the Intertidal Macroalga Ulva lactuca (Ulvophyceae, Chlorophyta)', Plant and Cell Physiology, vol. 55, no. 1, pp. 52-63.
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This study was carried out in order to understand the lipid and biochemical alterations resulting from different nutritional regimes of nitrate and phosphate in Ulva lactuca. The algal thalli cultured in artificial seawater (ASW) showed higher levels of carbohydrates and non-polar lipids and increased phosphatase activities, accompanied by degradation of polar lipids, proteins and pigments. Further, higher levels of lipid hydroperoxides indicated reative oxygen species (ROS)-mediated non-enzymatic lipid peroxidation due to nutritional limitation-induced oxidative stress. Those thalli cultured in ASW supplemented with nitrate showed responses corresponding to nitrate addition, such as an increase in pigments, monogalactosyldiacylglycerols, polyunsaturated fatty acids and nitrate reductase. In addition, these thalli showed partial induction of phosphatases, low phospholipids, and high sulfolipid and 1,2-diacylglyceryl-3-O-4′-(N,N,N-trimethyl)-homoserine (DGTS) due to phosphate limitation. Similarly, algal thalli cultured in ASW supplemented with phosphate showed down-regulation of phosphatases, an increase in phospholipids due to availability of phosphate as well as a decrease in nitrate reductase, pigment, monogalactosyldiacylglycerols and polyunsaturated fatty acids due to nitrate limitation. On the other hand, algal thalli cultured in ASW supplemented with both nitrate and phosphate showed recovery of lost pigments and proteins, a high monogalactosyldiacylglycerol/digalactosyldiacylglycerol ratio, high unsaturation and high oxylipin levels (both C18 and C20). Further, the accumulation of indole-3-acetic acid in nutrient-limited thalli and of kinetin and kinetin riboside in nutrient-supplemented thalli indicated their antagonistic roles under nutrient stress. Thus, U. lactuca copes with nitrate and phosphate nutritional stress by altering the metabolic pathways involved in lipid biosynthesis including a shift in lipid classes, fatty acids, oxylipins and...

Laczka, O, Labbate, M & Doblin, M 2014, 'Application of an ELISA-type amperometric assay to the detection of Vibrio species with screen-printed electrodes', ANALYTICAL METHODS, vol. 6, no. 7, pp. 2020-2023.
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Laczka, OF, Labbate, M, Seymour, JR, Bourne, DG, Fielder, SS & Doblin, MA 2014, 'Surface Immuno-Functionalisation for the Capture and Detection of Vibrio Species in the Marine Environment: A New Management Tool for Industrial Facilities', PLOS ONE, vol. 9, no. 10.
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Lauro, FM, Senstius, SJ, Cullen, J, Neches, R, Jensen, RM, Brown, MV, Darling, AE, Givskov, M, McDougald, D, Hoeke, R, Ostrowski, M, Philip, GK, Paulsen, IT & Grzymski, JJ 2014, 'The Common Oceanographer: Crowdsourcing the Collection of Oceanographic Data', PLOS BIOLOGY, vol. 12, no. 9, pp. e1001947-e1001947.
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Lavery, TJ, Roudnew, B, Seymour, J, Mitchell, JG, Smetacek, V & Nicol, S 2014, 'Whales sustain fisheries: Blue whales stimulate primary production in the Southern Ocean', Marine Mammal Science, vol. 30, no. 3, pp. 888-904.
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AbstractIt has previously been asserted that baleen whales compete with fisheries by consuming potentially harvestable marine resources. The regularly applied “surplus‐yield model” suggests that whale prey becomes available to fisheries if whales are removed, and has been presented as a justification for whaling. However, recent findings indicate that whales enhance ecosystem productivity by defecating iron that stimulates primary productivity in iron‐limited waters. While juvenile whales and whales that are pregnant or lactating retain iron for growth and milk production, nonbreeding adult whales defecate most of the iron they consume. Here, we modify the surplus‐yield model to incorporate iron defecation. After modeling a simplistic trajectory of blue whale recovery to historical abundances, the traditional surplus‐yield model predicts that 1011 kg of carbon yr−1 would become unavailable to fisheries. However, this ignores the nutrient recycling role of whales. Our model suggests the population of blue whales would defecate 3 × 106 kg of iron yr−1, which would stimulate primary production equivalent to that required to support prey consumption by the blue whale population. Thus, modifying the surplus‐yield model to include iron defecation indicates that blue whales do not render marine resources unavailable to fisheries. By defecating iron‐rich feces, blue whales promote Southern Ocean productivity, rather than reducing fishery yields.

Lockhart, PJ, Larkum, AWD, Becker, M & Penny, D 2014, 'We are Still Learning About the Nature of Species and Their Evolutionary Relationships¹', Annals of the Missouri Botanical Garden, vol. 100, no. 1-2, pp. 6-13.
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Macreadie, PI, Baird, ME, Trevathan-Tackett, SM, Larkum, AWD & Ralph, PJ 2014, 'Quantifying and modelling the carbon sequestration capacity of seagrass meadows - A critical assessment', MARINE POLLUTION BULLETIN, vol. 83, no. 2, pp. 430-439.
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Seagrasses are among the planet's most effective natural ecosystems for sequestering (capturing and storing) carbon (C); but if degraded, they could leak stored C into the atmosphere and accelerate global warming. Quantifying and modelling the C sequestration capacity is therefore critical for successfully managing seagrass ecosystems to maintain their substantial abatement potential. At present, there is no mechanism to support carbon financing linked to seagrass. For seagrasses to be recognised by the IPCC and the voluntary C market, standard stock assessment methodologies and inventories of seagrass C stocks are required. Developing accurate C budgets for seagrass meadows is indeed complex; we discuss these complexities, and, in addition, we review techniques and methodologies that will aid development of C budgets. We also consider a simple process-based data assimilation model for predicting how seagrasses will respond to future change, accompanied by a practical list of research priorities. © 2013 Elsevier Ltd.

Macreadie, PI, Schliepl, MT, Rasheed, MA, Chartrand, KM & Ralph, PJ 2014, 'Molecular indicators of chronic seagrass stress: A new era in the management of seagrass ecosystems?', ECOLOGICAL INDICATORS, vol. 38, pp. 279-281.
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Mondal, AK, Chen, S, Su, D, Liu, H & Wang, G 2014, 'Fabrication and enhanced electrochemical performances of MoO3/graphene composite as anode material for lithium-ion batteries', International Journal of Smart Grid and Clean Energy, vol. 3, no. 2, pp. 142-148.
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Molybdenum trioxide (Mo0#)/graphene composite were prepared by integrating Mo03 and graphene in dimethylformamide (DMF). The morphology and structure of the materials were characterized by X-ray diffraction, field emission scanning electron microscopy and transmission electron microscopy. The electrochemical properties of Mo03/graphene composite with different ratios were studied as anode materials for lithium-ion batteries using galavanostatic charge-discharge and cyclic voltammetry. We observed that the Mo03/graphene anode with a weight ratio of 1:1 (Mo03 graphene) exhibits a high lithium storage capacity of 967 mA h g-1 at the current density of 500 mA g-1, satisfactory cycling stability and good rate capability.

Mondal, AK, Su, D, Chen, S, Sun, B, Li, K & Wang, G 2014, 'A simple approach to prepare nickel hydroxide nanosheets for enhanced pseudocapacitive performance', RSC ADVANCES, vol. 4, no. 37, pp. 19476-19481.
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Nickel hydroxide nanosheets were synthesized by a simple microwave assisted heating method and investigated as electrochemical pseudo-capacitive materials for supercapacitors. The crystalline structure and morphology of the as-obtained Ni(OH)2 nanosheets were characterized by X-ray diffraction, nitrogen adsorption-desorption isotherms, field emission scanning electron microscopy and transmission electron microscopy. The electrochemical properties of the Ni(OH)2 nanosheets were evaluated by cyclic voltammetry and chronopotentiometry technology in 2 M KOH solution. The nickel hydroxide nanosheet electrode shows a maximum specific capacitance of 2570 F g -1 at a current density of 5 A g-1 and exhibits superior cycling stability. These results suggest its potential application as an electrode material for supercapacitors. © the Partner Organisations 2014.

Mondal, AK, Su, D, Chen, S, Xie, X & Wang, G 2014, 'Highly Porous NiCo₂O₄ Nanoflakes and Nanobelts as Anode Materials for Lithium-Ion Batteries with Excellent Rate Capability', ACS Applied Materials & Interfaces, vol. 6, no. 17, pp. 14827-14835.
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Mondal, AK, Su, D, Chen, S, Zhang, J, Ung, A & Wang, G 2014, 'Microwave-assisted synthesis of spherical β-Ni(OH) 2 superstructures for electrochemical capacitors with excellent cycling stability', Chemical Physics Letters, vol. 610-611, pp. 115-120.
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A novel single-step microwave-assisted process has been developed to synthesize spherical β-Ni(OH)2 superstructures without using any templates. Structure characterizations show that the spherical β-Ni(OH)2 composed of twisted nanosheets was obtained. The electrochemical properties of the as-prepared materials were evaluated by cyclic voltammetry and chronopotentiometry technology in 2 M KOH solution. Due to the unique morphology, the prepared β-Ni(OH)2 electrode displays a high specific capacitance of 2147 F g-1 at a discharge current of 1 A g-1 and outstanding cycling stability (99.5% capacitance retained after 2000 cycles), suggesting its potential application as an efficient electrode material for high-performance electrochemical capacitors. © 2014 Elsevier B.V.

Mondal, AK, Su, D, Wang, Y, Chen, S, Liu, Q & Wang, G 2014, 'Microwave hydrothermal synthesis of urchin-like NiO nanospheres as electrode materials for lithium-ion batteries and supercapacitors with enhanced electrochemical performances', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 582, no. 1, pp. 522-527.
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Urchin-like NiO nanospheres were synthesised by a microwave hydrothermal method. The as-synthesised NiO nanospheres were characterised by X-ray diffraction, field emission scanning electron microscopy and transmission electron microscopy. It was found that NiO nanosphere consists of a nanoporous structure and nanosize crystals. When applied as anode materials in lithium-ion batteries, NiO nanospheres exhibited a high reversible specific capacity of 1027 mA h g-1, an excellent cycling performance and a good high rate capability. NiO nanospheres also showed a high specific capacitance as electrode materials for supercapacitors. © 2013 Elsevier B.V. All rights reserved.

Mondal, AK, Wang, B, Su, D, Wang, Y, Chen, S, Zhang, X & Wang, G 2014, 'Graphene/MnO2 hybrid nanosheets as high performance electrode materials for supercapacitors', Materials Chemistry and Physics, vol. 143, no. 2, pp. 740-746.
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Graphene/MnO2 hybrid nanosheets were prepared by incorporating graphene and MnO2 nanosheets in ethylene glycol. Scanning electron microscopy and transmission electron microscopy analyses confirmed nanosheet morphology of the hybrid materials. Graphene/MnO2 hybrid nanosheets with different ratios were investigated as electrode materials for supercapacitors by cyclic voltammetry (CV) and galvanostatic charge-discharge in 1 M Na2SO4 electrolyte. We found that the graphene/MnO2 hybrid nanosheets with a weight ratio of 1:4 (graphene:MnO2) delivered the highest specific capacitance of 320 F g-1. Graphene/MnO2 hybrid nanosheets also exhibited good capacitance retention on 2000 cycles. © 2013 Elsevier B.V. All rights reserved.

Pandya‐Kumar, N, Shema, R, Kumar, M, Mayzlish‐Gati, E, Levy, D, Zemach, H, Belausov, E, Wininger, S, Abu‐Abied, M, Kapulnik, Y & Koltai, H 2014, 'Strigolactone analog GR24 triggers changes in PIN2 polarity, vesicle trafficking and actin filament architecture', New Phytologist, vol. 202, no. 4, pp. 1184-1196.
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SummaryStrigolactones (SLs) are plant hormones that regulate shoot and root development in a MAX2‐dependent manner. The mechanism underlying SLs' effects on roots is unclear.We used root hair elongation to measure root response to SLs. We examined the effects of GR24 (a synthetic, biologically active SL analog) on localization of the auxin efflux transporter PIN2, endosomal trafficking, and F‐actin architecture and dynamics in the plasma membrane (PM) of epidermal cells of the primary root elongation zone in wildtype (WT) Arabidopsis and the SL‐insensitive mutant max2. We also recorded the response to GR24 of trafficking (tir3), actin (der1) and PIN2 (eir1) mutants.GR24 increased polar localization of PIN2 in the PM of...

Pernice, M & Levy, O 2014, 'Novel tools integrating metabolic and gene function to study the impact of the environment on coral symbiosis', Frontiers in Microbiology, vol. 5, pp. 1-6.
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The symbiotic dinoflagellates (genus Symbiodinium) inhabiting coral endodermal tissues are well known for their role as keystone symbiotic partners, providing corals with enormous amounts of energy acquired via photosynthesis and the absorption of dissolved nutrients. In the past few decades, corals reefs worldwide have been increasingly affected by coral bleaching (i.e., the breakdown of the symbiosis between corals and their dinoflagellate symbionts), which carries important socio-economic implications. Consequently, the number of studies focusing on the molecular and cellular processes underlying this biological phenomenon has grown rapidly, and symbiosis is now widely recognized as a major topic in coral biology. However, obtaining a clear image of the interplay between the environment and this mutualistic symbiosis remains challenging. Here, we review the potential of recent technological advances in molecular biology and approaches using stable isotopes to fill critical knowledge gaps regarding coral symbiotic function. Finally, we emphasize that the largest opportunity to achieve the full potential in this field arises from the integration of these technological advances.

Pernice, M, Simpson, SJ & Ponton, F 2014, 'Towards an integrated understanding of gut microbiota using insects as model systems', Journal of Insect Physiology, vol. 69, pp. 12-18.
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Metazoans form symbioses with microorganisms that synthesize essential nutritional compounds and increase their efficiency to digest and absorb nutrients. Despite the growing awareness that microbes within the gut play key roles in metabolism, health and development of metazoans, symbiotic relationships within the gut are far from fully understood. Insects, which generally harbor a lower microbial diversity than vertebrates, have recently emerged as potential model systems to study these interactions. In this review, we give a brief overview of the characteristics of the gut microbiota in insects in terms of low diversity but high variability at intra- and interspecific levels and we investigate some of the ecological and methodological factors that might explain such variability. We then emphasize how studies integrating an array of techniques and disciplines have the potential to provide new understanding of the biology of this micro eco-system.

Petrou, K, Trimborn, S, Kuehl, M & Ralph, PJ 2014, 'Desiccation stress in two intertidal beachrock biofilms', MARINE BIOLOGY, vol. 161, no. 8, pp. 1765-1773.
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Chlorophyll a fluorescence was used to look at the effect of desiccation on the photophysiology in two beachrock microbial biofilms from the intertidal rock platform of Heron Island, Australia. The photophysiological response to desiccation differed between the beachrock microbial communities. The black biofilm from the upper shoreline, dominated by Calothrix sp., showed a response typical of desiccation-tolerant cyanobacteria, where photosynthesis closed down during air exposure with a rapid and complete recovery upon rehydration. In contrast, the pink biofilm from the mid-intertidal zone, dominated by Blennothrix sp., showed no distinct response to desiccation stress and instead maintained reduced photosynthesis throughout drying and re-wetting cycles. Spatial differences in photosynthetic activity within the black biofilm were evident with a faster recovery rate of photosynthesis in the surface cyanobacteria than in the deeper layers of the biofilm. There was no variation with depth in the pink biofilm. The photophysiological differences in desiccation responses between the beachrock biofilms exemplify the ecological niche specialisation of these complex microbial communities, where the functional differences help to explain their vertical distribution on the intertidal shoreline.

Petrou, K, Trimborn, S, Rost, B, Ralph, PJ & Hassler, CS 2014, 'The impact of iron limitation on the physiology of the Antarctic diatom Chaetoceros simplex', MARINE BIOLOGY, vol. 161, no. 4, pp. 925-937.
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Iron availability strongly governs the growth of Southern Ocean phytoplankton. To investigate how iron limitation affects photosynthesis as well as the uptake of carbon and iron in the Antarctic diatom Chaetoceros simplex, a combination of chlorophyll a fluorescence measurements and radiotracer incubations in the presence and absence of chemical inhibitors was conducted. Iron limitation in C. simplex led to a decline in growth rates, photochemical efficiency and structural changes in photosystem II (PSII), including a reorganisation of photosynthetic units in PSII and an increase in size of the functional absorption cross section of PSII. Iron-limited cells further exhibited a reduced plastoquinone pool and decreased photosynthetic electron transport rate, while non-photochemical quenching and relative xanthophyll pigment content were strongly increased, suggesting a photoprotective response. Additionally, iron limitation resulted in a strong decline in carbon fixation and thus the particulate organic carbon quotas. Inhibitor studies demonstrated that, independent of the iron supply, carbon fixation was dependent on internal, but not on extracellular carbonic anhydrase activity. Orthovanadate more strongly inhibited iron uptake in iron-limited cells, indicating that P-type ATPase transporters are involved in iron uptake. The stronger reduction in iron uptake by ascorbate in iron-limited cells suggests that the re-oxidation of iron is required before it can be taken up and further supports the presence of a high-affinity iron transport pathway. The measured changes to photosystem architecture and shifts in carbon and iron uptake strategies in C. simplex as a result of iron limitation provide evidence for a complex interaction of these processes to balance the iron requirements for photosynthesis and carbon demand for sustained growth in iron-limited waters. © 2014 The Author(s).

Poulton, AJ, Stinchcombe, MC, Achterberg, EP, Bakker, DCE, Dumousseaud, C, Lawson, HE, Lee, GA, Richier, S, Suggett, DJ & Young, JR 2014, 'Coccolithophores on the north-west European shelf: calcification rates and environmental controls', Biogeosciences Discussions, vol. 11, no. 2, pp. 2685-2733.
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Abstract. Coccolithophores are a key functional group in terms of the pelagic production of calcium carbonate (calcite), although their contribution to shelf-sea biogeochemistry, and how this relates to environmental conditions, is poorly constrained. Measurements of calcite production (CP) and coccolithophore abundance were made on the north-west European shelf to examine trends in coccolithophore calcification along natural gradients of carbonate chemistry, macronutrient availability and plankton composition. Similar measurements were also made in three bioassay experiments where nutrient (nitrate, phosphate) and pCO2 levels were manipulated. Nanoflagellates (< 10 μm) dominated chlorophyll biomass and primary production (PP) at all but one sampling site, with CP ranging from 0.6–9.6 mmol C m−2d−1. Highest CP and coccolithophore cell abundance occurred in a diatom bloom in fully mixed waters off Helgoland, rather than in two distinct coccolithophore blooms in the central North Sea and Western English Channel. Estimates of coccolithophore contributions to total PP and nanoplankton PP were generally < 5%, apart from in a coccolithophore bloom at the Western English Channel Observatory (E1) where coccolithophores contributed up to 11% and at Helgoland where they contributed ~23% to nanoplankton PP. Variability in CP was influenced by cell numbers, species composition and cell-normalised calcification rates under both in situ conditions and in the experimental bioassays. Water column structure and light availability had a strong influence on cellular calcification, whereas nitrate (N) to phosphate (P) ratios influenced bulk CP. Coccolithophore communities in the northern North Sea and over the Norwegian Trench showed responses to N and P addition whereas oceanic communities in the Bay of Biscay showed no response. Sharp decreases in pH and a rough halving of calcite saturation states in the bioassay experiments led to decreased CP in the Bay ...

Poulton, AJ, Stinchcombe, MC, Achterberg, EP, Bakker, DCE, Dumousseaud, C, Lawson, HE, Lee, GA, Richier, S, Suggett, DJ & Young, JR 2014, 'Coccolithophores on the north-west European shelf: calcification rates and environmental controls', Biogeosciences, vol. 11, no. 14, pp. 3919-3940.
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Abstract. Coccolithophores are a key functional group in terms of the pelagic production of calcium carbonate (calcite), although their contribution to shelf sea biogeochemistry, and how this relates to environmental conditions, is poorly constrained. Measurements of calcite production (CP) and coccolithophore abundance were made on the north-west European shelf to examine trends in coccolithophore calcification along natural gradients of carbonate chemistry, macronutrient availability and plankton composition. Similar measurements were also made in three bioassay experiments where nutrient (nitrate, phosphate) and pCO2 levels were manipulated. Nanoflagellates (< 10 μm) dominated chlorophyll biomass and primary production (PP) at all but one sampling site, with CP ranging from 0.6 to 9.6 mmol C m−2 d−1. High CP and coccolithophore abundance occurred in a diatom bloom in fully mixed waters off Heligoland, but not in two distinct coccolithophore blooms in the central North Sea and Western English Channel. Coccolithophore abundance and CP showed no correlation with nutrient concentrations or ratios, while significant (p < 0.01) correlations between CP, cell-specific calcification (cell-CF) and irradiance in the water column highlighted how light availability exerts a strong control on pelagic CP. In the experimental bioassays, Emiliania-huxleyi-dominated coccolithophore communities in shelf waters (northern North Sea, Norwegian Trench) showed a strong response in terms of CP to combined nitrate and phosphate addition, mediated by changes in cell-CF and growth rates. In contrast, an offshore diverse coccolithophore community (Bay of Biscay) showed no response to nutrient addition, while light availability or mortality may have been more important in controlling this community. Sharp decreases in pH and a rough halving of calcite saturation states in the bioassay experiments led to decreased CP in the Bay of Biscay and northern North Sea, but n...

Raven, JA & Doblin, MA 2014, 'Active water transport in unicellular algae: where, why, and how', JOURNAL OF EXPERIMENTAL BOTANY, vol. 65, no. 22, pp. 6279-6292.
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Richier, S, Achterberg, EP, Dumousseaud, C, Poulton, AJ, Suggett, DJ, Tyrrell, T, Zubkov, MV & Moore, CM 2014, 'Carbon cycling and phytoplankton responses within highly-replicated shipboard carbonate chemistry manipulation experiments conducted around Northwest European Shelf Seas', Biogeosciences Discussions, vol. 11, no. 3, pp. 3489-3534.
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Abstract. The ongoing oceanic uptake of anthropogenic carbon dioxide (CO2) is significantly altering the carbonate chemistry of seawater, a phenomenon referred to as ocean acidification. Experimental manipulations have been increasingly used to gauge how continued ocean acidification will potentially impact marine ecosystems and their associated biogeochemical cycles in the future; however, results amongst studies, particularly when performed on natural communities, are highly variable, which in part likely reflects inconsistencies in experimental approach. To investigate the potential for identification of more generic responses and greater experimentally reproducibility, we devised and implemented a series of highly replicated (n = 8), short term (2–4 days) multi-level (&amp;geq; 4 conditions) carbonate chemistry/nutrient manipulation experiments on a range of natural microbial communities sampled in Northwest European shelf seas. Carbonate chemistry manipulations and resulting biological responses were found to be highly reproducible within individual experiments and to a lesser extent between geographically different experiments. Statistically robust reproducible physiological responses of phytoplankton to increasing pCO2, characterized by a suppression of net growth for small sized cells (< 10 μm), were observed in the majority of the experiments, irrespective of nutrient status. Remaining between-experiment variability was potentially linked to initial community structure and/or other site-specific environmental factors. Analysis of carbon cycling within the experiments revealed the expected increased sensitivity of carbonate chemistry to biological processes at higher pCO2 and hence lower buffer capacity. The results thus emphasize how biological-chemical feedbacks may be altered in the future ocean.

Richier, S, Achterberg, EP, Dumousseaud, C, Poulton, AJ, Suggett, DJ, Tyrrell, T, Zubkov, MV & Moore, CM 2014, 'Phytoplankton responses and associated carbon cycling during shipboard carbonate chemistry manipulation experiments conducted around Northwest European shelf seas', Biogeosciences, vol. 11, no. 17, pp. 4733-4752.
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Abstract. The ongoing oceanic uptake of anthropogenic carbon dioxide (CO2) is significantly altering the carbonate chemistry of seawater, a phenomenon referred to as ocean acidification. Experimental manipulations have been increasingly used to gauge how continued ocean acidification will potentially impact marine ecosystems and their associated biogeochemical cycles in the future; however, results amongst studies, particularly when performed on natural communities, are highly variable, which may reflect community/environment-specific responses or inconsistencies in experimental approach. To investigate the potential for identification of more generic responses and greater experimentally reproducibility, we devised and implemented a series (n = 8) of short-term (2–4 days) multi-level (≥4 conditions) carbonate chemistry/nutrient manipulation experiments on a range of natural microbial communities sampled in Northwest European shelf seas. Carbonate chemistry manipulations and resulting biological responses were found to be highly reproducible within individual experiments and to a lesser extent between geographically separated experiments. Statistically robust reproducible physiological responses of phytoplankton to increasing pCO2, characterised by a suppression of net growth for small-sized cells (<10 μm), were observed in the majority of the experiments, irrespective of natural or manipulated nutrient status. Remaining between-experiment variability was potentially linked to initial community structure and/or other site-specific environmental factors. Analysis of carbon cycling within the experiments revealed the expected increased sensitivity of carbonate chemistry to biological processes at higher pCO2 and hence lower buffer capacity. The results thus emphasise how biogeochemical feedbacks may be altered in the future ocean.

Robinson, C, Suggett, DJ, Cherukuru, N, Ralph, PJ & Doblin, MA 2014, 'Performance of Fast Repetition Rate fluorometry based estimates of primary productivity in coastal waters', JOURNAL OF MARINE SYSTEMS, vol. 139, pp. 299-310.
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© 2014 Published by Elsevier B.V. Capturing the variability of primary productivity in highly dynamic coastal ecosystems remains a major challenge to marine scientists. To test the suitability of Fast Repetition Rate fluorometry (FRRf) for rapid assessment of primary productivity in estuarine and coastal locations, we conducted a series of paired analyses estimating 14C carbon fixation and primary productivity from electron transport rates with a Fast Repetition Rate fluorometer MkII, from waters on the Australian east coast. Samples were collected from two locations with contrasting optical properties and we compared the relative magnitude of photosynthetic traits, such as the maximum rate of photosynthesis (Pmax), light utilisation efficiency (α) and minimum saturating irradiance (EK) estimated using both methods. In the case of FRRf, we applied recent algorithm developments that enabled electron transport rates to be determined free from the need for assumed constants, as in most previous studies. Differences in the concentration and relative proportion of optically active substances at the two locations were evident in the contrasting attenuation of PAR (400-700nm), blue (431nm), green (531nm) and red (669nm) wavelengths. FRRF-derived estimates of photosynthetic parameters were positively correlated with independent estimates of 14C carbon fixation (Pmax: n=19, R2=0.66; α: n=21, R2=0.77; EK: n=19, R2=0.45; all p<0.05), however primary productivity was frequently underestimated by the FRRf method. Up to 81% of the variation in the relationship between FRRf and 14C estimates was explained by the presence of pico-cyanobacteria and chlorophyll-a biomass, and the proportion of photoprotective pigments, that appeared to be linked to turbidity. We discuss the potential importance of cyanobacteria in influencing the underestimations of FRRf productivity and steps to overcome this potential limitation.

Roudnew, B, Lavery, TJ, Seymour, JR, Jeffries, TC & Mitchell, JG 2014, 'Variability in Bacteria and Virus-Like Particle Abundances During Purging of Unconfined Aquifers', GROUND WATER, vol. 52, no. 1, pp. 118-124.
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Standard methodologies for sampling the physicochemical conditions of groundwater recommend purging a bore for three bore volumes to avoid sampling the stagnant water within a bore and instead gain samples representative of the aquifer. However, there are currently no methodological standards addressing the amount of purging required to gain representative biological samples to assess groundwater bacterial and viral abundances. The objective of this study was to examine how bacterial and viral abundances change during the purging of bore volumes. Six bores infiltrating into unconfined aquifers were pumped for five or six bore volumes each and bacteria and virus-like particles (VLPs) were enumerated from each bore volume using flow cytometry. In examination of the individual bores trends in bacterial abundances were observed to increase, decrease, or remain constant with each purged bore volume. Furthermore, triplicates taken at each bore volume indicated substantial variations in VLP and bacterial abundances that are often larger than the differences between bore volumes. This indicates a high level of small scale heterogeneity in microbial community abundance in groundwater samples, and we suggest that this may be an intrinsic feature of bore biology. The heterogeneity observed may be driven by bottom up processes (variability in the distribution of organic and inorganic nutrients), top-down processes (grazing and viral lysis), physical heterogeneities in the bore, or technical artifacts associated with the purging process. We suggest that a more detailed understanding of the ecology underpinning this variability is required to adequately describe the microbiological characteristics of groundwater ecosystems.

Sackett, O, Armand, L, Beardall, J, Hill, R, Doblin, M, Connelly, C, Howes, J, Stuart, B, Ralph, P & Heraud, P 2014, 'Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy', BIOGEOSCIENCES, vol. 11, no. 20, pp. 5795-5808.
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© 2014 Author(s). Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value-furthermore, data on taxon-specific responses are almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate/silicic acid and carbohydrates. In contrast to some previous studies, silicate/silicic acid levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately refle...

Sackett, O, Armand, L, Beardall, J, Hill, R, Doblin, M, Connelly, C, Howes, J, Stuart, B, Ralph, P & Heraud, P 2014, 'Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy', Biogeosciences Discussions, vol. 11, no. 5, pp. 7327-7357.
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Abstract. Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value, furthermore data on taxon-specific responses is almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate and carbohydrates. In contrast to some previous studies, silicate levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately reflected by bulk community meas...

Scanes, E, Parker, LM, O’Connor, WA & Ross, PM 2014, 'Mixed Effects of Elevated pCO2 on Fertilisation, Larval and Juvenile Development and Adult Responses in the Mobile Subtidal Scallop Mimachlamys asperrima (Lamarck, 1819)', PLoS ONE, vol. 9, no. 4, pp. e93649-e93649.
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Ocean acidification is predicted to have severe consequences for calcifying marine organisms especially molluscs. Recent studies, however, have found that molluscs in marine environments with naturally elevated or fluctuating CO2 or with an active, high metabolic rate lifestyle may have a capacity to acclimate and be resilient to exposures of elevated environmental pCO2. The aim of this study was to determine the effects of near future concentrations of elevated pCO2 on the larval and adult stages of the mobile doughboy scallop, Mimachlamys asperrima from a subtidal and stable physio-chemical environment. It was found that fertilisation and the shell length of early larval stages of M. asperrima decreased as pCO2 increased, however, there were less pronounced effects of elevated pCO2 on the shell length of later larval stages, with high pCO2 enhancing growth in some instances. Byssal attachment and condition index of adult M. asperrima decreased with elevated pCO2, while in contrast there was no effect on standard metabolic rate or pHe. The responses of larval and adult M. asperrima to elevated pCO2 measured in this study were more moderate than responses previously reported for intertidal oysters and mussels. Even this more moderate set of responses are still likely to reduce the abundance of M. asperrima and potentially other scallop species in the world's oceans at predicted future pCO2 levels.

Schrameyer, V, Wangpraseurt, D, Hill, R, Kuehl, M, Larkum, AWD & Ralph, PJ 2014, 'Light Respiratory Processes and Gross Photosynthesis in Two Scleractinian Corals', PLOS ONE, vol. 9, no. 10.
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© 2014 Schrameyer et al. The light dependency of respiratory activity of two scleractinian corals was examined using O2 microsensors and CO2 exchange measurements. Light respiration increased strongly but asymptotically with elevated irradiance in both species. Light respiration in Pocillopora damicornis was higher than in Pavona decussata under low irradiance, indicating species-specific differences in light-dependent metabolic processes. Overall, the coral P. decussata exhibited higher CO2 uptake rates than P. damicornis over the experimental irradiance range. P. decussata also harboured twice as many algal symbionts and higher total protein biomass compared to P. damicornis, possibly resulting in self-shading of the symbionts and/or changes in host tissue specific light distribution. Differences in light respiration and CO2 availability could be due to host-specific characteristics that modulate the symbiont microenvironment, its photosynthesis, and hence the overall performance of the coral holobiont.

Seymour, JR 2014, 'A sea of microbes: the diversity and activity of marine microorganisms', Microbiology Australia, vol. 35, no. 4, pp. 183-183.
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Covering 70% of the earth’s surface, with an average depth of 3.6 km, the ocean’s total volume of 1.3 billion cubic kilometres represents perhaps the largest inhabitable space in the biosphere. Within this vast ecosystem, 90% of all living biomass is microbial. Indeed, seawater from all marine environments, ranging from the warm and sunlit upper ocean to the cold, dark and anoxic deep sea floor, and from the tropics to the arctic, is teeming with microbial life. A single teaspoon of seawater typically contains over 50 million viruses, 5 million Bacteria, 100,000 Archaea and 50,000 eukaryotic microbes. The numerical importance of these microbes is matched only by their ecological and biogeochemical significance. By performing the bulk of oceanic primary production and mediating key chemical transformation processes, planktonic microbes form the base of the marine food-web and are the engines that drive the ocean’s major biogeochemical cycles (Figure 1). While marine microbes are the dominant biological feature throughout the entire water column and within ocean sediments, as well as being important symbionts and pathogens of marine animals and plants, this review will focus on the activity and diversity of microbes inhabiting seawater in the upper sun-lit depths of the global ocean.

Siboni, N, Abrego, D, Motti, CA, Tebben, J & Harder, T 2014, 'Gene Expression Patterns during the Early Stages of Chemically Induced Larval Metamorphosis and Settlement of the Coral Acropora millepora', PLOS ONE, vol. 9, no. 3, pp. 1-9.
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The morphogenetic transition of motile coral larvae into sessile primary polyps is triggered and genetically programmed upon exposure to environmental biomaterials, such as crustose coralline algae (CCA) and bacterial biofilms. Although the specific chemical cues that trigger coral larval morphogenesis are poorly understood there is much more information available on the genes that play a role in this early life phase. Putative chemical cues from natural biomaterials yielded defined chemical samples that triggered different morphogenetic outcomes: an extract derived from a CCA-associated Pseudoalteromonas bacterium that induced metamorphosis, characterized by non-attached metamorphosed juveniles; and two fractions of the CCA Hydrolithon onkodes (Heydrich) that induced settlement, characterized by attached metamorphosed juveniles. In an effort to distinguish the genes involved in these two morphogenetic transitions, competent larvae of the coral Acropora millepora were exposed to these predictable cues and the expression profiles of 47 coral genes of interest (GOI) were investigated after only 1 hour of exposure using multiplex RT-qPCR. Thirty-two GOI were differentially expressed, indicating a putative role during the early regulation of morphogenesis. The most striking differences were observed for immunity-related genes, hypothesized to be involved in cell recognition and adhesion, and for fluorescent protein genes. Principal component analysis of gene expression profiles resulted in separation between the different morphogenetic cues and exposure times, and not only identified those genes involved in the early response but also those which influenced downstream biological changes leading to larval metamorphosis or settlement. © 2014 Siboni et al.

Sinutok, S, Hill, R, Kuhl, M, Doblin, MA & Ralph, PJ 2014, 'Ocean acidification and warming alter photosynthesis and calcification of the symbiont-bearing foraminifera Marginopora vertebralis', MARINE BIOLOGY, vol. 161, no. 9, pp. 2143-2154.
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Szabo, M, Parker, K, Guruprasad, S, Kuzhiumparambil, U, Lilley, RM, Tamburic, B, Schliep, M, Larkum, AWD, Schreiber, U, Raven, JA & Ralph, PJ 2014, 'Photosynthetic acclimation of Nannochloropsis oculata investigated by multi-wavelength chlorophyll fluorescence analysis', BIORESOURCE TECHNOLOGY, vol. 167, pp. 521-529.
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Multi-wavelength chlorophyll fluorescence analysis was utilised to examine the photosynthetic efficiency of the biofuel-producing alga Nannochloropsis oculata, grown under two light regimes; low (LL) and high (HL) irradiance levels. Wavelength dependency was evident in the functional absorption cross-section of Photosystem II (σII(λ)), absolute electron transfer rates (ETR(II)), and non-photochemical quenching (NPQ) of chlorophyll fluorescence in both HL and LL cells. While σII(λ) was not significantly different between the two growth conditions, HL cells upregulated ETR(II) 1.6-1.8-fold compared to LL cells, most significantly in the wavelength range of 440-540nm. This indicates preferential utilisation of blue-green light, a highly relevant spectral region for visible light in algal pond conditions. Under these conditions, the HL cells accumulated saturated fatty acids, whereas polyunsaturated fatty acids were more abundant in LL cells. This knowledge is of importance for the use of N. oculata for fatty acid production in the biofuel industry. © 2014 Elsevier Ltd.

Szabo, M, Wangpraseurt, D, Tamburic, B, Larkum, AWD, Schreiber, U, Suggett, DJ, Kuehl, M & Ralph, PJ 2014, 'Effective light absorption and absolute electron transport rates in the coral Pocillopora damicornis', PLANT PHYSIOLOGY AND BIOCHEMISTRY, vol. 83, pp. 159-167.
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Pulse Amplitude Modulation (PAM) fluorometry has been widely used to estimate the relative photosynthetic efficiency of corals. However, both the optical properties of intact corals as well as past technical constrains to PAM fluorometers have prevented calculations of the electron turnover rate of PSII. We used a new Multi-colour PAM (MC-PAM) in parallel with light microsensors to determine for the first time the wavelength-specific effective absorption cross-section of PSII photochemistry, σII(λ), and thus PAM-based absolute electron transport rates of the coral photosymbiont Symbiodinium both in culture and in hospite in the coral Pocillopora damicornis. In both cases, σII of Symbiodinium was highest in the blue spectral region and showed a progressive decrease towards red wavelengths. Absolute values for σII at 440nm were up to 1.5-times higher in culture than in hospite. Scalar irradiance within the living coral tissue was reduced by 20% in the blue when compared to the incident downwelling irradiance. Absolute electron transport rates of P.damicornis at 440nm revealed a maximum PSII turnover rate of ca. 250 electrons PSII-1 s-1, consistent with one PSII turnover for every 4 photons absorbed by PSII; this likely reflects the limiting steps in electron transfer between PSII and PSI. Our results show that optical properties of the coral host strongly affect light use efficiency of Symbiodinium. Therefore, relative electron transport rates do not reflect the productivity rates (or indeed how the photosynthesis-light response is parameterised). Here we provide a non-invasive approach to estimate absolute electron transport rates in corals. © 2014 Elsevier Masson SAS.

Tamburic, B, Guruprasad, S, Radford, DT, Szabo, M, Lilley, RM, Larkum, AWD, Franklin, JB, Kramer, DM, Blackburn, SI, Raven, JA, Schliep, M & Ralph, PJ 2014, 'The Effect of Diel Temperature and Light Cycles on the Growth of Nannochloropsis oculata in a Photobioreactor Matrix', PLOS ONE, vol. 9, no. 1, p. e86047.
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A matrix of photobioreactors integrated with metabolic sensors was used to examine the combined impact of light and temperature variations on the growth and physiology of the biofuel candidate microalgal species Nannochloropsis oculata. The experiments were performed with algal cultures maintained at a constant 20u C versus a 15°C to 25°C diel temperature cycle, where light intensity also followed a diel cycle with a maximum irradiance of 1920 μmol photons m-2 s^-1. No differences in algal growth (Chlorophyll a) were found between the two environmental regimes; however, the metabolic processes responded differently throughout the day to the change in environmental conditions. The variable temperature treatment resulted in greater damage to photosystem II due to the combined effect of strong light and high temperature. Cellular functions responded differently to conditions before midday as opposed to the afternoon, leading to strong hysteresis in dissolved oxygen concentration, quantum yield of photosystem II and net photosynthesis. Overnight metabolism performed differently, probably as a result of the temperature impact on respiration. Our photobioreactor matrix has produced novel insights into the physiological response of Nannochloropsis oculata to simulated environmental conditions. This information can be used to predict the effectiveness of deploying Nannochloropsis oculata in similar field conditions for commercial biofuel production. © 2014 Tamburic et al.

Tamburic, B, Szabo, M, Tran, N-AT, Larkum, AWD, Suggett, DJ & Ralph, PJ 2014, 'Action spectra of oxygen production and chlorophyll a fluorescence in the green microalga Nannochloropsis oculata', BIORESOURCE TECHNOLOGY, vol. 169, pp. 320-327.
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The first complete action spectrum of oxygen evolution and chlorophyll a fluorescence was measured for the biofuel candidate alga Nannochloropsis oculata. A novel analytical procedure was used to generate a representative and reproducible action spectrum for microalgal cultures. The action spectrum was measured at 14 discrete wavelengths across the visible spectrum, at an equivalent photon flux density of 60μmolphotonsm-2s-1. Blue light (~414nm) was absorbed more efficiently and directed to photosystem II more effectively than red light (~679nm) at light intensities below the photosaturation limit. Conversion of absorbed photons into photosynthetic oxygen evolution was maximised at 625nm; however, this maximum is unstable since neighbouring wavelengths (646nm) resulted in the lowest photosystem II operating efficiency. Identifying the wavelength-dependence of photosynthesis has clear implications to optimising growth efficiency and hence important economic implications to the algal biofuels and bioproducts industries. © 2014 Elsevier Ltd.

Torres, MA, Ritchie, RJ, Lilley, RMC, Grillet, C & Larkum, AWD 2014, 'Measurement of photosynthesis and photosynthetic efficiency in two diatoms', NEW ZEALAND JOURNAL OF BOTANY, vol. 52, no. 1, pp. 6-27.
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Tout, J, Jeffries, TC, Webster, NS, Stocker, R, Ralph, PJ & Seymour, JR 2014, 'Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef', MICROBIAL ECOLOGY, vol. 67, no. 3, pp. 540-552.
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To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.

Trevathan-Tackett, S, Macreadie, P, Ralph, P & Seymour, J 2014, 'Detachment and flow cytometric quantification of seagrass-associated bacteria', JOURNAL OF MICROBIOLOGICAL METHODS, vol. 102, pp. 23-25.
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A new protocol was developed to detach bacteria from seagrass tissue and subsequently enumerate cells using flow cytometry (FCM). A method involving addition of the surfactant Tween 80 and vortexing resulted in maximum detachment efficiency of seagrass attached bacteria, providing a robust protocol for precisely enumerating seagrass-associated bacteria with FCM. Using this approach we detected cell concentrations between 2.0 × 105 and 8.0 × 106 cells mg- 1 DW tissue.

Ung, AT, Williams, SG, Angeloski, A, Ashmore, J, Kuzhiumparambil, U, Bhadbhade, M & Bishop, R 2014, 'Formation of 3-azabicyclo[3.3.1]non-3-enes: imino amides vs. imino alkenes', MONATSHEFTE FUR CHEMIE, vol. 145, no. 6, pp. 983-992.
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An effective method for synthesising alkaloidlike compounds containing the 3-azabicyclo[3.3.1]non-3-ene core structure was successfully carried out in a stereoselective manner via the bridged-Ritter reactions. Important optically active 6-alkyl(aryl)amido-4-alkyl( aryl)-2,2,6-trimethyl-3-azabicyclo[3.3.1]non-3-enes (imino amides) and 4-alkyl(aryl)-2,2,6-trimethyl-3-azabicyclo[3.3.1]nona-3,6-dienes (imino alkenes) were obtained in one step from (-)-b-pinene and the respective nitriles in the presence of concentrated H2SO4. The relative compositions of these products were controlled by varying the reaction conditions. Kinetic studies were conducted to enable a mechanistic understanding of the reaction pathways.

Wangpraseurt, D, Larkum, AWD, Franklin, J, Szabo, M, Ralph, PJ & Kuhl, M 2014, 'Lateral light transfer ensures efficient resource distribution in symbiont-bearing corals', JOURNAL OF EXPERIMENTAL BIOLOGY, vol. 217, no. 4, pp. 489-498.
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Coral tissue optics has received very little attention in the past, although the interaction between tissue and light is central to our basic understanding of coral physiology. Here we used fibre-optic and electrochemical microsensors along with variable chlorophyll fluorescence imaging to directly measure lateral light propagation within living coral tissues. Our results show that corals can transfer light laterally within their tissues to a distance of ∼2cm. Such light transport stimulates O2 evolution and photosystem II operating efficiency in areas >0.5-1 cm away from direct illumination. Light is scattered strongly in both coral tissue and skeleton, leading to photon trapping and lateral redistribution within the tissue. Lateral light transfer in coral tissue is a new mechanism by which light is redistributed over the coral colony and we argue that tissue optical properties are one of the key factors in explaining the high photosynthetic efficiency of corals. © 2014. Published by The Company of Biologists Ltd.

Wangpraseurt, D, Polerecky, L, Larkum, AWD, Ralph, PJ, Nielsen, DA, Pernice, M & Kuhl, M 2014, 'The in situ light microenvironment of corals', LIMNOLOGY AND OCEANOGRAPHY, vol. 59, no. 3, pp. 917-926.
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We used a novel diver-operated microsensor system to collect in situ spectrally resolved light fields on corals with a micrometer spatial resolution. The light microenvironment differed between polyp and coenosarc tissues with scalar irradiance (400700 nm) over polyp tissue, attenuating between 5.1- and 7.8-fold from top to base of small hemispherical coral colonies, whereas attenuation was at most 1.5-fold for coenosarc tissue. Fluctuations in ambient solar irradiance induced changes in light and oxygen microenvironments, which were more pronounced and faster in coenosarc compared with polyp tissue. Backscattered light from the surrounding benthos contributed . 20% of total scalar irradiance at the coral tissue surface and enhanced symbiont photosynthesis and the local O2 concentration, indicating an important role of benthos optics for coral ecophysiology. Light fields on corals are species and tissue specific and exhibit pronounced variation on scales from micrometers to decimeters. Consequently, the distribution, genetic diversity, and physiology of coral symbionts must be coupled with the measurements of their actual light microenvironment to achieve a more comprehensive understanding of coral ecophysiology.

Wangpraseurt, D, Tamburic, B, Szabo, M, Suggett, D, Ralph, PJ & Kuhl, M 2014, 'Spectral Effects on Symbiodinium Photobiology Studied with a Programmable Light Engine', PLOS ONE, vol. 9, no. 11.
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©2014 Wangpraseurt et al. The spectral light field of Symbiodinium within the tissue of the coral animal host can deviate strongly from the ambient light field on a coral reef and that of artificial light sources used in lab studies on coral photobiology. Here, we used a novel approach involving light microsensor measurements and a programmable light engine to reconstruct the spectral light field that Symbiodinium is exposed to inside the coral host and the light field of a conventional halogen lamp in a comparative study of Symbiodinium photobiology. We found that extracellular gross photosynthetic O 2 evolution was unchanged under different spectral illumination, while the more red-weighted halogen lamp spectrum decreased PSII electron transport rates and there was a trend towards increased light-enhanced dark respiration rates under excess irradiance. The approach provided here allows for reconstructing and comparing intra-tissue coral light fields and other complex spectral compositions of incident irradiance. This novel combination of sensor technologies provides a framework to studying the influence of macro- and microscale optics on Symbiodinium photobiology with unprecedented spectral resolution.

Wu, Y, Campbell, DA, Irwin, AJ, Suggett, DJ & Finkel, ZV 2014, 'Ocean acidification enhances the growth rate of larger diatoms', Limnology and Oceanography, vol. 59, no. 3, pp. 1027-1034.
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Ocean acidification is changing the nature of inorganic carbon availability in the global oceans. Diatoms account for µ 40% of all marine primary productivity and are major contributors to the export of atmospheric carbon to the deep ocean. Larger diatoms are more likely to be stimulated by future increases in CO2 availability as a result of their low surface area to volume ratio and lower diffusive flux of CO2 relative to their carbon demand for growth. Here we quantify the effect of the partial pressure of carbon dioxide (PCO2), at levels of 190, 380, and 750 µL L−1, on the growth rate, photosystem II electron transport rate (ETR), and elemental composition for five diatom species ranging over five orders of magnitude in cell volume. Growth rates for all species were enhanced under 750 relative to 190 and 380 µL L−1, with little change in ETR or elemental stoichiometries, indicating an enhanced allocation of photochemical energy to growth under elevated PCO2. PCO2 enhancement of growth rates was size dependent. Under 750 vs. 190 µL L−1 partial pressures, growth rate was enhanced by µ 5% for the smaller diatom species to µ 30% for the largest species examined. The size dependence of CO2‐stimulated growth enhancement indicates that ocean acidification may selectively favor an increase in the growth rates of larger vs. smaller phytoplankton species in the sea, with potentially significant consequences for carbon biochemistry.

Wu, Y, Jeans, J, Suggett, DJ, Finkel, ZV & Campbell, DA 2014, 'Large centric diatoms allocate more cellular nitrogen to photosynthesis to counter slower RUBISCO turnover rates', Frontiers in Marine Science, vol. 1, no. DEC, pp. 1-11.
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© 2014 Wu, Jeans, Suggett, Finkel and Campbell. Diatoms contribute ~40% of primary production in the modern ocean and encompass the largest cell size range of any phytoplankton group. Diatom cell size influences their nutrient uptake, photosynthetic light capture, carbon export efficiency, and growth responses to increasing pCO2. We therefore examined nitrogen resource allocations to the key protein complexes mediating photosynthesis across six marine centric diatoms, spanning 5 orders of magnitude in cell volume, under past, current and predicted future pCO2 levels, in balanced growth under nitrogen repletion. Membrane bound photosynthetic protein concentrations declined with cell volume in parallel with cellular concentrations of total protein, total nitrogen and chlorophyll. Larger diatom species, however, allocated a greater fraction (by 3.5-fold) of their total cellular nitrogen to the soluble Ribulose-1,5-bisphosphate Carboxylase Oxygenase (RUBISCO) carbon fixation complex than did smaller species. Carbon assimilation per unit of RUBISCO large subunit (C RbcL-1 s-1) decreased with cell volume, from ~8 to ~2 C RbcL-1 s-1 from the smallest to the largest cells. Whilst a higher allocation of cellular nitrogen to RUBISCO in larger cells increases the burden upon their nitrogen metabolism, the higher RUBISCO allocation buffers their lower achieved RUBISCO turnover rate to enable larger diatoms to maintain carbon assimilation rates per total protein comparable to small diatoms. Individual species responded to increased pCO2, but cell size effects outweigh pCO2 responses across the diatom species size range examined. In large diatoms a higher nitrogen cost for RUBISCO exacerbates the higher nitrogen requirements associated with light absorption, so the metabolic cost to maintain photosynthesis is a cell size-dependent trait.

Zhang, D, Glasby, TM, Ralph, PJ & Gribben, PE 2014, 'Mechanisms Influencing the Spread of a Native Marine Alga', PLOS ONE, vol. 9, no. 4.
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Klement, M, Děd, T, Šafránek, D, Červený, J, Müller, S & Steuer, R 1970, 'Biochemical Space: A Framework for Systemic Annotation of Biological Models', Electronic Notes in Theoretical Computer Science, Elsevier BV, pp. 31-44.
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In this tool paper, we target the problem of unique annotation of organism-specific computational models presented in a public model database. In particular, we present Biochemical Space, a novel annotation methodology accompanied with a set of software tools that allow to create, manage and maintain the Biochemical Space content. The main idea behind is to create a transparent well-annotated reaction network of chemical entities and elemental reactions onto which the mathematical models are projected. For a given organism, the Biochemical Space represents a unifying platform for understanding of the related biological processes. The contribution of the methodology is three-fold: (i) systemic projection of models to a well-structured biological knowledge, (ii) simplification of annotation procedure, (iii) targetting several problems such as the presence of lumped model variables, combinatorial explosion in chemical modifications of entities, and hierarchical organisation of locations of individual entities. In these aspects the Biochemical Space goes beyond the features of current standards such as SBML. Application of the framework is demonstrated on a set of annotation data compiled for complex cyanobacteria processes. © 2014 Elsevier B.V.