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Journal articles

Ajani, P.A., Harwood, D.T. & murray, S.A. 2017, 'Recent trends in marine phycotoxins from Australian coastal waters', Marine Drugs.

Ajani, P.A., Harwood, D.T. & Murray, S.A. 2017, 'Recent trends in marine phycotoxins from Australian coastal waters'.
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Ajani, P.A., Harwood, D.T. & murray, S.A. 2017, 'Recent trends in marine phycotoxins from Australian coastal waters', Marine Drugs.

Ajani, P.A., Harwood, D.T. & Murray, S.A. 2017, 'Recent trends in marine phycotoxins from Australian coastal waters.', Marine Drugs, vol. 15, no. 2.
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Barraza, V., Restrepo-Coupe, N., Huete, A., Grings, F., Beringer, J., Cleverly, J.R. & Eamus, D. 2017, 'Estimation of latent heat flux over savannah vegetation across the North Australian Tropical Transect from multiple sensors and global meteorological data', Agricultural and Forest Meteorology, vol. 232, pp. 689-703.
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Latent heat flux (LE) and corresponding water loss in non-moisture-limited ecosystems are well corre-lated to radiation and temperature. By contrast, in savannahs and arid and semi-arid lands LE is mostlydriven by available water and the vegetation exerts a strong control over the rate of transpiration.Therefore, LE models that use optical vegetation indices (VIs) to represent the vegetation component(transpiration as a function of surface conductance, Gs) generally overestimate water fluxes in water-limited ecosystems. In this study, we evaluated and compared optical and passive microwave indexbased retrievals of Gsand LE derived using the Penman-Monteith (PM) formulation over the North Aus-tralian Tropical Transect (NATT). The methodology was evaluated at six eddy covariance (EC) sites fromthe OzFlux network. To parameterize the PM equation for retrievals of LE (PM-Gs), a subset of Gsvalueswas derived from meteorological and EC flux observations and regressed against individual and com-bined satellite indices, from (1) MODIS AQUA: the Normalized Difference Water Index (NDWI) and theEnhanced Vegetation Index (EVI); and from (2) AMSR-E passive microwave: frequency index (FI), polar-ization index (PI), vegetation optical depth (VOD) and soil moisture (SM) products. Similarly, we combinedoptical and passive microwave indices (multi-sensor model) to estimate weekly Gsvalues, and evaluatedtheir spatial and temporal synergies. The multi-sensor approach explained 40–80% of LE variance at somesites, with root mean square errors (RMSE) lower than 20 W/m2and demonstrated better performanceto other satellite-based estimates of LE. The optical indices represented potential Gsassociated with thephenological status of the vegetation (e.g. leaf area index, chlorophyll content) at finer spatial resolution.The microwave indices provided information about water availability and moisture stress (e.g. watercontent in leaves and shallow soil depths, atmospheric demand) at a high tem...

Barraza, V., Restrepo-Coupe, N., Huete, A., Grings, F., Beringer, J., Cleverly, J.R. & Eamus, D. 2017, 'Estimation of latent heat flux over savannah vegetation across the North Australian Tropical Transect from multiple sensors and global meteorological data', Agricultural and Forest Meteorology, vol. 232, pp. 689-703.
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Latent heat flux (LE) and corresponding water loss in non-moisture-limited ecosystems are well corre-lated to radiation and temperature. By contrast, in savannahs and arid and semi-arid lands LE is mostlydriven by available water and the vegetation exerts a strong control over the rate of transpiration.Therefore, LE models that use optical vegetation indices (VIs) to represent the vegetation component(transpiration as a function of surface conductance, Gs) generally overestimate water fluxes in water-limited ecosystems. In this study, we evaluated and compared optical and passive microwave indexbased retrievals of Gsand LE derived using the Penman-Monteith (PM) formulation over the North Aus-tralian Tropical Transect (NATT). The methodology was evaluated at six eddy covariance (EC) sites fromthe OzFlux network. To parameterize the PM equation for retrievals of LE (PM-Gs), a subset of Gsvalueswas derived from meteorological and EC flux observations and regressed against individual and com-bined satellite indices, from (1) MODIS AQUA: the Normalized Difference Water Index (NDWI) and theEnhanced Vegetation Index (EVI); and from (2) AMSR-E passive microwave: frequency index (FI), polar-ization index (PI), vegetation optical depth (VOD) and soil moisture (SM) products. Similarly, we combinedoptical and passive microwave indices (multi-sensor model) to estimate weekly Gsvalues, and evaluatedtheir spatial and temporal synergies. The multi-sensor approach explained 40–80% of LE variance at somesites, with root mean square errors (RMSE) lower than 20 W/m2and demonstrated better performanceto other satellite-based estimates of LE. The optical indices represented potential Gsassociated with thephenological status of the vegetation (e.g. leaf area index, chlorophyll content) at finer spatial resolution.The microwave indices provided information about water availability and moisture stress (e.g. watercontent in leaves and shallow soil depths, atmospheric demand) at a high tem...

Bellgrove, A., van Rooyen, A., Weeks, A.R., Clark, J.S., Doblin, M.A. & Miller, A.D. 2017, 'New resource for population genetics studies on the Australasian intertidal brown alga, Hormosira banksii: isolation and characterization of 15 polymorphic microsatellite loci through next generation DNA sequencing', Journal of Applied Phycology, vol. 29, no. 3, pp. 1721-1727.
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© 2016, Springer Science+Business Media Dordrecht. The Australasian fucoid, Hormosira banksii, commonly known as ‘Neptune’s necklace’ or ‘bubbleweed’ is regarded as an autogenic ecosystem engineer with no functional equivalents. Population declines resulting from climate change and other anthropogenic disturbances pose significant threats to intertidal biodiversity. For effective conservation strategies, patterns of gene flow and po pulation genetic structure across the species distribution need to be clearly understood. We developed a suite of 15 polymorphic microsatellite markers using next generation sequencing of 53–55 individuals from two sites (south-western Victoria and central New South Wales, Australia) and a replicated spatially hierarchical sampling design. We observed low to moderate genetic variation across most loci (mean number of alleles per locus =3.26; mean expected heterozygosity =0.38) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Independent spatial autocorrelation analyses were performed for each site using multilocus genotypes and different relatedness measures. Both analyses indicated no significant patterns between relatedness and geographic distance, complemented by non-significant Hardy-Weinberg estimates (P  <  0.05), suggesting that individuals from each site represent a randomly mating, outcrossing population. A preliminary investigation of population structure indicates that gene flow among sites is limited (F ST  = 0.49), however more comprehensive sampling is needed to determine the extent of population structure across the species range ( > 10,000 km). The genetic markers described provide a valuable resource for future population genetic assessments that will help guide conservation planning for H. banksii and the associated intertidal communities.

Brodersen, K.E., Hammer, K.J., Schrameyer, V., Floytrup, A., Rasheed, M.A., Ralph, P.J., Kühl, M. & Pedersen, O. 2017, 'Sediment Resuspension and Deposition on Seagrass Leaves Impedes Internal Plant Aeration and Promotes Phytotoxic H2S Intrusion.', Front Plant Sci, vol. 8, p. 657.
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HIGHLIGHTS: Sedimentation of fine sediment particles onto seagrass leaves severely hampers the plants' performance in both light and darkness, due to inadequate internal plant aeration and intrusion of phytotoxic H2S. Anthropogenic activities leading to sediment re-suspension can have adverse effects on adjacent seagrass meadows, owing to reduced light availability and the settling of suspended particles onto seagrass leaves potentially impeding gas exchange with the surrounding water. We used microsensors to determine O2 fluxes and diffusive boundary layer (DBL) thickness on leaves of the seagrass Zostera muelleri with and without fine sediment particles, and combined these laboratory measurements with in situ microsensor measurements of tissue O2 and H2S concentrations. Net photosynthesis rates in leaves with fine sediment particles were down to ~20% of controls without particles, and the compensation photon irradiance increased from a span of 20-53 to 109-145 μmol photons m(-2) s(-1). An ~2.5-fold thicker DBL around leaves with fine sediment particles impeded O2 influx into the leaves during darkness. In situ leaf meristematic O2 concentrations of plants exposed to fine sediment particles were lower than in control plants and exhibited long time periods of complete meristematic anoxia during night-time. Insufficient internal aeration resulted in H2S intrusion into the leaf meristematic tissues when exposed to sediment resuspension even at relatively high night-time water-column O2 concentrations. Fine sediment particles that settle on seagrass leaves thus negatively affect internal tissue aeration and thereby the plants' resilience against H2S intrusion.

Camp, E.F., Dong, L.F., Suggett, D.J., Smith, D.J., Boatman, T.G., Crosswel, J.R., Evenhuis, C., Scorfield, S., Walinjkar, A., Woods, J. & Lawson, T. 2017, 'A novel membrane inlet-infrared gas analysis (MI-IRGA) system for monitoring of seawater carbonate system', Limnology and Oceanography: Methods, vol. 15, no. 1, pp. 38-53.
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© 2016 The Authors Limnology and Oceanography: Methods published by Wiley Periodicals, Inc. Increased atmospheric CO 2 concentrations are driving changes in ocean chemistry at unprecedented rates resulting in ocean acidification, which is predicted to impact the functioning of marine biota, in particular of marine calcifiers. However, the precise understanding of such impacts relies on an analytical system that determines the mechanisms and impact of elevated pCO 2 on the physiology of organisms at scales from species to entire communities. Recent work has highlighted the need within experiments to control all aspects of the carbonate system to resolve the role of different inorganic carbon species on the physiological responses observed across taxa in real-time. Presently however, there are limited options available for continuous quantification of physiological responses, coupled with real-time calculation of the seawater carbonate chemistry system within microcosm environments. Here, we describe and characterise the performance of a novel pCO 2 membrane equilibrium system (the Membrane Inlet Infra-Red Gas Analyser, MI-IRGA) integrated with a continuous pH and oxygen monitoring platform. The system can detect changes in the seawater carbonate chemistry and determine organism physiological responses, while providing the user with real-time control over the microcosm system. We evaluate the systems control, response time and associated error, and demonstrate the flexibility of the system to operate under field conditions and within a laboratory. We use the system to measure physiological parameters (photosynthesis and respiration) for the corals Pocillipora damicornis and Porites cylindrica; in doing so we present a novel dataset examining the interactive role of temperature, light and pCO 2 on the physiology of P. cylindrica.

Camp, E.F., Nitschke, M.R., Rodolfo-Metalpa, R., Houlbreque, F., Gardner, S.G., Smith, D.J., Zampighi, M. & Suggett, D.J. 2017, 'Reef-building corals thrive within hot-acidified and deoxygenated waters.', Sci Rep, vol. 7, no. 1, p. 2434.
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Coral reefs are deteriorating under climate change as oceans continue to warm and acidify and thermal anomalies grow in frequency and intensity. In vitro experiments are widely used to forecast reef-building coral health into the future, but often fail to account for the complex ecological and biogeochemical interactions that govern reefs. Consequently, observations from coral communities under naturally occurring extremes have become central for improved predictions of future reef form and function. Here, we present a semi-enclosed lagoon system in New Caledonia characterised by diel fluctuations of hot-deoxygenated water coupled with tidally driven persistently low pH, relative to neighbouring reefs. Coral communities within the lagoon system exhibited high richness (number of species = 20) and cover (24-35% across lagoon sites). Calcification rates for key species (Acropora formosa, Acropora pulchra, Coelastrea aspera and Porites lutea) for populations from the lagoon were equivalent to, or reduced by ca. 30-40% compared to those from the reef. Enhanced coral respiration, alongside high particulate organic content of the lagoon sediment, suggests acclimatisation to this trio of temperature, oxygen and pH changes through heterotrophic plasticity. This semi-enclosed lagoon therefore provides a novel system to understand coral acclimatisation to complex climatic scenarios and may serve as a reservoir of coral populations already resistant to extreme environmental conditions.

Cartaxana, P., Trampe, E., Kühl, M. & Cruz, S. 2017, 'Kleptoplast photosynthesis is nutritionally relevant in the sea slug Elysia viridis.', Sci Rep, vol. 7, no. 1, p. 7714.
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Several sacoglossan sea slug species feed on macroalgae and incorporate chloroplasts into tubular cells of their digestive diverticula. We investigated the role of the "stolen" chloroplasts (kleptoplasts) in the nutrition of the sea slug Elysia viridis and assessed how their abundance, distribution and photosynthetic activity were affected by light and starvation. Elysia viridis individuals feeding on the macroalga Codium tomentosum were compared with starved specimens kept in dark and low light conditions. A combination of variable Chl a fluorescence and hyperspectral imaging, and HPLC pigment analysis was used to evaluate the spatial and temporal variability of photopigments and of the photosynthetic capacity of kleptoplasts. We show increased loss of weight and body length in dark-starved E. viridis as compared to low light-starved sea slugs. A more pronounced decrease in kleptoplast abundance and lower photosynthetic electron transport rates were observed in dark-starved sea slugs than in low light-starved animals. This study presents strong evidence of the importance of kleptoplast photosynthesis for the nutrition of E. viridis in periods of food scarcity. Deprived of photosynthates, E. viridis could accelerate the breakdown of kleptoplasts in the dark to satisfy its' energy requirements.

Chekli, L., Corjon, E., Tabatabai, S.A.A., Naidu, G., Tamburic, B., Park, S.H. & Shon, H.K. 2017, 'Performance of titanium salts compared to conventional FeCl3 for the removal of algal organic matter (AOM) in synthetic seawater: Coagulation performance, organic fraction removal and floc characteristics.', J Environ Manage, vol. 201, pp. 28-36.
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During algal bloom periods, operation of seawater reverse osmosis (SWRO) pretreatment processes (e.g. ultrafiltration (UF)) has been hindered due to the high concentration of algal cells and algal organic matter (AOM). The present study evaluated for the first time the performance of titanium salts (i.e. titanium tetrachloride (TiCl4) and polytitanium tetrachloride (PTC)) for the removal of AOM in seawater and results were compared with the conventional FeCl3 coagulant. Previous studies already demonstrated that titanium salts not only provide a cost-effective alternative to conventional coagulants by producing a valuable by-product but also minimise the environmental impact of sludge production. Results from this study showed that both TiCl4 and PTC achieved better performance than FeCl3 in terms of turbidity, UV254 and dissolved organic carbon (DOC) removal at similar coagulant dose. Liquid chromatography - organic carbon detection (LC-OCD) was used to determine the removal of AOM compounds based on their molecular weight (MW). This investigation revealed that both humic substances and low MW organics were preferentially removed (i.e. up to 93% removal) while all three coagulants showed poorer performance for the removal of high MW biopolymers (i.e. less than 50% removal). The detailed characterization of flocs indicated that both titanium coagulants can grow faster, reach larger size and present a more compact structure, which is highly advantageous for the design of smaller and more compact mixing and sedimentation tanks. Both titanium coagulants also presented a higher ability to withstand shear force, which was related to the higher amount of DOC adsorbed with the aggregated flocs. Finally, TiCl4 had a better recovery after breakage suggesting that charge neutralization may be the dominant mechanism for this coagulant, while the lower recovery of both PTC and FeCl3 indicated that sweep flocculation is also a contributing mechanism for the coagulation of AOM...

Chekli, L., Eripret, C., Park, S.H., Tabatabai, S.A.A., Vronska, O., Tamburic, B., Kim, J.H. & Shon, H.K. 2017, 'Coagulation performance and floc characteristics of polytitanium tetrachloride (PTC) compared with titanium tetrachloride (TiCl4) and ferric chloride (FeCl3) in algal turbid water', Separation and Purification Technology, vol. 175, pp. 99-106.
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© 2016 Elsevier B.V. Seasonal green algae blooms in freshwaters have raised attention on the need to develop novel effective treatment processes for the removal of algae in water. In the present study, the performance of newly developed polytitanium tetrachloride (PTC) coagulant for the removal of freshwater microalga Chlorella vulgaris has been investigated and compared with titanium tetrachloride (TiCl 4 ) coagulant and the conventional ferric chloride (FeCl 3 ) coagulant. The main benefit of using titanium-based coagulants is that the sludge produced after flocculation may be recycled into a valuable product: titanium dioxide photocatalyst. Both titanium-based coagulants achieved good flocculation over a broader pH range and coagulant dose compared to conventional FeCl 3 coagulant. All three coagulants achieved comparable performance in terms of turbidity removal (i.e. turbidity removal efficiency > 97%); although TiCl 4 performed slightly better at the lower tested dose (i.e. < 9 mg/L). Zeta potential measurements indicated that charge neutralisation may not be the sole mechanism involved in the coagulation of algae for all three coagulants. Analysis of the dynamic floc size variation during floc breakage showed no regrowth after floc breakage for the three coagulants. The flocs formed by both Ti-based coagulants were larger than those formed by FeCl 3 and also grew at a faster rate. This study indicates that Ti-based coagulants are effective and promising coagulants for algae removal in water.

Commault, A.S., Laczka, O., Siboni, N., Tamburic, B., Crosswell, J.R., Seymour, J.R. & Ralph, P.J. 2017, 'Electricity and biomass production in a bacteria-Chlorella based microbial fuel cell treating wastewater', Journal of Power Sources, vol. 356, pp. 299-309.
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© 2017 Elsevier B.V. The chlorophyte microalga Chlorella vulgaris has been exploited within bioindustrial settings to treat wastewater and produce oxygen at the cathode of microbial fuel cells (MFCs), thereby accumulating algal biomass and producing electricity. We aimed to couple these capacities by growing C. vulgaris at the cathode of MFCs in wastewater previously treated by anodic bacteria. The bioelectrochemical performance of the MFCs was investigated with different catholytes including phosphate buffer and anode effluent, either in the presence or absence of C. vulgaris. The power output fluctuated diurnally in the presence of the alga. The maximum power when C. vulgaris was present reached 34.2 ± 10.0 mW m −2 , double that observed without the alga (15.6 ± 9.7 mW m −2 ), with a relaxation of 0.19 gL −1  d −1 chemical oxygen demand and 5 mg L −1  d −1 ammonium also removed. The microbial community associated with the algal biofilm included nitrogen-fixing (Rhizobiaceae), denitrifying (Pseudomonas stutzeri and Thauera sp., from Pseudomonadales and Rhodocyclales orders, respectively), and nitrate-reducing bacteria (Rheinheimera sp. from the Alteromonadales), all of which likely contributed to nitrogen cycling processes at the cathode. This paper highlights the importance of coupling microbial community screening to electrochemical and chemical analyses to better understand the processes involved in photo-cathode MFCs.

Davis, A., Abbriano, R., Smith, S.R. & Hildebrand, M. 2017, 'Clarification of Photorespiratory Processes and the Role of Malic Enzyme in Diatoms', PROTIST, vol. 168, no. 1, pp. 134-153.
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Del Campo, J., Pombert, J.F., Šlapeta, J., Larkum, A. & Keeling, P.J. 2017, 'The 'other' coral symbiont: Ostreobium diversity and distribution.', The ISME journal, vol. 11, pp. 296-299.
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Ostreobium is an endolithic algal genus thought to be an early-diverging lineage of the Bryopsidales (Ulvophyceae, Chlorophyta). Ostreobium can live in low-light conditions on calcium carbonate substrata in tropical conditions. It is best known as a symbiont of corals, where it lives deep within the animal skeleton and exchanges nitrogen and carbon, as well as providing nutrients and photoassimilates. In contrast to the relatively well-studied role of the photosynthetic zooxanthellae symbionts in coral (Symbiodinium), Ostreobium phylogeny, diversity and distribution are all poorly understood. Here, we describe the phylogenetic position and diversity of Ostreobium based on plastid 16S ribosomal DNA (rDNA), 18S rDNA and rbcL genes from a nuclear genome survey and complete plastid genome, and determined its environmental diversity and distribution by screening the publicly available environmental data for those genes. The results shed light on the phylogeny and the ecology of the 'other' coral symbiont.The ISME Journal advance online publication, 15 July 2016; doi:10.1038/ismej.2016.101.

Dorantes-Aranda, J.J., Campbell, K., Bradbury, A., Elliott, C.T., Harwood, D.T., Murray, S.A., Ugalde, S.C., Wilson, K., Burgoyne, M. & Hallegraeff, G.M. 2017, 'Comparative performance of four immunological test kits for the detection of Paralytic Shellfish Toxins in Tasmanian shellfish.', Toxicon, vol. 125, pp. 110-119.
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Blooms of the toxic dinoflagellate Alexandrium tamarense (Group 1) seriously impacted the Tasmanian shellfish industry during 2012 and 2015, necessitating product recalls and intensive paralytic shellfish toxin (PST) product testing. The performance of four commercial PST test kits, Abraxis™, Europroxima™, Scotia™ and Neogen™, was compared with the official AOAC LC-FLD method for contaminated mussels and oysters. Abraxis and Europroxima kits underestimated PST in 35-100% of samples when using standard protocols but quantification improved when concentrated extracts were further diluted (underestimation ≤18%). The Scotia kit (cut off 0.2-0.7 mg STX-diHCl eq/kg) delivered 0% false negatives, but 27% false positives. Neogen produced 5% false negatives and 13% false positives when the cut off was altered to 0.5-0.6 mg STX-diHCl eq/kg, the introduction of a conversion step eliminated false negatives. Based on their sensitivity, ease of use and performance, the Neogen kit proved the most suitable kit for use with Tasmanian mussels and oysters. Once formally validated for regulatory purposes, the Neogen kit could provide shellfish growers with a rapid tool for harvesting decisions at the farm gate. Effective rapid screening preventing compliant samples undergoing testing using the more expensive and time consuming LC-FLD method will result in significant savings in analytical costs.

Flynn, K.J. & Raven, J.A. 2017, 'What is the limit for photoautotrophic plankton growth rates?', Journal of Plankton Research, vol. 39, no. 1, pp. 13-22.
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© 2016 The Author. Knowing the potential maximum photoautotrophic growth rate for planktonic primary producers is fundamental to our understanding of trophic and biogeochemical processes, and of importance in applied phycology. When dayintegrated C-specific growth is considered over natural light:dark cycles, plausible RuBisCO activity (K cat coupled with cellular RuBisCO content) caps growth to less than a few doubling per day. Prolonged periods of C-specific growth rates above ca. 1.3 d thus appear increasingly implausible. Discrepancies between RuBisCO-capped rates and reported microalgal-specific growth rates, including temperature-growth rate relationships, may be explained by transformational errors in growth rate determinations made by reference to cell counts or most often chlorophyll, or by extrapolations from short-Term measurements. Coupled studies of enzyme activity and day-on-day C-specific growth rates are required to provide definitive evidence of high growth rates. It seems likely, however, that selective pressure to evolve a RuBisCO with a high K cat (with a likely concomitant increase in K m for CO 2 ) would be low, as other factors such as light limitation (developing during biomass growth due to self-shading), nutrient limitations, CO 2 depletion and pH elevation, would all rapidly depress realized specific growth rates.

Fransen, J., Bush, S., Woodcock, S., Novak, A., Deprez, D., Baxter-Jones, A.D.G., Vaeyens, R. & Lenoir, M. 2017, 'Improving the Prediction of Maturity From Anthropometric Variables Using a Maturity Ratio', Pediatric Exercise Science, pp. 1-28.
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Gardner, S.G., Raina, J.-.B., Ralph, P.J. & Petrou, K. 2017, 'Reactive oxygen species (ROS) and dimethylated sulphur compounds in coral explants under acute thermal stress.', Journal of Experimental Biology, vol. 220, no. Pt 10, pp. 1787-1791.
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Coral bleaching is intensifying with global climate change. Although the causes for these catastrophic events are well understood, the cellular mechanism that triggers bleaching is not well established. Our understanding of coral bleaching processes is hindered by the lack of robust methods for studying interactions between host and symbiont at the single-cell level. Here, we exposed coral explants to acute thermal stress and measured oxidative stress, more specifically, reactive oxygen species (ROS), in individual symbiont cells. Furthermore, we measured concentrations of dimethylsulphoniopropionate (DMSP) and dimethylsulphoxide (DMSO) to elucidate the role of these compounds in coral antioxidant function. This work demonstrates the application of coral explants for investigating coral physiology and biochemistry under thermal stress and delivers a new approach to study host-symbiont interactions at the microscale, allowing us to directly link intracellular ROS with DMSP and DMSO dynamics.

Goodwin, K.D., Thompson, L.R., Duarte, B., Kahlke, T., Thompson, A.R., Marques, J.C. & Caçador, I. 2017, 'DNA sequencing as a tool to monitor marine ecological status', Frontiers in Marine Science, vol. 4, no. MAY.
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© 2017 Goodwin, Thompson, Duarte, Kahlke, Thompson, Marques and Caçador. Many ocean policies mandate integrated, ecosystem-based approaches to marine monitoring, driving a global need for efficient, low-cost bioindicators of marine ecological quality. Most traditional methods to assess biological quality rely on specialized expertise to provide visual identification of a limited set of specific taxonomic groups, a time-consuming process that can provide a narrow view of ecological status. In addition, microbial assemblages drive food webs but are not amenable to visual inspection and thus are largely excluded from detailed inventory. Molecular-based assessments of biodiversity and ecosystem function offer advantages over traditional methods and are increasingly being generated for a suite of taxa using a "microbes to mammals" or "barcodes to biomes" approach. Progress in these efforts coupled with continued improvements in high-throughput sequencing and bioinformatics pave the way for sequence data to be employed in formal integrated ecosystem evaluation, including food web assessments, as called for in the European Union Marine Strategy Framework Directive. DNA sequencing of bioindicators, both traditional (e.g., benthic macroinvertebrates, ichthyoplankton) and emerging (e.g., microbial assemblages, fish via eDNA), promises to improve assessment of marine biological quality by increasing the breadth, depth, and throughput of information and by reducing costs and reliance on specialized taxonomic expertise.

Goyen, S., Pernice, M., Szabó, M., Warner, M.E., Ralph, P.J. & Suggett, D.J. 2017, 'A molecular physiology basis for functional diversity of hydrogen peroxide production amongst Symbiodinium spp. (Dinophyceae)', Marine Biology: international journal on life in oceans and coastal waters, vol. 164, no. 3.
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Hildebrand, M., Manandhar-Shrestha, K. & Abbriano, R. 2017, 'Effects of chrysolaminarin synthase knockdown in the diatom Thalassiosira pseudonana: Implications of reduced carbohydrate storage relative to green algae', ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, vol. 23, pp. 66-77.
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Jensen, P.Ø., Kolpen, M., Kragh, K.N. & Kühl, M. 2017, 'Microenvironmental characteristics and physiology of biofilms in chronic infections of CF patients are strongly affected by the host immune response.', APMIS, vol. 125, no. 4, pp. 276-288.
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In vitro studies of Pseudomonas aeruginosa and other pathogenic bacteria in biofilm aggregates have yielded detailed insight into their potential growth modes and metabolic flexibility under exposure to gradients of substrate and electron acceptor. However, the growth pattern of P. aeruginosa in chronic lung infections of cystic fibrosis (CF) patients is very different from what is observed in vitro, for example, in biofilms grown in flow chambers. Dense in vitro biofilms of P. aeruginosa exhibit rapid O2 depletion within <50-100 μm due to their own aerobic metabolism. In contrast, in vivo investigations show that P. aeruginosa persists in the chronically infected CF lung as relatively small cell aggregates that are surrounded by numerous PMNs, where the activity of PMNs is the major cause of O2 depletion rendering the P. aeruginosa aggregates anoxic. High levels of nitrate and nitrite enable P. aeruginosa to persist fueled by denitrification in the PMN-surrounded biofilm aggregates. This configuration creates a potentially long-term stable ecological niche for P. aeruginosa in the CF lung, which is largely governed by slow growth and anaerobic metabolism and enables persistence and resilience of this pathogen even under the recurring aggressive antimicrobial treatments of CF patients. As similar slow growth of other CF pathogens has recently been observed in endobronchial secretions, there is now a clear need for better in vitro models that simulate such in vivo growth patterns and anoxic microenvironments in order to help unravel the efficiency of existing or new antimicrobials targeting anaerobic metabolism in P. aeruginosa and other CF pathogens. We also advocate that host immune responses such as PMN-driven O2 depletion play a central role in the formation of anoxic microniches governing bacterial persistence in other chronic infections such as chronic wounds.

Klein, S.G., Pitt, K.A., Nitschke, M.R., Goyen, S., Welsh, D.T., Suggett, D.J. & Carroll, A.R. 2017, 'Symbiodinium mitigate the combined effects of hypoxia and acidification on a noncalcifying cnidarian.', Glob Chang Biol, vol. 23, no. 9, pp. 3690-3703.
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Anthropogenic nutrient inputs enhance microbial respiration within many coastal ecosystems, driving concurrent hypoxia and acidification. During photosynthesis, Symbiodinium spp., the microalgal endosymbionts of cnidarians and other marine phyla, produce O2 and assimilate CO2 and thus potentially mitigate the exposure of the host to these stresses. However, such a role for Symbiodinium remains untested for noncalcifying cnidarians. We therefore contrasted the fitness of symbiotic and aposymbiotic polyps of a model host jellyfish (Cassiopea sp.) under reduced O2 (~2.09 mg/L) and pH (~ 7.63) scenarios in a full-factorial experiment. Host fitness was characterized as asexual reproduction and their ability to regulate internal pH and Symbiodinium performance characterized by maximum photochemical efficiency, chla content and cell density. Acidification alone resulted in 58% more asexual reproduction of symbiotic polyps than aposymbiotic polyps (and enhanced Symbiodinium cell density) suggesting Cassiopea sp. fitness was enhanced by CO2 -stimulated Symbiodinium photosynthetic activity. Indeed, greater CO2 drawdown (elevated pH) was observed within host tissues of symbiotic polyps under acidification regardless of O2 conditions. Hypoxia alone produced 22% fewer polyps than ambient conditions regardless of acidification and symbiont status, suggesting Symbiodinium photosynthetic activity did not mitigate its effects. Combined hypoxia and acidification, however, produced similar numbers of symbiotic polyps compared with aposymbiotic kept under ambient conditions, demonstrating that the presence of Symbiodinium was key for mitigating the combined effects of hypoxia and acidification on asexual reproduction. We hypothesize that this mitigation occurred because of reduced photorespiration under elevated CO2 conditions where increased net O2 production ameliorates oxygen debt. We show that Symbiodinium play an important role in facilitating enhanced fitness of Cassiopea sp. ...

Kohli, G.S., Campbell, K., John, U., Smith, K.F., Fraga, S., Rhodes, L.L. & Murray, S.A. 2017, 'Role of Modular Polyketide Synthases in the Production of Polyether Ladder Compounds in Ciguatoxin-Producing Gambierdiscus polynesiensis and G. excentricus (Dinophyceae).', Journal of Eukaryotic Microbiology, pp. 1-16.
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Gambierdiscus, a benthic dinoflagellate, produces ciguatoxins that cause the human illness Ciguatera. Ciguatoxins are polyether ladder compounds that have a polyketide origin, indicating that polyketide synthases (PKS) are involved in their production. We sequenced transcriptomes of Gambierdiscus excentricus and Gambierdiscus polynesiensis and found 264 contigs encoding single domain ketoacyl synthases (KS; G. excentricus: 106, G. polynesiensis: 143) and ketoreductases (KR; G. excentricus: 7, G. polynesiensis: 8) with sequence similarity to type I PKSs, as reported in other dinoflagellates. In addition, 24 contigs (G. excentricus: 3, G. polynesiensis: 21) encoding multiple PKS domains (forming typical type I PKSs modules) were found. The proposed structure produced by one of these megasynthases resembles a partial carbon backbone of a polyether ladder compound. Seventeen contigs encoding single domain KS, KR, s-malonyltransacylase, dehydratase and enoyl reductase with sequence similarity to type II fatty acid synthases (FAS) in plants were found. Type I PKS and type II FAS genes were distinguished based on the arrangement of domains on the contigs and their sequence similarity and phylogenetic clustering with known PKS/FAS genes in other organisms. This differentiation of PKS and FAS pathways in Gambierdiscus is important, as it will facilitate approaches to investigating toxin biosynthesis pathways in dinoflagellates.

Kretzschmar, A.L., Verma, A., Harwood, T., Hoppenrath, M. & Murray, S. 2017, 'Characterization of Gambierdiscus lapillus sp. nov. (Gonyaulacales, Dinophyceae): a new toxic dinoflagellate from the Great Barrier Reef (Australia).', J Phycol, vol. 53, no. 2, pp. 283-297.
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Gambierdiscus is a genus of benthic dinoflagellates found worldwide. Some species produce neurotoxins (maitotoxins and ciguatoxins) that bioaccumulate and cause ciguatera fish poisoning (CFP), a potentially fatal food-borne illness that is common worldwide in tropical regions. The investigation of toxigenic species of Gambierdiscus in CFP endemic regions in Australia is necessary as a first step to determine which species of Gambierdiscus are related to CFP cases occurring in this region. In this study, we characterized five strains of Gambierdiscus collected from Heron Island, Australia, a region in which ciguatera is endemic. Clonal cultures were assessed using (i) light microscopy; (ii) scanning electron microscopy; (iii) DNA sequencing based on the nuclear encoded ribosomal 18S and D8-D10 28S regions; (iv) toxicity via mouse bioassay; and (v) toxin profile as determined by Liquid Chromatography-Mass Spectrometry. Both the morphological and phylogenetic data indicated that these strains represent a new species of Gambierdiscus, G. lapillus sp. nov. (plate formula Po, 3', 0a, 7″, 6c, 7-8s, 5‴, 0p, 2″″ and distinctive by size and hatchet-shaped 2' plate). Culture extracts were found to be toxic using the mouse bioassay. Using chemical analysis, it was determined that they did not contain maitotoxin (MTX1) or known algal-derived ciguatoxin analogs (CTX3B, 3C, CTX4A, 4B), but that they contained putative MTX3, and likely other unknown compounds.

Larsson, M., Ajani, P.A., Rubio, A.M., Guise, K., MacPherson, R.G., Brett, S.J., Davies, K.P. & Doblin, M. 2017, 'Long-term perspective on the relationship between phytoplankton and nutrient concentrations in a southeastern Australian estuary', Marine Pollution Bulletin, vol. 114, no. 1, pp. 227-238.
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Levin, R.A., Suggett, D.J., Nitschke, M.R., van Oppen, M.J.H. & Steinberg, P.D. 2017, 'Expanding the Symbiodinium (Dinophyceae, Suessiales) Toolkit Through Protoplast Technology.', J Eukaryot Microbiol.
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Dinoflagellates within the genus Symbiodinium are photosymbionts of many tropical reef invertebrates, including corals, making them central to the health of coral reefs. Symbiodinium have therefore gained significant research attention, though studies have been constrained by technical limitations. In particular, the generation of viable cells with their cell walls removed (termed protoplasts) has enabled a wide range of experimental techniques for bacteria, fungi, plants, and algae such as ultrastructure studies, virus infection studies, patch clamping, genetic transformation, and protoplast fusion. However, previous studies have struggled to remove the cell walls from armored dinoflagellates, potentially due to the internal placement of their cell walls. Here, we produce the first Symbiodinium protoplasts from three genetically and physiologically distinct strains via incubation with cellulase and osmotic agents. Digestion of the cell walls was verified by a lack of Calcofluor White fluorescence signal and by cell swelling in hypotonic culture medium. Fused protoplasts were also observed, motivating future investigation into intra- and inter-specific somatic hybridization of Symbiodinium. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Generation of Symbiodinium protoplasts opens exciting, new avenues for researching these crucial symbiotic dinoflagellates, including genetic modification.

Levin, R.A., Voolstra, C.R., Agrawal, S., Steinberg, P.D., Suggett, D.J. & van Oppen, M.J.H. 2017, 'Engineering Strategies to Decode and Enhance the Genomes of Coral Symbionts.', Front Microbiol, vol. 8, p. 1220.
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Elevated sea surface temperatures from a severe and prolonged El Niño event (2014-2016) fueled by climate change have resulted in mass coral bleaching (loss of dinoflagellate photosymbionts, Symbiodinium spp., from coral tissues) and subsequent coral mortality, devastating reefs worldwide. Genetic variation within and between Symbiodinium species strongly influences the bleaching tolerance of corals, thus recent papers have called for genetic engineering of Symbiodinium to elucidate the genetic basis of bleaching-relevant Symbiodinium traits. However, while Symbiodinium has been intensively studied for over 50 years, genetic transformation of Symbiodinium has seen little success likely due to the large evolutionary divergence between Symbiodinium and other model eukaryotes rendering standard transformation systems incompatible. Here, we integrate the growing wealth of Symbiodinium next-generation sequencing data to design tailored genetic engineering strategies. Specifically, we develop a testable expression construct model that incorporates endogenous Symbiodinium promoters, terminators, and genes of interest, as well as an internal ribosomal entry site from a Symbiodinium virus. Furthermore, we assess the potential for CRISPR/Cas9 genome editing through new analyses of the three currently available Symbiodinium genomes. Finally, we discuss how genetic engineering could be applied to enhance the stress tolerance of Symbiodinium, and in turn, coral reefs.

Lichtenberg, M., Brodersen, K.E. & Kühl, M. 2017, 'Radiative Energy Budgets of Phototrophic Surface-Associated Microbial Communities and their Photosynthetic Efficiency Under Diffuse and Collimated Light.', Front Microbiol, vol. 8, p. 452.
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We investigated the radiative energy budgets of a heterogeneous photosynthetic coral reef sediment and a compact uniform cyanobacterial biofilm on top of coastal sediment. By combining electrochemical, thermocouple and fiber-optic microsensor measurements of O2, temperature and light, we could calculate the proportion of the absorbed light energy that was either dissipated as heat or conserved by photosynthesis. We show, across a range of different incident light regimes, that such radiative energy budgets are highly dominated by heat dissipation constituting up to 99.5% of the absorbed light energy. Highest photosynthetic energy conservation efficiency was found in the coral sediment under low light conditions and amounted to 18.1% of the absorbed light energy. Additionally, the effect of light directionality, i.e., diffuse or collimated light, on energy conversion efficiency was tested on the two surface-associated systems. The effects of light directionality on the radiative energy budgets of these phototrophic communities were not unanimous but, resulted in local spatial differences in heat-transfer, gross photosynthesis, and light distribution. The light acclimation index, Ek, i.e., the irradiance at the onset of saturation of photosynthesis, was >2 times higher in the coral sediment compared to the biofilm and changed the pattern of photosynthetic energy conservation under light-limiting conditions. At moderate to high incident irradiances, the photosynthetic conservation of absorbed energy was highest in collimated light; a tendency that changed in the biofilm under sub-saturating incident irradiances, where higher photosynthetic efficiencies were observed under diffuse light. The aim was to investigate how the physical structure and light propagation affected energy budgets and light utilization efficiencies in loosely organized vs. compact phototrophic sediment under diffuse and collimated light. Our results suggest that the optical properties and the st...

Lichtenberg, M., Nørregaard, R.D. & Kühl, M. 2017, 'Diffusion or advection? Mass transfer and complex boundary layer landscapes of the brown alga Fucus vesiculosus.', J R Soc Interface, vol. 14, no. 128.
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The role of hyaline hairs on the thallus of brown algae in the genus Fucus is long debated and several functions have been proposed. We used a novel motorized set-up for two-dimensional and three-dimensional mapping with O2 microsensors to investigate the spatial heterogeneity of the diffusive boundary layer (DBL) and O2 flux around single and multiple tufts of hyaline hairs on the thallus of Fucus vesiculosus. Flow was a major determinant of DBL thickness, where higher flow decreased DBL thickness and increased O2 flux between the algal thallus and the surrounding seawater. However, the topography of the DBL varied and did not directly follow the contour of the underlying thallus. Areas around single tufts of hyaline hairs exhibited a more complex mass-transfer boundary layer, showing both increased and decreased thickness when compared with areas over smooth thallus surfaces. Over thallus areas with several hyaline hair tufts, the overall effect was an apparent increase in the boundary layer thickness. We also found indications for advective O2 transport driven by pressure gradients or vortex shedding downstream from dense tufts of hyaline hairs that could alleviate local mass-transfer resistances. Mass-transfer dynamics around hyaline hair tufts are thus more complex than hitherto assumed and may have important implications for algal physiology and plant-microbe interactions.

Macreadie, P.I., Nielsen, D.A., Kelleway, J.J., Atwood, T.B., Seymour, J.R., Petrou, K., Connolly, R.M., Thomson, A.C.G., Trevathan-Tackett, S.M. & Ralph, P.J. 2017, 'Can we manage coastal ecosystems to sequester more blue carbon?', Frontiers in Ecology and the Environment, vol. 15, no. 4, pp. 206-213.
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© The Ecological Society of America To promote the sequestration of blue carbon, resource managers rely on best-management practices that have historically included protecting and restoring vegetated coastal habitats (seagrasses, tidal marshes, and mangroves), but are now beginning to incorporate catchment-level approaches. Drawing upon knowledge from a broad range of environmental variables that influence blue carbon sequestration, including warming, carbon dioxide levels, water depth, nutrients, runoff, bioturbation, physical disturbances, and tidal exchange, we discuss three potential management strategies that hold promise for optimizing coastal blue carbon sequestration: (1) reducing anthropogenic nutrient inputs, (2) reinstating top-down control of bioturbator populations, and (3) restoring hydrology. By means of case studies, we explore how these three strategies can minimize blue carbon losses and maximize gains. A key research priority is to more accurately quantify the impacts of these strategies on atmospheric greenhouse-gas emissions in different settings at landscape scales.

Maeda, E., Ma, X., Wagner, F., Kim, H., Oki, T., Eamus, D. & Huete, A. 2017, 'Evapotranspiration seasonality across the Amazon basin', Earth System Dynamics Discussions, vol. 8, pp. 438-454.
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Evapotranspiration (ET) of Amazon forests is a main driver of regional climate patterns and an important indicator of ecosystem functioning. Despite its importance, the seasonal variability of ET over Amazon forests, and its relationship with environmental drivers, is still poorly understood. In this study, we carry out a water balance approach to analyse seasonal patterns in ET and their relationships with water and energy drivers over five sub-basins across the Amazon basin. We used in-situ measurements of river discharge, and remotely sensed estimates of terrestrial water storage, rainfall, and solar radiation. We show that the characteristics of ET seasonality in all sub-basins differ in timing and magnitude. The highest mean annual ET was found in the northern Rio Negro basin (~ 1497 mm year−1) and the lowest values in the Solimões River basin (~ 986 mm year−1). For the first time in a basin-scale study, using observational data, we show that factors limiting ET vary across climatic gradients in the Amazon, confirming local-scale eddy covariance studies. Both annual mean and seasonality in ET are driven by a combination of energy and water availability, as neither rainfall nor radiation alone could explain patterns in ET. In southern basins, despite seasonal rainfall deficits, deep root water uptake allows increasing rates of ET during the dry season, when radiation is usually higher than in the wet season. We demonstrate contrasting ET seasonality with satellite greenness across Amazon forests, with strong asynchronous relationships in ever-wet watersheds, and positive correlations observed in seasonally dry watersheds. Finally, we compared our results with estimates obtained by two ET models, and we conclude that neither of the two tested models could provide a consistent representation of ET seasonal patterns across the Amazon.

Maeda, E.E., Ma, X., Wagner, F.H., Kim, H., Oki, T., Eamus, D. & Huete, A. 2017, 'Evapotranspiration seasonality across the Amazon Basin', Earth System Dynamics, vol. 8, no. 2, pp. 439-454.
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Matthijs, M., Fabris, M., Obata, T., Foubert, I., Franco-Zorrilla, M.J., Solano, R., Fernie, A.F., Vyverman, W. & Goossens, A. 2017, 'The transcription factor bZIP14 regulates the TCA cycle in the diatom Phaeodactylum tricornutum', EMBO Journal, vol. e201696392.
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Diatoms are amongst the most important marine microalgae in terms of biomass, but little is known concerning the molecular mechanisms that regulate their versatile metabolism. Here, the pennate diatom Phaeodactylum tricornutum was studied at the metabolite and transcriptome level during nitrogen starvation and following imposition of three other stresses that impede growth. The coordinated upregulation of the tricarboxylic acid (TCA) cycle during the nitrogen stress response was the most striking observation. Through co‐expression analysis and DNA binding assays, the transcription factor bZIP14 was identified as a regulator of the TCA cycle, also beyond the nitrogen starvation response, namely in diurnal regulation. Accordingly, metabolic and transcriptional shifts were observed upon overexpression of bZIP14 in transformed P. tricornutum cells. Our data indicate that the TCA cycle is a tightly regulated and important hub for carbon reallocation in the diatom cell during nutrient starvation and that bZIP14 is a conserved regulator of this cycle.

McLaughlin, R.L., Schijven, D., van Rheenen, W., van Eijk, K.R., O'Brien, M., Kahn, R.S., Ophoff, R.A., Goris, A., Bradley, D.G., Al-Chalabi, A., van den Berg, L.H., Luykx, J.J., Hardiman, O., Veldink, J.H., Project MinE GWAS Consortium & Schizophrenia Working Group of the Psychiatric Genomics Consortium 2017, 'Genetic correlation between amyotrophic lateral sclerosis and schizophrenia.', Nat Commun, vol. 8, p. 14774.
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We have previously shown higher-than-expected rates of schizophrenia in relatives of patients with amyotrophic lateral sclerosis (ALS), suggesting an aetiological relationship between the diseases. Here, we investigate the genetic relationship between ALS and schizophrenia using genome-wide association study data from over 100,000 unique individuals. Using linkage disequilibrium score regression, we estimate the genetic correlation between ALS and schizophrenia to be 14.3% (7.05-21.6; P=1 × 10(-4)) with schizophrenia polygenic risk scores explaining up to 0.12% of the variance in ALS (P=8.4 × 10(-7)). A modest increase in comorbidity of ALS and schizophrenia is expected given these findings (odds ratio 1.08-1.26) but this would require very large studies to observe epidemiologically. We identify five potential novel ALS-associated loci using conditional false discovery rate analysis. It is likely that shared neurobiological mechanisms between these two disorders will engender novel hypotheses in future preclinical and clinical studies.

Messer, L.F., Brown, M.V., Furnas, M.J., Carney, R.L., McKinnon, A.D. & Seymour, J.R. 2017, 'Diversity and Activity of Diazotrophs in Great Barrier Reef Surface Waters.', Frontiers in Microbiology, vol. 8, pp. 1-16.
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Discrepancies between bioavailable nitrogen (N) concentrations and phytoplankton growth rates in the oligotrophic waters of the Great Barrier Reef (GBR) suggest that undetermined N sources must play a significant role in supporting primary productivity. One such source could be biological dinitrogen (N2) fixation through the activity of "diazotrophic" bacterioplankton. Here, we investigated N2 fixation and diazotroph community composition over 10° S of latitude within GBR surface waters. Qualitative N2 fixation rates were found to be variable across the GBR but were relatively high in coastal, inner and outer GBR waters, reaching 68 nmol L(-1) d(-1). Diazotroph assemblages, identified by amplicon sequencing of the nifH gene, were dominated by the cyanobacterium Trichodesmium erythraeum, γ-proteobacteria from the Gamma A clade, and δ-proteobacterial phylotypes related to sulfate-reducing genera. However, diazotroph communities exhibited significant spatial heterogeneity, correlated with shifts in dissolved inorganic nutrient concentrations. Specifically, heterotrophic diazotrophs generally increased in relative abundance with increasing concentrations of phosphate and N, while Trichodesmium was proportionally more abundant when concentrations of these nutrients were low. This study provides the first in-depth characterization of diazotroph community composition and N2 fixation dynamics within the oligotrophic, N-limited surface waters of the GBR. Our observations highlight the need to re-evaluate N cycling dynamics within oligotrophic coral reef systems, to include diverse N2 fixing assemblages as a potentially significant source of dissolved N within the water column.

Morelato, M., Barash, M., Blanes, L., Chadwick, S., Dilag, J., Kuzhiumparambil, U., Nizio, K.D., Spindler, X. & Moret, S. 2017, 'Forensic Science: Current State and Perspective by a Group of Early Career Researchers', Foundations of Science, pp. 1-27.
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Forensic science and its influence on policing and the criminal justice system have increased since the beginning of the twentieth century. While the philosophies of the forensic science pioneers remain the pillar of modern practice, rapid advances in technology and the underpinning sciences have seen an explosion in the number of disciplines and tools. Consequently, the way in which we exploit and interpret the remnant of criminal activity are adapting to this changing environment. In order to best exploit the trace, an interdisciplinary approach to both research and investigation is required. In this paper, nine postdoctoral research fellows from a multidisciplinary team discuss their vision for the future of forensic science at the crime scene, in the laboratory and beyond. This paper does not pretend to be exhaustive of all fields of forensic science, but describes a portion of the postdoctoral fellows’ interests and skills.

Murphy, C.D., Ni, G., Li, G., Barnett, A., Xu, K., Grant-Burt, J., Liefer, J.D., Suggett, D.J. & Campbell, D.A. 2017, 'Quantitating active photosystem II reaction center content from fluorescence induction transients', Limnology and Oceanography: Methods, vol. 15, no. 1, pp. 54-69.
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© 2016 The Authors Limnology and Oceanography: Methods published by Wiley Periodicals, Inc. Photosystem II (PSII) is a pigment-protein complex that photochemically extracts electrons from water, generating the reductant that supports biological productivity in all biomes. Estimating the content of active PSII reaction centers in a liquid sample is a key input for estimating aquatic photosynthesis rates, as well as for analyzing phytoplankton stress responses. Established procedures for PSII content quantification based on oxygen evolution are slow, imprecise and require dense cell suspensions, and are thus inapplicable to many laboratory or field studies. A new approach uses baseline chlorophyll fluorescence emission divided by the effective absorbance cross section for PSII photochemistry, with both variables derivable from single turnover fluorescence induction protocols. This approach has not been widely tested and is potentially subject to variation in samples suffering progressive photoinactivation or induction of non-photochemical quenching under variable light. We evaluated the validity of this approach for a marine picocyanobacteria, low and high light Prochlorococcus ecotypes, arctic and temperate prasinophyte green alga and two centric diatoms, generating 209 paired determinations from a range of growth and treatment conditions. We successfully calibrated the fluorescence derived estimator for PSII reaction center content, and demonstrate a modification that corrects for the short term influence of photoinactivation. The modified parameter shows little response to induction of non-photochemical quenching. In doing so we show the potential and limitations of an estimator of active PSII reaction center content that is sufficiently robust to support rapid, time-resolved autonomous measures of primary productivity from lakes and oceans.

Murray, S.A., Ajani, P., Kretzschmar, A.L. & Verma, A. 2017, 'Response to "More surprises in the global greenhouse: Human health impacts form recent toxic marine aerosol formulations, due to centennial alterations or world-wide coastal food webs".', Mar Pollut Bull.
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Najafpour, M.M., Heidari, S., Balaghi, S.E., Hołyńska, M., Sadr, M.H., Soltani, B., Khatamian, M., Larkum, A.W. & Allakhverdiev, S.I. 2017, 'Proposed mechanisms for water oxidation by Photosystem II and nanosized manganese oxides.', Biochim Biophys Acta, vol. 1858, no. 2, pp. 156-174.
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Plants, algae and cyanobacteria capture sunlight, extracting electrons from H2O to reduce CO2 into sugars while releasing O2 in the oxygenic photosynthetic process. Because of the important role of water oxidation in artificial photosynthesis and many solar fuel systems, understanding the structure and function of this unique biological catalyst forms a requisite research field. Herein the structure of the water-oxidizing complex and its ligand environment are described with reference to the 1.9Å resolution X-ray-derived crystallographic model of the water-oxidizing complex from the cyanobacterium Thermosynechococcus vulcanus. Proposed mechanisms for water oxidation by Photosystem II and nanosized manganese oxides are also reviewed and discussed in the paper.

Pandey, A.K., Mishra, A.K., Kumar, R., Berwal, S., Devadas, R., Huete, A. & Kumar, K. 2017, 'CO variability and its association with household cooking fuels consumption over the Indo-Gangetic Plains.', Environ Pollut, vol. 222, pp. 83-93.
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This study examines the spatio-temporal trends obtained from decade long (Jan 2003-Dec 2014) satellite observational data of Atmospheric Infrared Sounder (AIRS) and Measurements of Pollution in the Troposphere (MOPITT) on carbon monoxide (CO) concentration over the Indo-Gangetic Plains (IGP) region. The time sequence plots of columnar CO levels over the western, central and eastern IGP regions reveal marked seasonal behaviour, with lowest CO levels occurring during the monsoon months and the highest CO levels occurring during the pre-monsoon period. A negative correlation between CO levels and rainfall is observed. CO vertical profiles show relatively high values in the upper troposphere at ∼200 hPa level during the monsoon months, thus suggesting the role of convective transport and advection in addition to washout behind the decreased CO levels during this period. MOPITT and AIRS observations show a decreasing trend of 9.6 × 10(15) and 1.5 × 10(16) molecules cm(-2) yr(-1), respectively, in columnar CO levels over the IGP region. The results show the existence of a spatial gradient in CO from the eastern (higher levels) to western IGP region (lower levels). Data from the Census of India on the number of households using various cooking fuels in the IGP region shows the prevalence of biomass-fuel (i.e. firewood, crop residue, cowdung etc.) use over the eastern and central IGP regions and that of liquefied petroleum gas over the western IGP region. CO emission estimates from cooking activity over the three IGP regions are found to be in the order east > central > west, which support the existence of the spatial gradient in CO from eastern to the western IGP region. Our results support the intervention of present Indian government on limiting the use of biomass-fuels in domestic cooking to achieve the benefits in terms of the better air quality, household health and regional/global climate change mitigation.

Peng, D., Zhang, B., Wu, C., Huete, A.R., Gonsamo, A., Lei, L., Ponce-Campos, G.E., Liu, X. & Wu, Y. 2017, 'Country-level net primary production distribution and response to drought and land cover change', Science of the Total Environment, vol. 574, pp. 65-77.
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© 2016 Elsevier B.V. Carbon sequestration by terrestrial ecosystems can offset emissions and thereby offers an alternative way of achieving the target of reducing the concentration of CO 2 in the atmosphere. Net primary production (NPP) is the first step in the sequestration of carbon by terrestrial ecosystems. This study quantifies moderate-resolution imaging spectroradiometer (MODIS) NPP from 2000 to 2014 at the country level along with its response to drought and land cover change. Our results indicate that the combined NPP for 53 countries represents >  90% of global NPP. From 2000 to 2014, 29 of these 53 countries had increasing NPP trends, most notably the Central African Republic (23 g C/m 2 /y). The top three and top 12 countries accounted for 30% and 60% of total global NPP, respectively, whereas the mean national NPP per unit area in the countries with the 12 lowest values was only around ~ 300 g C/m 2 /y - the exception to this was Brazil, which had an NPP of 850 g C/m 2 /y. Large areas of Russia, Argentina, Peru and several countries in southeast Asia showed a marked decrease in NPP (~ 15 g C/m 2 /y). About 37% of the NPP decrease was caused by drought while ~ 55% of NPP variability was attributed to changes in water availability. Land cover change explained about 20% of the NPP variability. Our findings support the idea that government policies should aim primarily to improve water management in drought-afflicted countries; land use/land cover change policy could also be used as an alternative method of increasing NPP.

Peng, D., Zhang, X., Wu, C., Huang, W., Gonsamo, A., Huete, A.R., Didan, K., Tan, B., Liu, X. & Zhang, B. 2017, 'Intercomparison and evaluation of spring phenology products using National Phenology Network and AmeriFlux observations in the contiguous United States', Agricultural and Forest Meteorology, vol. 242, pp. 33-46.
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© 2017 Elsevier B.V. Many remote sensing based spring phenology products have been developed to monitor and study vegetation phenology at regional and global scales. It is important to understand how these products perform relative to each other and to ground observations. In this study, we extracted spring green-up onset dates (GUD) over the contiguous United States (CONUS) from six major land surface phenology (LSP) products: (1) Moderate Resolution Imaging Spectroradiometer (MODIS) Land Cover Dynamics Phenology (MCD12Q2); (2) Vegetation Index and Phenology Multi-sensor Phenology (VIPPHENEVI2); (3) Global Long-Term Climate Modeling Grid Land Surface Phenology (CMGLSP); (4 and 5) North American Carbon Program (NACP) Phenology (MOD09Q1PEVI and MOD15PHN); and (6) USGS/EROS advanced very high resolution radiometer (AVHRR) phenology (AVHRRP). We characterized and compared the GUD data in these LSP products, and evaluated their accuracy using ground-based phenology observations [i.e., human observations of first leaf and sensor readings of gross primary productivity (GPP)] from the USA National Phenology Network (USA-NPN) and AmeriFlux. The results revealed the consistencies and discrepancies of GUD estimates among LSP products. Intercomparison of the six products indicated that the root mean square error (RMSE) of these products range from 17.8 days to 31.5 days, whereas AVHRRP GUD has the lowest correlation and largest RMSE (∼30 days) relative to other products. When compared to ground observations, GUD estimates in six LSP products generally have RMSE values of ∼20 days and significant correlations (p  <  0.001). For the products (MCD12Q2, AVHRRP, MOD09Q1PEVI, and MOD15PHN) available for comparisons in the short-term period (from 2001–2007), AVHRRP GUD presented relatively weaker correlations and a lower index of agreement (IOA), however, MCD12Q2 GUD showed overall slightly better consistencies with ground observations. In the two long-term products (CMGLSP and VI...

Petrou, K., Ralph, P.J. & Nielsen, D.A. 2017, 'A novel mechanism for host-mediated photoprotection in endosymbiotic foraminifera.', ISME J, vol. 11, no. 2, pp. 453-462.
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Light underpins the health and function of coral reef ecosystems, where symbiotic partnerships with photosynthetic algae constitute the life support system of the reef. Decades of research have given us detailed knowledge of the photoprotective capacity of phototrophic organisms, yet little is known about the role of the host in providing photoprotection in symbiotic systems. Here we show that the intracellular symbionts within the large photosymbiotic foraminifera Marginopora vertebralis exhibit phototactic behaviour, and that the phototactic movement of the symbionts is accomplished by the host, through rapid actin-mediated relocation of the symbionts deeper into the cavities within the calcium carbonate test. Using a photosynthetic inhibitor, we identified that the infochemical signalling for host regulation is photosynthetically derived, highlighting the presence of an intimate communication between the symbiont and the host. Our results emphasise the central importance of the host in photosymbiotic photoprotection via a new mechanism in foraminifera that can serve as a platform for exploring host-symbiont communication in other photosymbiotic organisms.

Pierangelini, M., Raven, J.A. & Giordano, M. 2017, 'The relative availability of inorganic carbon and inorganic nitrogen influences the response of the dinoflagellate Protoceratium reticulatum to elevated CO2.', Journal of phycology.
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This work originates from three facts: 1) changes in CO2 availability influence metabolic processes in algal cells. 2) Spatial and temporal variations of nitrogen availability cause repercussions on phytoplankton physiology. 3) Growth and cell composition are dependent on the stoichiometry of nutritional resources. In this study we assess whether the impact of rising pCO2 is influenced by N availability, through the impact that it would have on the C/N stoichiometry, in condition of N sufficiency. Our experiments used the dinoflagellate Protoceratium reticulatum, which we cultured under three CO2 regimes (400, 1000 and 5000 ppmv, pH of 8.1) and either variable (the NO3 (-) concentration was always 2.5 mmol • L(-1) ) or constant (NO3 (-) concentration varied to maintain the same Ci /NO3 (-) ratio at all pCO2 ) Ci  /NO3 (-) ratio. Regardless of N availability, cells had higher specific growth rates, but lower cell dry weight and C and N quotas, at elevated CO2 . The carbohydrate pool size and the C/N was unaltered in all treatments. The lipid content only decreased at high pCO2 at constant Ci  /NO3 (-) ratio. In the variable Ci  /NO3 (-) conditions, the relative abundance of Rubisco (and other proteins) also changed; this did not occur at constant Ci  /NO3 (-) . Thus, the biomass quality of P. reticulatum for grazers was affected by the Ci  /NO3 (-) ratio in the environment and not only by the pCO2 , both with respect to the size of the main organic pools and the composition of the expressed proteome. This article is protected by copyright. All rights reserved.

Raina, J.-.B., Clode, P.L., Cheong, S., Bougoure, J., Kilburn, M.R., Reeder, A., Forêt, S., Stat, M., Beltran, V., Thomas-Hall, P., Tapiolas, D., Motti, C.M., Gong, B., Pernice, M., Marjo, C.E., Seymour, J.R., Willis, B.L. & Bourne, D.G. 2017, 'Subcellular tracking reveals the location of dimethylsulfoniopropionate in microalgae and visualises its uptake by marine bacteria.', eLife, vol. 6, pp. 1-17.
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Phytoplankton-bacteria interactions drive the surface ocean sulfur cycle and local climatic processes through the production and exchange of a key compound: dimethylsulfoniopropionate (DMSP). Despite their large-scale implications, these interactions remain unquantified at the cellular-scale. Here we use secondary-ion mass spectrometry to provide the first visualization of DMSP at sub-cellular levels, tracking the fate of a stable sulfur isotope ((34)S) from its incorporation by microalgae as inorganic sulfate to its biosynthesis and exudation as DMSP, and finally its uptake and degradation by bacteria. Our results identify for the first time the storage locations of DMSP in microalgae, with high enrichments present in vacuoles, cytoplasm and chloroplasts. In addition, we quantify DMSP incorporation at the single-cell level, with DMSP-degrading bacteria containing seven times more (34)S than the control strain. This study provides an unprecedented methodology to label, retain, and image small diffusible molecules, which can be transposable to other symbiotic systems.

Raven, J.A. 2017, 'Chloride: essential micronutrient and multifunctional beneficial ion.', J Exp Bot, vol. 68, no. 3, pp. 359-367.
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Cl(-) is an essential micronutrient for oxygenic photolithotrophs. About half of global primary productivity is carried out by oxygenic photolithotrophs exposed to saline waters with Cl(-) concentrations orders of magnitude higher than that needed to satisfy the micronutrient requirement. The other half of primary productivity involves terrestrial and freshwater glycophytes sometimes in environments containing significantly more Cl(-) than is needed for the micronutrient requirement, but less than the toxic Cl(-) concentration for glycophytes. Intracellular Cl(-) acts in regulation of cell turgor and volume, including that of stomatal and pulvinar nastic movements, is a major ion in streptophyte and ulvophycean action potentials, and is involved in ion currents flowing around apices of pollen tubes and Acetabularia cells. More work is needed on the essentiality of Cl(-) in these processes, as well as the recent finding that Cl(-) at 1-5 mol m(-3) increases water use efficiency of growth and leaf area in Nicotiana tabacum.

Restrepo-Coupe, N., Levine, N., Christoffersen, B.O., Albert, L.P., Wu, J., Costa, M.H., Galbraith, D., Imbuzeiro, H., Martins, G., da Araujo, A.C., Malhi, Y.S., Zeng, X., Moorcroft, P. & Saleska, S.R. 2017, 'Do dynamic global vegetation models capture the seasonality of carbon fluxes in the Amazon basin? A data-model intercomparison.', Global Change Biology, vol. 23, no. 1, pp. 191-208.
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To predict forest response to long-term climate change with high confidence requires that dynamic global vegetation models (DGVMs) be successfully tested against ecosystem response to short-term variations in environmental drivers, including regular seasonal patterns. Here, we used an integrated dataset from four forests in the Brasil flux network, spanning a range of dry season intensities and lengths, to determine how well four state-of-the-art models (IBIS, ED2, JULES, and CLM3.5) simulated the seasonality of carbon exchanges in Amazonian tropical forests. We found that most DGVMs poorly represented the annual cycle of gross primary productivity (GPP), of photosynthetic capacity (Pc), and of other fluxes and pools. Models simulated consistent dry season declines in GPP in the equatorial Amazon (Manaus K34, Santarem K67, and Caxiuanã CAX); a contrast to observed GPP increases. Model simulated dry season GPP reductions were driven by an external environmental factor, "soil water stress" and consequently by a constant or decreasing photosynthetic infrastructure (Pc), while observed dry-season GPP resulted from a combination of internal biological (leaf-flush and abscission and increased Pc) and environmental (incoming radiation) causes. Moreover, we found models generally overestimated observed seasonal net ecosystem exchange (NEE) and respiration (Re) at equatorial locations. In contrast, a southern Amazon forest (Jarú RJA) exhibited dry season declines in GPP and Re consistent with most DGVMs simulations. While water-limitation was represented in models and the primary driver of seasonal photosynthesis in southern Amazonia, changes in internal biophysical processes, light harvesting adaptations (e.g. variations in leaf area index (LAI) and increasing leaf-level assimilation rate related to leaf demography), and allocation lags between leaf and wood, dominated equatorial Amazon carbon flux dynamics and were deficient or absent from current model formulations. Co...

Rhodes, L., Smith, K.F., Verma, A., Curley, B.G., Harwood, D.T., Murray, S., Kohli, G.S., Solomona, D., Rongo, T., Munday, R. & Murray, S.A. 2017, 'A new species of Gambierdiscus (Dinophyceae) from the south-west Pacific: Gambierdiscus honu sp. nov.', Harmful Algae, vol. 65, pp. 61-70.
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Two isolates of a new tropical, epiphytic dinoflagellate species, Gambierdiscus honu sp. nov., were obtained from macroalgae sampled in Rarotonga, Cook Islands, and from North Meyer Island, Kermadec Islands. Gambierdiscus honu sp. nov. had the common Gambierdiscus Kofoidian plate formula: Po, 3', 6″, 6C?, 6 or 7S, 5‴, 1p and 2⁗. The characteristic morphological features of this species were its relatively small short dorsoventral length and width and the shape of individual plates, in particular the combination of the hatchet-shaped 2' and pentagonal 3' plates and the length to width ratio of the antapical 1p plate. The combination of these characteristics plus the smooth thecal surface and equal sized 1⁗ and 2⁗ plates differentiated this species from other Gambierdiscus species. The phylogenetic analyses supported the unique description. Both isolates of G. honu produced the putative maitotoxin (MTX)-3 analogue, but neither produced ciguatoxin (CTX) or MTX. Extracts of G. honu were shown to be highly toxic to mice by intraperitoneal injection (0.2mg/kg), although less toxic by gavage. It is possible that toxins other than putative MTX-3 are produced.

Robinson, C.M., Cherukuru, N., Hardman-Mountford, N.J., Everett, J.D., McLaughlin, M.J., Davies, K.P., Van Dongen-Vogels, V., Ralph, P.J. & Doblin, M.A. 2017, 'Phytoplankton absorption predicts patterns in primary productivity in Australian coastal shelf waters', Estuarine, Coastal and Shelf Science, vol. 192, pp. 1-16.
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© 2017 Elsevier Ltd The phytoplankton absorption coefficient (a PHY ) has been suggested as a suitable alternate first order predictor of net primary productivity (NPP). We compiled a dataset of surface bio-optical properties and phytoplankton NPP measurements in coastal waters around Australia to examine the utility of an in-situ absorption model to estimate NPP. The magnitude of surface NPP (0.20–19.3 mmol C m −3 d −1 ) across sites was largely driven by phytoplankton biomass, with higher rates being attributed to the microplankton ( > 20 μm) size class. The phytoplankton absorption coefficient a PHY for PAR (photosynthetically active radiation; ā PHY )) ranged from 0.003 to 0.073 m -1 , influenced by changes in phytoplankton community composition, physiology and environmental conditions. The a PHY coefficient also reflected changes in NPP and the absorption model-derived NPP could explain 73% of the variability in measured surface NPP (n = 41; RMSE = 2.49). The absorption model was applied to two contrasting coastal locations to examine NPP dynamics: a high chlorophyll-high variation (HCHV; Port Hacking National Reference Station) and moderate chlorophyll-low variation (MCLV; Yongala National Reference Station) location in eastern Australia using the GIOP-DC satellite a PHY product. Mean daily NPP rates between 2003 and 2015 were higher at the HCHV site (1.71 ± 0.03 mmol C m −3 d −1 ) with the annual maximum NPP occurring during the austral winter. In contrast, the MCLV site annual NPP peak occurred during the austral wet season and had lower mean daily NPP (1.43 ± 0.03 mmol C m −3 d −1 ) across the time-series. An absorption-based model to estimate NPP is a promising approach for exploring the spatio-temporal dynamics in phytoplankton NPP around the Australian continental shelf.

Seymour, J.R., Amin, S.A., Raina, J. & Stocker, R. 2017, 'Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships', Nature Microbiology, vol. 2, pp. 1-12.
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By controlling nutrient cycling and biomass production at the base of the food web, interactions between phytoplankton and bacteria represent a fundamental ecological relationship in aquatic environments. Although typically studied over large spatiotemporal scales, emerging evidence indicates that this relationship is often governed by microscale interactions played out within the region immediately surrounding individual phytoplankton cells. This microenvironment, known as the phycosphere, is the planktonic analogue of the rhizosphere in plants. The exchange of metabolites and infochemicals at this interface governs phytoplankton–bacteria relationships, which span mutualism, commensalism, antagonism, parasitism and competition. The importance of the phycosphere has been postulated for four decades, yet only recently have new technological and conceptual frameworks made it possible to start teasing apart the complex nature of this unique microbial habitat. It has subsequently become apparent that the chemical exchanges and ecological interactions between phytoplankton and bacteria are far more sophisticated than previously thought and often require close proximity of the two partners, which is facilitated by bacterial colonization of the phycosphere. It is also becoming increasingly clear that while interactions taking place within the phycosphere occur at the scale of individual microorganisms, they exert an ecosystem-scale influence on fundamental processes including nutrient provision and regeneration, primary production, toxin biosynthesis and biogeochemical cycling. Here we review the fundamental physical, chemical and ecological features of the phycosphere, with the goal of delivering a fresh perspective on the nature and importance of phytoplankton–bacteria interactions in aquatic ecosystems.

Shi, H., Li, L., Eamus, D., Huete, A., Cleverly, J., Tian, X., Yu, Q., Wang, S., Montagnani, L., Magliulo, V., Rotenberg, E., Pavelka, M. & Carrara, A. 2017, 'Assessing the ability of MODIS EVI to estimate terrestrial ecosystem gross primary production of multiple land cover types', Ecological Indicators, vol. 72, pp. 153-164.
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tTerrestrial ecosystem gross primary production (GPP) is the largest component in the global carbon cycle.The enhanced vegetation index (EVI) has been proven to be strongly correlated with annual GPP withinseveral biomes. However, the annual GPP-EVI relationship and associated environmental regulationshave not yet been comprehensively investigated across biomes at the global scale. Here we exploredrelationships between annual integrated EVI (iEVI) and annual GPP observed at 155 flux sites, whereGPP was predicted with a log-log model: ln(GPP) = a × ln(iEVI) + b. iEVI was computed from MODISmonthly EVI products following removal of values affected by snow or cold temperature and withoutcalculating growing season duration. Through categorisation of flux sites into 12 land cover types, theability of iEVI to estimate GPP was considerably improved (R2from 0.62 to 0.74, RMSE from 454.7 to368.2 g C m−2yr−1). The biome-specific GPP-iEVI formulae generally showed a consistent performancein comparison to a global benchmarking dataset (R2= 0.79, RMSE = 387.8 g C m−2yr−1). Specifically, iEVIperformed better in cropland regions with high productivity but poorer in forests. The ability of iEVI inestimating GPP was better in deciduous biomes (except deciduous broadleaf forest) than in evergreendue to the large seasonal signal in iEVI in deciduous biomes. Likewise, GPP estimated from iEVI was ina closer agreement to global benchmarks at mid and high-latitudes, where deciduous biomes are morecommon and cloud cover has a smaller effect on remote sensing retrievals. Across biomes, a significant andnegative correlation (R2= 0.37, p < 0.05) was observed between the strength (R2) of GPP-iEVI relationshipsand mean annual maximum leaf area index (LAImax), and the relationship between the strength andmean annual precipitation followed a similar trend. LAImaxalso revealed a scaling effect on GPP-iEVIrelationships. Our results suggest that iEVI provides a very simple but robust approach to ...

Smith, K.F., Kohli, G.S., Murray, S.A. & Rhodes, L.L. 2017, 'Assessment of the metabarcoding approach for community analysis of benthic-epiphytic dinoflagellates using mock communities', New Zealand Journal of Marine and Freshwater Research, pp. 1-22.
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© 2017 The Royal Society of New Zealand In this study, we assessed the use of DNA metabarcoding as a method for biodiversity assessment of benthic-epiphytic dinoflagellate communities and for detecting rare, toxin-producing taxa. Mock communities and three primer pairs were used to establish the recovery of species signal and quantitative representation of species in the samples, as well as to determine primer biases, bioinformatic filtering steps, and threshold levels. Samples were analysed using high-throughput sequencing Illumina ™ MiSeq technology. We did not find a relationship between read number and cell abundance for all treatments. However, the method was extremely sensitive, with two of the primer pairs detecting a single cell representing less than 0.001% of the cells in the sample. Benthic and epiphytic dinoflagellate communities were also collected from the Bay of Islands (Northland, New Zealand). Dinophyceae species richness was much higher when samples were analysed using metabarcoding than when analysed by microscopy, and we detected several new taxonomic records for New Zealand.

Sønderholm, M., Kragh, K.N., Koren, K., Jakobsen, T.H., Darch, S.E., Alhede, M., Jensen, P.Ø., Whiteley, M., Kühl, M. & Bjarnsholt, T. 2017, 'Pseudomonas aeruginosa Aggregate Formation in an Alginate Bead Model System Exhibits In Vivo-Like Characteristics.', Appl Environ Microbiol, vol. 83, no. 9.
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Alginate beads represent a simple and highly reproducible in vitro model system for diffusion-limited bacterial growth. In this study, alginate beads were inoculated with Pseudomonas aeruginosa and followed for up to 72 h. Confocal microscopy revealed that P. aeruginosa formed dense clusters similar in size to in vivo aggregates observed ex vivo in cystic fibrosis lungs and chronic wounds. Bacterial aggregates primarily grew in the bead periphery and decreased in size and abundance toward the center of the bead. Microsensor measurements showed that the O2 concentration decreased rapidly and reached anoxia ∼100 μm below the alginate bead surface. This gradient was relieved in beads supplemented with NO3(-) as an alternative electron acceptor allowing for deeper growth into the beads. A comparison of gene expression profiles between planktonic and alginate-encapsulated P. aeruginosa confirmed that the bacteria experienced hypoxic and anoxic growth conditions. Furthermore, alginate-encapsulated P. aeruginosa exhibited a lower respiration rate than the planktonic counterpart and showed a high tolerance toward antibiotics. The inoculation and growth of P. aeruginosa in alginate beads represent a simple and flexible in vivo-like biofilm model system, wherein bacterial growth exhibits central features of in vivo biofilms. This was observed by the formation of small cell aggregates in a secondary matrix with O2-limited growth, which was alleviated by the addition of NO3(-) as an alternative electron acceptor, and by reduced respiration rates, as well as an enhanced tolerance to antibiotic treatment.IMPORTANCEPseudomonas aeruginosa has been studied intensively for decades due to its involvement in chronic infections, such as cystic fibrosis and chronic wounds, where it forms biofilms. Much research has been dedicated to biofilm formation on surfaces; however, in chronic infections, most biofilms form small aggregates of cells not attached to a surface, but embedded in hos...

Tan, Z.H., Zeng, J., Zhang, Y.J., Slot, M., Gamo, M., Hirano, T., Kosugi, Y., Da Rocha, H.R., Saleska, S.R., Goulden, M.L., Wofsy, S.C., Miller, S.D., Manzi, A.O., Nobre, A.D., De Camargo, P.B. & Restrepo-Coupe, N. 2017, 'Optimum air temperature for tropical forest photosynthesis: Mechanisms involved and implications for climate warming', Environmental Research Letters, vol. 12, no. 5.
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Trevathan-Tackett, S.M., Seymour, J.R., Nielsen, D.A., Macreadie, P.I., Jeffries, T.C., Sanderman, J., Baldock, J., Howes, J.M., Steven, A.D.L. & Ralph, P.J. 2017, 'Sediment anoxia limits microbial-driven seagrass carbon remineralization under warming conditions.', FEMS Microbiology Ecology, vol. 93, no. 6.
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Seagrass ecosystems are significant carbon sinks, and their resident microbial communities ultimately determine the quantity and quality of carbon sequestered. However, environmental perturbations have been predicted to affect microbial-driven seagrass decomposition and subsequent carbon sequestration. Utilizing techniques including 16S-rDNA sequencing, solid-state NMR and microsensor profiling, we tested the hypothesis that elevated seawater temperatures and eutrophication enhance the microbial decomposition of seagrass leaf detritus and rhizome/root tissues. Nutrient additions had a negligible effect on seagrass decomposition, indicating an absence of nutrient limitation. Elevated temperatures caused a 19% higher biomass loss for aerobically decaying leaf detritus, coinciding with changes in bacterial community structure and enhanced lignocellulose degradation. Although, community shifts and lignocellulose degradation were also observed for rhizome/root decomposition, anaerobic decay was unaffected by temperature. These observations suggest that oxygen availability constrains the stimulatory effects of temperature increases on bacterial carbon remineralization, possibly through differential temperature effects on bacterial functional groups, including putative aerobic heterotrophs (e.g. Erythrobacteraceae, Hyphomicrobiaceae) and sulfate reducers (e.g. Desulfobacteraceae). Consequently, under elevated seawater temperatures, carbon accumulation rates may diminish due to higher remineralization rates at the sediment surface. Nonetheless, the anoxic conditions ubiquitous to seagrass sediments can provide a degree of carbon protection under warming seawater temperatures.

Venuleo, M., Raven, J.A. & Giordano, M. 2017, 'Intraspecific chemical communication in microalgae.', New Phytol, vol. 215, no. 2, pp. 516-530.
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Contents 516 I. 516 II. 518 III. 518 IV. 521 V. 523 VI. 523 VII. 526 526 References 526 SUMMARY: The relevance of infochemicals in the relationships between organisms is emerging as a fundamental aspect of aquatic ecology. Exchanges of chemical cues are likely to occur not only between organisms of different species, but also between conspecific individuals. Especially intriguing is the investigation of chemical communication in microalgae, because of the relevance of these organisms for global primary production and their key role in trophic webs. Intraspecific communication between algae has been investigated mostly in relation to sexuality and mating. The literature also contains information on other types of intraspecific chemical communication that have not always been explicitly tagged as ways to communicate to conspecifics. However, the proposed role of certain compounds as intraspecific infochemicals appears questionable. In this article, we make use of this plethora of information to describe the various instances of intraspecific chemical communication between conspecific microalgae and to identify the common traits and ecological significance of intraspecific communication. We also discuss the evolutionary implications of intraspecific chemical communication and the mechanisms by which it can be inherited. A special focus is the genetic diversity among conspecific algae, including the possibility that genetic diversity is an absolute requirement for intraspecific chemical communication.

Walpersdorf, E., Kuehl, M., Elberling, B., Andersen, T.J., Hansen, B.U., Pejrup, M. & Glud, R.N. 2017, 'In situ oxygen dynamics and carbon turnover in an intertidal sediment (Skallingen, Denmark)', MARINE ECOLOGY PROGRESS SERIES, vol. 566, pp. 49-65.
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Wangpraseurt, D., Holm, J.B., Larkum, A.W.D., Pernice, M., Ralph, P.J., Suggett, D.J. & Kühl, M. 2017, 'In vivo Microscale Measurements of Light and Photosynthesis during Coral Bleaching: Evidence for the Optical Feedback Loop?', Front Microbiol, vol. 8, p. 59.
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Climate change-related coral bleaching, i.e., the visible loss of zooxanthellae from the coral host, is increasing in frequency and extent and presents a major threat to coral reefs globally. Coral bleaching has been proposed to involve accelerating light stress of their microalgal endosymbionts via a positive feedback loop of photodamage, symbiont expulsion and excess in vivo light exposure. To test this hypothesis, we used light and O2 microsensors to characterize in vivo light exposure and photosynthesis of Symbiodinium during a thermal stress experiment. We created tissue areas with different densities of Symbiodinium cells in order to understand the optical properties and light microenvironment of corals during bleaching. Our results showed that in bleached Pocillopora damicornis corals, Symbiodinium light exposure was up to fivefold enhanced relative to healthy corals, and the relationship between symbiont loss and light enhancement was well-described by a power-law function. Cell-specific rates of Symbiodinium gross photosynthesis and light respiration were enhanced in bleached P. damicornis compared to healthy corals, while areal rates of net photosynthesis decreased. Symbiodinium light exposure in Favites sp. revealed the presence of low light microniches in bleached coral tissues, suggesting that light scattering in thick coral tissues can enable photoprotection of cryptic symbionts. Our study provides evidence for the acceleration of in vivo light exposure during coral bleaching but this optical feedback mechanism differs between coral hosts. Enhanced photosynthesis in relation to accelerating light exposure shows that coral microscale optics exerts a key role on coral photophysiology and the subsequent degree of radiative stress during coral bleaching.

Wangpraseurt, D., Wentzel, C., Jacques, S.L., Wagner, M. & Kühl, M. 2017, 'In vivo imaging of coral tissue and skeleton with optical coherence tomography.', J R Soc Interface, vol. 14, no. 128.
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Application of optical coherence tomography (OCT) for in vivo imaging of tissue and skeleton structure of intact living corals enabled the non-invasive visualization of coral tissue layers (endoderm versus ectoderm), skeletal cavities and special structures such as mesenterial filaments and mucus release from intact living corals. Coral host chromatophores containing green fluorescent protein-like pigment granules appeared hyper-reflective to near-infrared radiation allowing for excellent optical contrast in OCT and a rapid characterization of chromatophore size, distribution and abundance. In vivo tissue plasticity could be quantified by the linear contraction velocity of coral tissues upon illumination resulting in dynamic changes in the live coral tissue surface area, which varied by a factor of 2 between the contracted and expanded state of a coral. Our study provides a novel view on the in vivo organization of coral tissue and skeleton and highlights the importance of microstructural dynamics for coral ecophysiology.

Watanabe, S., Kuzhiumparambil, U., Nguyen, M.A., Cameron, J. & Fu, S. 2017, 'Metabolic Profile of Synthetic Cannabinoids 5F-PB-22, PB-22, XLR-11 and UR-144 by Cunninghamella elegans.', AAPS J, vol. 19, no. 4, pp. 1148-1162.
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The knowledge of metabolic profile of synthetic cannabinoids is important for the detection of drugs in urinalysis due to the typical absence or low abundance of parent cannabinoids in human urine. The fungus Cunninghamella elegans has been reported to be a useful tool for metabolism study and thus applicability to synthetic cannabinoid metabolism was examined. In this study, 8-quinolinyl 1-(5-fluoropentyl)-1H-indole-3-carboxylate (5F-PB-22), 8-quinolinyl 1-pentyl-1H-indole-3-carboxylate (PB-22), [1-(5-fluoropentyl)-1H-indol-3-yl](2,2,3,3-tetramethylcyclopropyl)methanone (XLR-11) and (1-pentyl-1H-indol-3-yl)(2,2,3,3-tetramethylcyclopropyl)methanone (UR-144) were incubated with C. elegans and the metabolites were identified using liquid chromatography-quadrupole time-of-flight mass spectrometry. The obtained metabolites were compared with reported human metabolites to assess the suitability of the fungus to extrapolate human metabolism. 5F-PB-22 underwent dihydroxylation, dihydrodiol formation, oxidative defluorination, oxidative defluorination to carboxylic acid, ester hydrolysis and glucosidation, alone and/or in combination. The metabolites of PB-22 were generated by hydroxylation, dihydroxylation, trihydroxylation, dihydrodiol formation, ketone formation, carboxylation, ester hydrolysis and glucosidation, alone and/or in combination. XLR-11 was transformed through hydroxylation, dihydroxylation, aldehyde formation, carboxylation, oxidative defluorination, oxidative defluorination to carboxylic acid and glucosidation, alone and/or in combination. UR-144 was metabolised by hydroxylation, dihydroxylation, trihydroxylation, aldehyde formation, ketone formation, carboxylation, N-dealkylation and combinations. These findings were consistent with previously reported human metabolism except for the small extent of ester hydrolysis observed and the absence of glucuronidation. Despite the limitations, C. elegans demonstrated the capacity to produce a wide variety of met...

Wells, M.L., Potin, P., Craigie, J.S., Raven, J.A., Merchant, S.S., Helliwell, K.E., Smith, A.G., Camire, M.E. & Brawley, S.H. 2017, 'Algae as nutritional and functional food sources: revisiting our understanding', Journal of Applied Phycology, vol. 29, no. 2, pp. 949-982.
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© 2016 The Author(s)Global demand for macroalgal and microalgal foods is growing, and algae are increasingly being consumed for functional benefits beyond the traditional considerations of nutrition and health. There is substantial evidence for the health benefits of algal-derived food products, but there remain considerable challenges in quantifying these benefits, as well as possible adverse effects. First, there is a limited understanding of nutritional composition across algal species, geographical regions, and seasons, all of which can substantially affect their dietary value. The second issue is quantifying which fractions of algal foods are bioavailable to humans, and which factors influence how food constituents are released, ranging from food preparation through genetic differentiation in the gut microbiome. Third is understanding how algal nutritional and functional constituents interact in human metabolism. Superimposed considerations are the effects of harvesting, storage, and food processing techniques that can dramatically influence the potential nutritive value of algal-derived foods. We highlight this rapidly advancing area of algal science with a particular focus on the key research required to assess better the health benefits of an alga or algal product. There are rich opportunities for phycologists in this emerging field, requiring exciting new experimental and collaborative approaches.

Wilkinson, A.D., Collier, C.J., Flores, F., Langlois, L., Ralph, P.J. & Negri, A.P. 2017, 'Combined effects of temperature and the herbicide diuron on Photosystem II activity of the tropical seagrass Halophila ovalis.', Sci Rep, vol. 7, p. 45404.
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Tropical seagrasses are at their highest risk of exposure to photosystem II (PSII) herbicides when elevated rainfall and runoff from farms transports these toxicants into coastal habitats during summer, coinciding with periods of elevated temperature. PSII herbicides, such as diuron, can increase the sensitivity of corals to thermal stress, but little is known of the potential for herbicides to impact the thermal optima of tropical seagrass. Here we employed a well-plate approach to experimentally assess the effects of diuron on the photosynthetic performance of Halophila ovalis leaves across a 25 °C temperature range (36 combinations of these stressors across 15-40 °C). The thermal optimum for photosynthetic efficiency (▵) in H. ovalis was 31 °C while lower and higher temperatures reduced ▵ as did all elevated concentrations of diuron. There were significant interactions between the effects of temperature and diuron, with a majority of the combined stresses causing sub-additive (antagonistic) effects. However, both stressors caused negative responses and the sum of the responses was greater than that caused by temperature or diuron alone. These results indicate that improving water quality (reducing herbicide in runoff) is likely to maximise seagrass health during extreme temperature events that will become more common as the climate changes.

Woodcock, S. & Sloan, W.T. 2017, 'Biofilm community succession: a neutral perspective.', Microbiology, vol. 163, no. 5, pp. 664-668.
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Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested. Here, we further develop spatially resolved neutral community models and demonstrate that these can also explain these patterns and offer alternative explanations of microbial succession. The success of neutral models suggests that stochastic effects alone may have a much greater influence on microbial community succession than previously acknowledged. Furthermore, such models are much more readily parameterised and can be used as the foundation of more complex and realistic models of microbial community succession.

Conferences

Natarajan, S., Kumar, M.A. & Sundareswaran, A.U.M. 2017, 'Computational Analysis of an Early Direct Injected HCCI Engine Using Bio Ethanol and Diesel Blends as Fuel', Energy Procedia, pp. 350-357.
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© 2017 The Authors. Published by Elsevier Ltd. In this paper the work deals with the Experimental analysis of the early direct injected HCCI. The computational analysis of the engine was carried out using CHEMKIN-PRO Software. The computational analysis was carried out using the auto ignition chemistry by means of reduced chemical kinetics. For these investigations, the neat diesel and bio ethanol - diesel blend (E20) fuels were used as fuel and the pressure, combustion and emission characteristics were studied in the equivalence ratio of 0.6 (φ= 0.6). The injection timing was advanced to 18°rather than the normal 23°before top dead centre (BTDC) as specified engine conditions. Since pressure and temperature profiles plays a vital role in reaction path at certain operating conditions, an effort has been made here to present a comprehensive reaction path analysis on the formation/destruction of chemical species at peak temperature and pressure conditions.

Wilkinson, S.J., Stoller, P., Ralph, P., Hamdorf, B., Navarro Catana, L. & Santana Kuzava, G. 2016, 'Exploring the feasibility of algae building technology in NSW', SBE16 International High Performance Built Environments Conference, Sydney NSW.
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For some time, Biochemists have been exploring the potential to produce biofuels as an alternative to fossil fuel energy. Biofuels can be derived from crops such as corn, soybean and sugarcane however these crops can contribute to water scarcity and deforestation. Furthermore, large areas of land are used that could otherwise be used for food production. Another possibility is to use microalgae, which does not have the disadvantages associated with crop-based biofuels. Depending on conditions, microalgae can produce bio compounds that are converted into biofuels. The built environment is responsible for around 40 to 50% of total greenhouse gas emissions through fossil fuel consumption. Not only is it necessary to design and to retrofit our built environment to be more energy efficient, but it is also necessary to consider alternative fuel sources. To date, this has mostly focused on solar, wind and geothermal sources, however one residential building in Hamburg Germany has adopted algae building technology in the form of façade panels which act as a source of energy for heating the apartments and for hot water. The climate in northern Germany is very different to Australia, and the question arises; what is the feasibility to adopt algae building technology in New South Wales? There are issues around the physical and technical aspects of the technology, the social and environmental aspects, the regulatory and planning aspects, as well as the economic considerations. This paper reports on a study with key stakeholders in New South Wales to explore barriers and drivers associated with the adoption of algae building technology.

Reports

Lassudrie, M., Ajani, P.A. & Murray, S.A. 2017, Microalgal Community Composition Assessment in Warringah Lagoons 2016-2017, 1-33.

Other

Ajani, P.A., Hallegraeff, G.M., Allen, D., Coughlan, A., Richardson, A.J., Armand, L., Ingleton, I. & Murray, S.A. 2017, 'Establishing baselines: eighty years of phytoplankton diversity and biomass in south-eastern Australia. ALSO Aquatic Science Meeting Hawaii.'.
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(Oral Presentation)

Davies, C.H., Coughlan, A., Hallegraeff, G., Ajani, P., Armbrecht, L., Atkins, N., Bonham, P., Brett, S., Brinkman, R., Burford, M., Clementson, L., Coad, P., Coman, F., Davies, D., Dela-Cruz, J., Devlin, M., Edgar, S., Eriksen, R., Furnas, M., Hassler, C., Hill, D., Holmes, M., Ingleton, T., Jameson, I., Leterme, S.C., Lønborg, C., McLaughlin, J., McEnnulty, F., McKinnon, A.D., Miller, M., Murray, S., Nayar, S., Patten, R., Pausina, S.A., Pritchard, T., Proctor, R., Purcell-Meyerink, D., Raes, E., Rissik, D., Ruszczyk, J., Slotwinski, A., Swadling, K.M., Tattersall, K., Thompson, P., Thomson, P., Tonks, M., Trull, T.W., Uribe-Palomino, J., Waite, A.M., Yauwenas, R., Zammit, A. & Richardson, A.J. 2017, 'Corrigendum: A database of marine phytoplankton abundance, biomass and species composition in Australian waters.', Nature Publishing Group, pp. 1-1.
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The authors regret that Sarah A. Pausina was omitted in error from the author list of the original version of this Data Descriptor. This omission has now been corrected in the HTML and PDF versions of this Data Descriptor, as well as the accompanying Corrigendum

Woodcock, S. 2017, 'How predictable are the Oscars? More than you might think', The Conversation.

Woodcock, S. 2017, 'Paradoxes of probability and other statistical strangeness', The Conversation.