Publications

Larkum, AW 2016, 'Photosynthesis and Light Harvesting in Algae' in The Physiology of Microalgae, Springer International Publishing, pp. 67-87.
View/Download from: Publisher's site

Mondal, A & Wang, G 2016, 'Advances in Solar Photovoltaic Power Plants' in Islam, MR, Rahman, F & Xu, W (eds), Advances in Solar Photovoltaic Power Plants, Springer Berlin Heidelberg, Berlin Heidelberg, pp. 231-251.
View/Download from: Publisher's site
View description>>

Among various renewable energy resources, solar energy has gained tremendous attention for future energy because of its cleanliness, availability and environmental friendliness. Many countries around the globe are intensely considering solar energy technologies for their future energy expansion. The major disadvantage for use of solar technology is its intermittent and unpredictable nature. This influence the power quality and consistency of the power grid, particularly at large-scale solar energy systems. Solar power is the conversion of sunlight into electricity, either directly using photovoltaic (PV) or indirectly using concentrated solar power. The variation of sun light may lead to over-production of electricity at one time and lack of production at another time. The variable nature of solar power causes significant challenges for the electric grid operators. To smooth out the intermittency of solar energy production, electrical energy storage technology will become necessary. In order to increase the solar energy penetration with appropriate reliability, this chapter presents a range of energy storage systems that could technically and economically be used in association with solar photovoltaic energy.

Warner, ME & Suggett, DJ 2016, 'The Photobiology of Symbiodinium spp.: Linking Physiological Diversity to the Implications of Stress and Resilience' in The Cnidaria, Past, Present and Future, Springer International Publishing, pp. 489-509.
View/Download from: Publisher's site
View description>>

© Springer International Publishing Switzerland 2016. Over the past two decades, our knowledge of Symbiodinium genetic diversity and ecological distribution has grown at an incredible pace, while the physiological diversity and how it may be compared to the phylogenetic and evolutionary constraints of these dinoflagellates is still catching up. Our knowledge of the photobiology of Symbiodinium has been driven largely by the desire to explain cellular mechanisms of stress and reaction to global events driven by climate change. We tend to focus more on the former in this chapter since this is where the majority of work has been performed to date. However, it is imperative that we return to the first principles of phytoplankton physiological ecology to form a more complete understanding of the photobiology of these algae and the physiological constraints expected in an algal cell capable of living benthic, pelagic and symbiotic life styles. In order to understand not only the pathways of cellular dysfunction, but also resilience, we address specific patterns of light harvesting balance, reaction centre turnover, inorganic carbon acquisition and utilisation, and alternative electron transport across this genus. Symbiodinium - focused research, and physiology in particular, poses several challenges that demand a broad perspective gleaned from working with these algae in culture as well as in hospite in controlled ‘model’ and natural cnidarian hosts across many different environments. We outline several key processes related to photosynthesis as well as new directions integrating many of these processes that are required to more fully understand how environmental change shapes the role of photobiology in governing the ecological success of these important algae.

Ajani, P, Larsson, ME, Rubio, A, Bush, S, Brett, S & Farrell, H 2016, 'Modelling bloom formation of the toxic dinoflagellates Dinophysis acuminata and Dinophysis caudata in a highly modified estuary, south eastern Australia', Estuarine, Coastal and Shelf Science, vol. 183, pp. 95-106.
View/Download from: Publisher's site
View description>>

© 2016 Elsevier Ltd Dinoflagellates belonging to the toxigenic genus Dinophysis are increasing in abundance in the Hawkesbury River, south-eastern Australia. This study investigates a twelve year time series of abundance and physico-chemical data to model these blooms. Four species were reported over the sampling campaign - Dinophysis acuminata, Dinophysis caudata, Dinophysis fortii and Dinophysis tripos-with D. acuminata and D. caudata being most abundant. Highest abundance of D. acuminata occurred in the austral spring (max. abundance 4500 cells l−1), whilst highest D. caudata occurred in the summer to autumn (max. 12,000 cells l−1). Generalised additive models revealed abundance of D. acuminata was significantly linked to season, thermal stratification and nutrients, whilst D. caudata was associated with nutrients, salinity and dissolved oxygen. The models’ predictive capability was up to 60% for D. acuminata and 53% for D. caudata. Altering sampling strategies during blooms accompanied with in situ high resolution monitoring will further improve Dinophysis bloom prediction capability.

Baird, ME, Adams, MP, Babcock, RC, Oubelkheir, K, Mongin, M, Wild-Allen, KA, Skerratt, J, Robson, BJ, Petrou, K, Ralph, PJ, O'Brien, KR, Carter, AB, Jarvis, JC & Rasheed, MA 2016, 'A biophysical representation of seagrass growth for application in a complex shallow-water biogeochemical model', ECOLOGICAL MODELLING, vol. 325, pp. 13-27.
View/Download from: Publisher's site
View description>>

Seagrasses are a critical component of the healthy functioning of many coastal marine ecosystems. Capturing the dynamics of seagrass communities requires both a detailed representation of processes such as seagrass nutrient uptake and photosynthesis, as well as models of light penetration, water column and sediment biogeochemical processes and other ecosystem characteristics that determine the environmental state. Here we develop a new two-state, 13-parameter seagrass model with the aim of providing sufficient detail to represent light and nutrient limitation, but simple enough to be coupled into a 60 state variable biogeochemical model. The novel formulation is built around a nitrogen-specific leaf area parameter, Ω, that is well-constrained and is used in calculating both the rate of photosynthesis and the fraction of the seafloor covered by seagrass, Aeff, where Aeff=1-exp(-ΩSGA) and SGA is the aboveground areal seagrass biomass. The model also contains terms for the uptake of nutrients from multiple layers of varying-porosity sediments, translocation of organic matter between leaves and roots, respiration and simple mortality terms. The model is applied to Gladstone Harbour, a macro-tidal sub-tropical estuary in northeast Australia, and is able to simulate realistic spatial seagrass distributions. A simplified form of the model is derived, which can be used to predict seagrass light-limited growth based on five measurable species-specific parameters (maximum growth rate, mortality rate, compensation irradiance, leaf blade angle and nitrogen-specific leaf area). The steady-state percent coverage of seagrass achieved at varying light levels and mortality intensity is calculated as a means of understanding the dynamics of the new seagrass model.

Baird, ME, Cherukuru, N, Jones, E, Margvelashvili, N, Mongin, M, Oubelkheir, K, Ralph, PJ, Rizwi, F, Robson, BJ, Schroeder, T, Skerratt, J, Steven, ADL & Wild-Allen, KA 2016, 'Remote-sensing reflectance and true colour produced by a coupled hydrodynamic, optical, sediment, biogeochemical model of the Great Barrier Reef, Australia: Comparison with satellite data', ENVIRONMENTAL MODELLING & SOFTWARE, vol. 78, pp. 79-96.
View/Download from: Publisher's site

Baker, KG, Robinson, CM, Radford, DT, McInnes, AS, Evenhuis, C & Doblin, MA 2016, 'Thermal Performance Curves of Functional Traits Aid Understanding of Thermally Induced Changes in Diatom-Mediated Biogeochemical Fluxes', Frontiers in Marine Science, vol. 3, pp. 1-14.
View/Download from: Publisher's site
View description>>

© 2016 Baker, Robinson, Radford, McInnes, Evenhuis and Doblin.How the functional traits (FTs) of phytoplankton change with temperature is important for understanding the impacts of ocean warming on phytoplankton mediated biogeochemical fluxes. This study quantifies the thermal performance curves (TPCs) of FTs in the cosmopolitan model diatom, Thalassiosira pseudonana, to advance understanding of trade-offs between physiological (photoacclimation, carbon fixation, nitrate, phosphate, and silicate uptake) and morphological traits (cell volume and frustule silicification). We show that each FT has substantial phenotypic plasticity and exhibits a unique TPC, varying in both shape and thermal optimum, and diverging from the growth response. The TPC for growth was symmetric with a thermal optimum (Topt) of 18°C. In comparison, the TPC for primary productivity was warm-skewed with a Topt around 21°C, whereas frustule silicification decreased linearly with increasing temperature. Together, this suggests that the optimal temperature for overall fitness is a balance of trade-offs in the underlying functional traits. Moreover, these results demonstrate that growth is not necessarily an accurate estimate of overall biogeochemical performance and that temperature change will likely influence elemental fluxes such as carbon and silicon. Finally, we show that temperature-driven changes in individual traits e.g., photoacclimation, can mimic responses experienced under other environmental stressors (high light) and so a multi-trait assessment is essential for accurate interpretation of the cellular impact of warming. This study also reveals that multi-trait analysis, in the context of TPCs, provides insight into the cellular physiology regulating the whole cell response and has the potential to provide better estimates of how diatom-mediated biogeochemical fluxes are likely to be impacted in the context of ocean warming. Analyzing the response of multiple traits more comprehensiv...

Bao, W, Mondal, AK, Xu, J, Wang, C, Su, D & Wang, G 2016, '3D hybrid–porous carbon derived from carbonization of metal organic frameworks for high performance supercapacitors', Journal of Power Sources, vol. 325, pp. 286-291.
View/Download from: Publisher's site

Bibiloni‐Isaksson, J, Seymour, JR, Ingleton, T, van de Kamp, J, Bodrossy, L & Brown, MV 2016, 'Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia', Environmental Microbiology, vol. 18, no. 12, pp. 4485-4500.
View/Download from: Publisher's site
View description>>

SummaryAerobic Anoxygenic Phototrophic Bacteria (AAnPB) are ecologically important microorganisms, widespread in oceanic photic zones. However, the key environmental drivers underpinning AAnPB abundance and diversity are still largely undefined. The temporal patterns in AAnPB dynamics at three oceanographic reference stations spanning at approximately 15° latitude along the Australian east coast were examined. AAnPB abundance was highly variable, with pufM gene copies ranging from 1.1 × 102 to 1.4 × 105 ml−1 and positively correlated with day length and solar radiation. pufM gene Miseq sequencing revealed that the majority of sequences were closely related to those obtained previously, suggesting that key AAnPB groups are widely distributed across similar environments globally. Temperature was a major structuring factor for AAnPB assemblages across large spatial scales, correlating positively with richness and Gammaproteobacteria (phylogroup K) abundance but negatively with Roseobacter‐clade (phylogroup E) abundance, with temperatures between 16°C and 18°C identified as a potential transition zone between these groups. Network analysis revealed that discrete AAnPB populations exploit specific niches defined by varying temperature, light and nutrient conditions in the Tasman Sea system, with evidence for both niche sharing and partitioning amongst closely related operational taxonomic units.

Camp, EF, Smith, DJ, Evenhuis, C, Enochs, I, Manzello, D, Woodcock, S & Suggett, DJ 2016, 'Acclimatization to high-variance habitats does not enhance physiological tolerance of two key Caribbean corals to future temperature and pH', Proceedings of the Royal Society B: Biological Sciences, vol. 283, no. 1831, pp. 20160442-20160442.
View/Download from: Publisher's site
View description>>

Corals are acclimatized to populate dynamic habitats that neighbour coral reefs. Habitats such as seagrass beds exhibit broad diel changes in temperature and pH that routinely expose corals to conditions predicted for reefs over the next 50–100 years. However, whether such acclimatization effectively enhances physiological tolerance to, and hence provides refuge against, future climate scenarios remains unknown. Also, whether corals living in low-variance habitats can tolerate present-day high-variance conditions remains untested. We experimentally examined how pH and temperature predicted for the year 2100 affects the growth and physiology of two dominant Caribbean corals ( Acropora palmata and Porites astreoides ) native to habitats with intrinsically low (outer-reef terrace, LV) and/or high (neighbouring seagrass, HV) environmental variance. Under present-day temperature and pH, growth and metabolic rates (calcification, respiration and photosynthesis) were unchanged for HV versus LV populations. Superimposing future climate scenarios onto the HV and LV conditions did not result in any enhanced tolerance to colonies native to HV. Calcification rates were always lower for elevated temperature and/or reduced pH. Together, these results suggest that seagrass habitats may not serve as refugia against climate change if the magnitude of future temperature and pH changes is equivalent to neighbouring reef habitats.

Camp, EF, Suggett, DJ, Gendron, G, Jompa, J, Manfrino, C & Smith, DJ 2016, 'Mangrove and Seagrass Beds Provide Different Biogeochemical Services for Corals Threatened by Climate Change', Frontiers in Marine Science, vol. 3, no. APR, pp. 1-16.
View/Download from: Publisher's site
View description>>

© 2016 Camp, Suggett, Gendron, Jompa, Manfrino and Smith. Rapidly rising atmospheric CO2 concentrations are driving acidification in parallel with warming of the oceans. Future ocean acidification scenarios have the potential to impact coral growth and associated reef function, although reports suggest such affects could be reduced in adjacent seagrass habitats as a result of physio-chemical buffering. To-date, it remains unknown whether these habitats can actually support the metabolic function of a diverse range of corals. Similarly, whether mangroves provide the same ecological buffering service remains unclear. We examine whether reef-associated habitat sites (seagrass and mangroves) can act as potential refugia to future climate change by maintaining favorable chemical conditions (elevated pH and aragonite saturation state relative to the open-ocean), but by also assessing whether the metabolic function (photosynthesis, respiration and calcification) of important reef-building corals are sustained. We investigated three sites in the Atlantic, Indian, and Pacific Oceans and consistently observed that seagrass beds experience an overall elevation in mean pH (8.15 ± 0.01) relative to the adjacent outer-reef (8.12 ± 0.03), but with periods of high and low pH. Corals in the seagrass habitats either sustained calcification or experienced an average reduction of 17.0 ± 6.1% relative to the outer-reef. In contrast, mangrove habitats were characterized by a low mean pH (8.04 ± 0.01) and a relatively moderate pH range. Corals within mangrove-dominated habitats were thus pre-conditioned to low pH but with significant suppression to calcification (70.0 ± 7.3% reduction relative to the outer-reef). Both habitats also experienced more variable temperatures (diel range up to 2.5°C) relative to the outer-reef (diel range less than 0.7°C), which did not correspond with changes in calcification rates. Here we report, for the first time, the biological costs for cora...

Carney, RL, Seymour, JR, Westhorpe, D & Mitrovic, SM 2016, 'Lotic bacterioplankton and phytoplankton community changes under dissolved organic-carbon amendment: evidence for competition for nutrients', Marine and Freshwater Research, vol. 67, no. 9, pp. 1362-1362.
View/Download from: Publisher's site
View description>>

During periods of low river discharge, bacterial growth is typically limited by dissolved organic carbon (DOC) and is tightly regulated by phytoplankton production. However, import of allochthonous DOC into rivers by freshwater inflows may diminish bacterial reliance on phytoplankton-produced carbon, leading to competition for nitrogen (N) and phosphorus (P). To investigate phytoplankton–bacterial competition in response to allochthonous inputs, we conducted a mesocosm experiment, comparing microbial responses to the following two manipulation treatments: (1) addition of N and P, and (2) addition of a DOC and N and P. Measurement of chlorophyll-a estimated phytoplankton biomass and microscopic counts were performed to discriminate community change. Bacterial abundance was tracked using flow cytometry and community assemblages were characterised using automated ribosomal intergenic spacer analyses and 16S rRNA-amplicon sequencing. We found that bacterial abundance increased in the leachate addition, whereas chlorophyll-a was reduced and the bacterial community shifted to one dominated by heterotrophic genera, and autotrophic microbes including Synechococcus and Cyclotella increased significantly in the nutrient treatment. These observations indicated that DOC and nutrient inputs can lead to shifts in the competitive dynamics between bacteria and phytoplankton, reducing phytoplankton biomass, which may potentially shift the major pathway of carbon to higher trophic organisms, from the phytoplankton grazer chain to the microbial food web.

Chartrand, KM, Bryant, CV, Carter, AB, Ralph, PJ & Rasheed, MA 2016, 'Light Thresholds to Prevent Dredging Impacts on the Great Barrier Reef Seagrass, Zostera muelleri ssp. capricorni', Frontiers in Marine Science, vol. 3, no. JUL, pp. 1-17.
View/Download from: Publisher's site
View description>>

© 2016 Chartrand, Bryant, Carter, Ralph and Rasheed. Coastal seagrass habitats are at risk from a range of anthropogenic activities that modify the natural light environment, including dredging activities associated with coastal and port developments. On Australia's east coast, the tropical seagrass Zostera muelleri ssp. capricorni dominates intertidal mudbanks in sheltered embayments which are also preferred locations for harbors and port facilities. Dredging to establish and maintain shipping channels in these areas can degrade water quality and diminish light conditions that are required for seagrass growth. Based on this potential conflict, we simulated in-situ light attenuation events to measure effects on Z. muelleri ssp. capricorni condition. Semi-annual in situ shading studies conducted over 3 years were used to quantify the impact of prolonged light reduction on seagrass morphometrics (biomass, percent cover, and shoot density). Experimental manipulations were complimented with an assessment of 46 months of light history and concurrent natural seagrass change at the study site in Gladstone Harbour. There was a clear light-dependent effect on seagrass morphometrics during seagrass growing seasons, but no effect during senescent periods. Significant seagrass declines occurred between 4 and 8 weeks after shading during the growing seasons with light maintained in the range of 4-5 mol photons m-2 d-1. Sensitivity to shading declined when applied in 2-week intervals (fortnightly) rather than continuous over the same period. Field observations were correlated to manipulative experiments to derive an applied threshold of 6 mol photons m-2 d-1 which formed the basis of a reactive light-based management strategy which has been successfully implemented to ensure positive ecological outcomes for seagrass during a large-scale dredging program.

Cherukuru, N, Davies, PL, Brando, VE, Anstee, JM, Baird, ME, Clementson, LA & Doblin, MA 2016, 'Physical oceanographic processes influence bio-optical properties in the Tasman Sea', JOURNAL OF SEA RESEARCH, vol. 110, pp. 1-7.
View/Download from: Publisher's site

Cole, VJ, Parker, LM, O’Connor, SJ, O’Connor, WA, Scanes, E, Byrne, M & Ross, PM 2016, 'Effects of multiple climate change stressors: ocean acidification interacts with warming, hyposalinity, and low food supply on the larvae of the brooding flat oyster Ostrea angasi', Marine Biology, vol. 163, no. 5.
View/Download from: Publisher's site
View description>>

Ocean acidification, rising temperatures, and increased intensity of rain events are occurring due to climate change. Individually, each of these stressors has the potential to influence the growth and survival of many marine organisms, particularly during early development. Together the interactive and multiple impacts of elevated pCO2, temperature, and salinity may be exacerbated by a lack of food. Life history traits are important in determining the response of organisms to climate change. Larvae that develop within a brood chamber, such as the flat oyster, Ostrea angasi, may be pre-exposed to living a higher CO2 environment. This study determined the pH of the fluid surrounding the gills of adult oysters where larvae are brooded and investigated the interactive effects of the multiple climate-related stressors: ocean acidification, warming, hyposalinity, and reduced food availability, on development of O. angasi larvae. The fluid surrounding the larvae was of pH 7.88 ± 0.04, lower than that of surrounding sea water, and was significantly reduced (to pH 7.46 ± 0.05) when oysters remained closed as occurs in nature during periods of stress caused by low salinity. Elevated pCO2 [853–1194 µatm (pHNBS 7.79)] resulted in larvae being 3 % smaller, but it had no effect on the timing of progression through developmental stages, percentage of abnormalities, or survival of larvae. Exposure to elevated pCO2 together with increased temperature (+4 °C) or reduced salinity (20) had a negative effect on the time to the eyed larval stage and with an increase in the percentage of abnormal larvae. Unexpectedly, larvae did not meet their higher metabolic requirements to survive under elevated pCO2 by eating more. In a sublethal effect of elevated pCO2, larval feeding was impaired. We found that O. angasi larva were relatively resilient to elevated pCO2, a trait that may be due to the acclimatisation of hypercapnic conditions in the brood cavity or because they are rele...

Davey, PA, Pernice, M, Sablok, G, Larkum, A, Lee, HT, Golicz, A, Edwards, D, Dolferus, R & Ralph, P 2016, 'The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses', FUNCTIONAL & INTEGRATIVE GENOMICS, vol. 16, no. 5, pp. 465-480.
View/Download from: Publisher's site
View description>>

Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events.

Doblin, MA & van Sebille, E 2016, 'Drift in ocean currents impacts intergenerational microbial exposure to temperature', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 113, no. 20, pp. 5700-5705.
View/Download from: Publisher's site
View description>>

Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034-1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming.

Doblin, MA, Petrou, K, Sinutok, S, Seymour, JR, Messer, LF, Brown, MV, Norman, L, Everett, JD, McInnes, AS, Ralph, PJ, Thompson, PA & Hassler, CS 2016, 'Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current', PEERJ, vol. 4, no. 4.
View/Download from: Publisher's site
View description>>

© 2016 Doblin et al. The intensification of western boundary currents in the global ocean will potentially influence meso-scale eddy generation, and redistribute microbes and their associated ecological and biogeochemical functions. To understand eddy-induced changes in microbial community composition as well as how they control growth, we targeted the East Australian Current (EAC) region to sample microbes in a cyclonic (cold-core) eddy (CCE) and the adjacent EAC. Phototrophic and diazotrophic microbes were more diverse (2-10 times greater Shannon index) in the CCE relative to the EAC, and the cell size distribution in the CCE was dominated (67%) by larger micro-plankton (≥ 20μm), as opposed to pico- and nano-sized cells in the EAC. Nutrient addition experiments determined that nitrogen was the principal nutrient limiting growth in the EAC, while iron was a secondary limiting nutrient in the CCE. Among the diazotrophic community, heterotrophic NifH gene sequences dominated in the EAC and were attributable to members of the gamma-, beta-, and delta-proteobacteria, while the CCE contained both phototrophic and heterotrophic diazotrophs, including Trichodesmium, UCYN- A and gamma-proteobacteria. Daily sampling of incubation bottles following nutrient amendment captured a cascade of effects at the cellular, population and community level, indicating taxon-specific differences in the speed of response of microbes to nutrient supply. Nitrogen addition to the CCE community increased picoeukaryote chlorophyll a quotas within 24 h, suggesting that nutrient uplift by eddies causes a 'greening' effect as well as an increase in phytoplankton biomass. After three days in both the EAC and CCE, diatoms increased in abundance with macronutrient (N, P, Si) and iron amendment, whereas haptophytes and phototrophic dinoflagellates declined. Our results indicate that cyclonic eddies increase delivery of nitrogen to the upper ocean to potentially mitigate the negative conse...

Farrant, GK, Doré, H, Cornejo-Castillo, FM, Partensky, F, Ratin, M, Ostrowski, M, Pitt, FD, Wincker, P, Scanlan, DJ, Iudicone, D, Acinas, SG & Garczarek, L 2016, 'Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria', Proceedings of the National Academy of Sciences, vol. 113, no. 24, pp. E3365-E3374.
View/Download from: Publisher's site
View description>>

Significance Metagenomics has become an accessible approach to study complex microbial communities thanks to the advent of high-throughput sequencing technologies. However, molecular ecology studies often face interpretation issues, notably due to the lack of reliable reference databases for assigning reads to the correct taxa and use of fixed cutoffs to delineate taxonomic groups. Here, we considerably refined the phylogeography of marine picocyanobacteria, responsible for about 25% of global marine productivity, by recruiting reads targeting a high-resolution marker from Tara Oceans metagenomes. By clustering lineages based on their distribution patterns, we showed that there is significant diversity at a finer resolution than the currently defined “ecotypes,” a diversity that is tightly controlled by environmental cues.

Gardner, SG, Nielsen, DA, Laczka, O, Shimmon, R, Beltran, VH, Ralph, PJ & Petrou, K 2016, 'Dimethylsulfoniopropionate, superoxide dismutase and glutathione as stress response indicators in three corals under short-term hyposalinity stress', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 283, no. 1824, pp. 1-9.
View/Download from: Publisher's site
View description>>

© 2016 The Author(s) Published by the Royal Society. All rights reserved. Corals are among the most active producers of dimethylsulfoniopropionate (DMSP), a key molecule in marine sulfur cycling, yet the specific physiological role of DMSP in corals remains elusive. Here, we examine the oxidative stress response of three coral species (Acropora millepora, Stylophora pistillata and Pocillopora damicornis) and explore the antioxidant role of DMSP and its breakdown products under short-termhyposalinity stress. Symbiont photosynthetic activity declined with hyposalinity exposure in all three reef-building corals. This corresponded with the upregulation of superoxide dismutase and glutathione in the animal host of all three species. For the symbiont component, there were differences in antioxidant regulation, demonstrating differential responses to oxidative stress between the Symbiodinium subclades. Of the three coral species investigated, only A. millepora provided any evidence of the role of DMSP in the oxidative stress response. Our study reveals variability in antioxidant regulation in corals and highlights the influence life-history traits, and the subcladal differences can have on coral physiology.Our data expand on the emerging understanding of the role of DMSP in coral stress regulation and emphasizes the importance of exploring both the host and symbiont responses for defining the threshold of the coral holobiont to hyposalinity stress.

Garren, M, Son, K, Tout, J, Seymour, JR & Stocker, R 2016, 'Temperature-induced behavioral switches in a bacterial coral pathogen', The ISME Journal, vol. 10, no. 6, pp. 1363-1372.
View/Download from: Publisher's site
View description>>

Abstract Evidence to date indicates that elevated seawater temperatures increase the occurrence of coral disease, which is frequently microbial in origin. Microbial behaviors such as motility and chemotaxis are often implicated in coral colonization and infection, yet little is known about the effect of warming temperatures on these behaviors. Here we present data demonstrating that increasing water temperatures induce two behavioral switches in the coral pathogen Vibrio coralliilyticus that considerably augment the bacterium’s performance in tracking the chemical signals of its coral host, Pocillopora damicornis. Coupling field-based heat-stress manipulations with laboratory-based observations in microfluidic devices, we recorded the swimming behavior of thousands of individual pathogen cells at different temperatures, associated with current and future climate scenarios. When temperature reached ⩾23 °C, we found that the pathogen’s chemotactic ability toward coral mucus increased by >60%, denoting an enhanced capability to track host-derived chemical cues. Raising the temperature further, to 30 °C, increased the pathogen’s chemokinetic ability by >57%, denoting an enhanced capability of cells to accelerate in favorable, mucus-rich chemical conditions. This work demonstrates that increasing temperature can have strong, multifarious effects that enhance the motile behaviors and host-seeking efficiency of a marine bacterial pathogen.

Hassan, KA, Cain, AK, Huang, T, Liu, Q, Elbourne, LDH, Boinett, CJ, Brzoska, AJ, Li, L, Ostrowski, M, Nhu, NTK, Nhu, TDH, Baker, S, Parkhill, J & Paulsen, IT 2016, 'Fluorescence-Based Flow Sorting in Parallel with Transposon Insertion Site Sequencing Identifies Multidrug Efflux Systems in Acinetobacter baumannii', mBio, vol. 7, no. 5.
View/Download from: Publisher's site
View description>>

ABSTRACT Multidrug efflux pumps provide clinically significant levels of drug resistance in a number of Gram-negative hospital-acquired pathogens. These pathogens frequently carry dozens of genes encoding putative multidrug efflux pumps. However, it can be difficult to determine how many of these pumps actually mediate antimicrobial efflux, and it can be even more challenging to identify the regulatory proteins that control expression of these pumps. In this study, we developed an innovative high-throughput screening method, combining transposon insertion sequencing and cell sorting methods (TraDISort), to identify the genes encoding major multidrug efflux pumps, regulators, and other factors that may affect the permeation of antimicrobials, using the nosocomial pathogen Acinetobacter baumannii . A dense library of more than 100,000 unique transposon insertion mutants was treated with ethidium bromide, a common substrate of multidrug efflux pumps that is differentially fluorescent inside and outside the bacterial cytoplasm. Populations of cells displaying aberrant accumulations of ethidium were physically enriched using fluorescence-activated cell sorting, and the genomic locations of transposon insertions within these strains were determined using transposon-directed insertion sequencing. The relative abundance of mutants in the input pool compared to the selected mutant pools indicated that the AdeABC, AdeIJK, and AmvA efflux pumps are the major ethidium efflux systems in A. baumannii . Furthermore, the method identified a new transcriptional regulator that controls expression of amvA . In addition to the identification of efflux pumps and their regulators, TraD...

Hopkins, FE, Bell, TG, Yang, M, Suggett, DJ & Steinke, M 2016, 'Air exposure of coral is a significant source of dimethylsulfide (DMS) to the atmosphere', Scientific Reports, vol. 6, no. 1.
View/Download from: Publisher's site
View description>>

AbstractCorals are prolific producers of dimethylsulfoniopropionate (DMSP). High atmospheric concentrations of the DMSP breakdown product dimethylsulfide (DMS) have been linked to coral reefs during low tides. DMS is a potentially key sulfur source to the tropical atmosphere, but DMS emission from corals during tidal exposure is not well quantified. Here we show that gas phase DMS concentrations (DMSgas) increased by an order of magnitude when three Indo-Pacific corals were exposed to air in laboratory experiments. Upon re-submersion, an additional rapid rise in DMSgas was observed, reflecting increased production by the coral and/or dissolution of DMS-rich mucus formed by the coral during air exposure. Depletion in DMS following re-submersion was likely due to biologically-driven conversion of DMS to dimethylsulfoxide (DMSO). Fast Repetition Rate fluorometry showed downregulated photosynthesis during air exposure but rapid recovery upon re-submersion, suggesting that DMS enhances coral tolerance to oxidative stress during a process that can induce photoinhibition. We estimate that DMS emission from exposed coral reefs may be comparable in magnitude to emissions from other marine DMS hotspots. Coral DMS emission likely comprises a regular and significant source of sulfur to the tropical marine atmosphere, which is currently unrecognised in global DMS emission estimates and Earth System Models.

Jeffries, TC, Curlevski, NJ, Brown, MV, Harrison, DP, Doblin, MA, Petrou, K, Ralph, PJ & Seymour, JR 2016, 'Partitioning of fungal assemblages across different marine habitats', ENVIRONMENTAL MICROBIOLOGY REPORTS, vol. 8, no. 2, pp. 235-238.
View/Download from: Publisher's site
View description>>

© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd. Fungi are a highly diverse group of microbes that fundamentally influence the biogeochemistry of the biosphere, but we currently know little about the diversity and distribution of fungi in aquatic habitats. Here we describe shifts in marine fungal community composition across different marine habitats, using targeted pyrosequencing of the fungal Internal Transcribed Spacer (ITS) region. Our results demonstrate strong partitioning of fungal community composition between estuarine, coastal and oceanic samples, with each habitat hosting discrete communities that are controlled by patterns in salinity, temperature, oxygen and nutrients. Whereas estuarine habitats comprised a significant proportion of fungal groups often found in terrestrial habitats, the open ocean sites were dominated by previously unidentified groups. The patterns observed here indicate that fungi are potentially a significant, although largely overlooked, feature of the ocean's microbiota, but greater efforts to characterize marine species are required before the full ecological and biogeochemical importance of marine fungi can be ascertained.

Jeffries, TC, Fontes, MLS, Harrison, DP, Van-Dongen-Vogels, V, Eyre, BD, Ralph, PJ & Seymour, JR 2016, 'Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary', FRONTIERS IN MICROBIOLOGY, vol. 6, no. JAN, pp. 1-17.
View/Download from: Publisher's site
View description>>

© 2016 Jeffries, Schmitz Fontes, Harrison, Van-Dongen-Vogels, Eyre, Ralph and Seymour. The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide i...

Jin, YK, Lundgren, P, Lutz, A, Raina, J-B, Howells, EJ, Paley, AS, Willis, BL & van Oppen, MJH 2016, 'Genetic markers for antioxidant capacity in a reef-building coral', Science Advances, vol. 2, no. 5.
View/Download from: Publisher's site
View description>>

We identify the first quantitative trait loci for antioxidant capacity in corals, providing possible new avenues for management and restoration approaches.

Kelleway, JJ, Saintilan, N, Macreadie, PI & Ralph, PJ 2016, 'Sedimentary Factors are Key Predictors of Carbon Storage in SE Australian Saltmarshes', ECOSYSTEMS, vol. 19, no. 5, pp. 865-880.
View/Download from: Publisher's site

Kelleway, JJ, Saintilan, N, Macreadie, PI, Skilbeck, CG, Zawadzki, A & Ralph, PJ 2016, 'Seventy years of continuous encroachment substantially increases 'blue carbon' capacity as mangroves replace intertidal salt marshes', GLOBAL CHANGE BIOLOGY, vol. 22, no. 3, pp. 1097-1109.
View/Download from: Publisher's site

Koyyalamudi, SR, Kuzhiumparambil, U, Nath, CE, Byrne, JA, Fraser, CJ, O'Brien, TA, Earl, JW & Shaw, PJ 2016, 'Development and Validation of a High Pressure Liquid Chromatography-UV Method for the Determination of Treosulfan and Its Epoxy Metabolites in Human Plasma and Its Application in Pharmacokinetic Studies', JOURNAL OF CHROMATOGRAPHIC SCIENCE, vol. 54, no. 3, pp. 326-333.
View/Download from: Publisher's site

Kumar, M, Kuzhiumparambil, U, Pernice, M, Jiang, Z & Ralph, PJ 2016, 'Metabolomics: an emerging frontier of systems biology in marine macrophytes', ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, vol. 16, pp. 76-92.
View/Download from: Publisher's site
View description>>

© 2016. Metabolomics is a rapidly emerging discipline within functional genomics which is increasingly being applied to understand biochemical phenotypes across a range of biological systems. Metabolomics measures all (or a subset) metabolites in a cell at a specific time point, reflecting a snapshot of all the regulatory events responding to the external environmental conditions. Although metabolomics and systems biology approaches have been applied to the study of terrestrial plants, few marine macrophytes have been examined using these novel technologies. Marine macrophytes (including seaweeds and seagrasses) are marine ecosystem engineers delivering a range of ecologically and economically valuable biological services; however they are under threat from a wide range of anthropogenic stressors, climate variation, invasive species and pathogens. Investigating metabolomic regulation in these organisms is crucial to understand their acclimation, adaptation and defence responses to environmental challenges. This review describes the current analytical tools available to study metabolomics in marine macrophytes, along with their limitations for both targeted and non-targeted workflows. To illustrate recent advances in systems biology studies in marine macrophytes, we describe how metabolites are used in chemical defence to deter a broad range of invasive species and pathogens, as well as metabolomic reprogramming leading to acclimation or adaptive strategies to environmental and anthropogenic stresses. Where possible, the mechanistic processes associated with primary and secondary plant metabolism governing cellular homeostasis under extreme environments are discussed. Further, we provide a comprehensive overview of an in silico plant metabolome database that can be utilized to advance our knowledge from a system biology approach to marine macrophytes. Finally, functional integration of metabolomics with the allied 'omics' disciplines of transcriptomics a...

Labbate, M, Seymour, JR, Lauro, F & Brown, MV 2016, 'Editorial: Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments', Frontiers in Microbiology, vol. 7, no. JUL.
View/Download from: Publisher's site

Laiolo, L, McInnes, AS, Matear, R & Doblin, MA 2016, 'Key Drivers of Seasonal Plankton Dynamics in Cyclonic and Anticyclonic Eddies off East Australia', Frontiers in Marine Science, vol. 3, no. AUG, pp. 1-14.
View/Download from: Publisher's site
View description>>

© 2016 Laiolo, McInnes, Matear and Doblin. Mesoscale eddies in the south west Pacific region are prominent ocean features that represent distinctive environments for phytoplankton. Here, we examine the seasonal plankton dynamics associated with averaged cyclonic and anticyclonic eddies (CE and ACE, respectively) off eastern Australia. We do this through building seasonal climatologies of mixed layer depth (MLD) and surface chlorophyll-a for both CE and ACE by combining remotely sensed sea surface height (TOPEX/Poseidon, Envisat, Jason-1, and OSTM/Jason-2), remotely sensed ocean color (GlobColour) and in situ profiles of temperature, salinity and pressure from Argo floats. Using the CE and ACE seasonal climatologies, we assimilate the surface chlorophyll-a data into both a single (WOMBAT), and multi-phytoplankton class (EMS) biogeochemical model to investigate the level of complexity required to simulate the phytoplankton chlorophyll-a. For the two eddy types, the data assimilation showed both biogeochemical models only needed one set of parameters to represent phytoplankton but needed different parameters for zooplankton. To assess the simulated phytoplankton behavior we compared EMS model simulations with a ship-based experiment that involved incubating a winter phytoplankton community sampled from below the mixed layer under ambient and two higher light intensities with and without nutrient enrichment. By the end of the 5-day field experiment, large diatom abundance was four times greater in all treatments compared to the initial community, with a corresponding decline in pico-cyanobacteria. The experimental results were consistent with the simulated behavior in CE and ACE, where the seasonal deepening of the mixed layer during winter produced a rapid increase in large phytoplankton. Our model simulations suggest that CE off East Australia are not only characterized by a higher chlorophyll-a concentration compared to ACE, but also by a higher concentr...

Lee, H, Golicz, AA, Bayer, PE, Jiao, Y, Tang, H, Paterson, AH, Sablok, G, Krishnaraj, RR, Chan, C-KK, Batley, J, Kendrick, GA, Larkum, AWD, Ralph, PJ & Edwards, D 2016, 'The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri)', Plant Physiology, vol. 172, no. 1, pp. 272-283.
View/Download from: Publisher's site
View description>>

Seagrasses are marine angiosperms that evolved from land plants but returned to the sea around 140 million years ago during the early evolution of monocotyledonous plants. They successfully adapted to abiotic stresses associated with growth in the marine environment, and today, seagrasses are distributed in coastal waters worldwide. Seagrass meadows are an important oceanic carbon sink and provide food and breeding grounds for diverse marine species. Here, we report the assembly and characterization of the Zostera muelleri genome, a southern hemisphere temperate species. Multiple genes were lost or modified in Z. muelleri compared with terrestrial or floating aquatic plants that are associated with their adaptation to life in the ocean. These include genes for hormone biosynthesis and signaling and cell wall catabolism. There is evidence of whole-genome duplication in Z. muelleri; however, an ancient pan-commelinid duplication event is absent, highlighting the early divergence of this species from the main monocot lineages.

Lepère, C, Ostrowski, M, Hartmann, M, Zubkov, MV & Scanlan, DJ 2016, 'In situ associations between marine photosynthetic picoeukaryotes and potential parasites – a role for fungi?', Environmental Microbiology Reports, vol. 8, no. 4, pp. 445-451.
View/Download from: Publisher's site
View description>>

SummaryPhotosynthetic picoeukaryotes (PPEs) are important components of the marine picophytoplankton community playing a critical role in CO2 fixation but also as bacterivores, particularly in the oligotrophic gyres. Despite an increased interest in these organisms and an improved understanding of the genetic diversity of this group, we still know little of the environmental factors controlling the abundance of these organisms. Here, we investigated the quantitative importance of eukaryotic parasites in the free‐living fraction as well as in associations with PPEs along a transect in the South Atlantic. Using tyramide signal amplification‐fluorescence in situ hybridization (TSA‐FISH), we provide quantitative evidence of the occurrence of free‐living fungi in open ocean marine systems, while the Perkinsozoa and Syndiniales parasites were not abundant in these waters. Using flow cytometric cell sorting of different PPE populations followed by a dual‐labelled TSA‐FISH approach, we also demonstrate fungal associations, potentially parasitic, occurring with both pico‐Prymnesiophyceae and pico‐Chrysophyceae. These data highlight the necessity for fur...

Lichtenberg, M, Larkum, AWD & Kuehl, M 2016, 'Photosynthetic Acclimation of Symbiodinium in hospite Depends on Vertical Position in the Tissue of the Scleractinian Coral Montastrea curta', FRONTIERS IN MICROBIOLOGY, vol. 7.
View/Download from: Publisher's site

Mazard, S, Penesyan, A, Ostrowski, M, Paulsen, I & Egan, S 2016, 'Tiny Microbes with a Big Impact: The Role of Cyanobacteria and Their Metabolites in Shaping Our Future', Marine Drugs, vol. 14, no. 5, pp. 97-97.
View/Download from: Publisher's site
View description>>

© 2016 by the authors; licensee MDPI. Cyanobacteria are among the first microorganisms to have inhabited the Earth. Throughout the last few billion years, they have played a major role in shaping the Earth as the planet we live in, and they continue to play a significant role in our everyday lives. Besides being an essential source of atmospheric oxygen, marine cyanobacteria are prolific secondary metabolite producers, often despite the exceptionally small genomes. Secondary metabolites produced by these organisms are diverse and complex; these include compounds, such as pigments and fluorescent dyes, as well as biologically-active compounds with a particular interest for the pharmaceutical industry. Cyanobacteria are currently regarded as an important source of nutrients and biofuels and form an integral part of novel innovative energy-efficient designs. Being autotrophic organisms, cyanobacteria are well suited for large-scale biotechnological applications due to the low requirements for organic nutrients. Recent advances in molecular biology techniques have considerably enhanced the potential for industries to optimize the production of cyanobacteria secondary metabolites with desired functions. This manuscript reviews the environmental role of marine cyanobacteria with a particular focus on their secondary metabolites and discusses current and future developments in both the production of desired cyanobacterial metabolites and their potential uses in future innovative projects.

McElroy, DJ, Doblin, MA, Murphy, RJ, Hochuli, DF & Coleman, RA 2016, 'A limited legacy effect of copper in marine biofilms', MARINE POLLUTION BULLETIN, vol. 109, no. 1, pp. 117-127.
View/Download from: Publisher's site
View description>>

The effects of confounding by temporal factors remains understudied in pollution ecology. For example, there is little understanding of how disturbance history affects the development of assemblages. To begin addressing this gap in knowledge, marine biofilms were subjected to temporally-variable regimes of copper exposure and depuration. It was expected that the physical and biological structure of the biofilms would vary in response to copper regime. Biofilms were examined by inductively coupled plasma optical emission spectrometry, chlorophyll-a fluorescence and field spectrometry and it was found that (1) concentrations of copper were higher in those biofilms exposed to copper, (2) concentrations of copper remain high in biofilms after the source of copper is removed, and (3) exposure to and depuration from copper might have comparable effects on the photosynthetic microbial assemblages in biofilms. The persistence of copper in biofilms after depuration reinforces the need for consideration of temporal factors in ecology.

Messer, LF, Mahaffey, C, Robinson, CM, Jeffries, TC, Baker, KG, Isaksson, JB, Ostrowski, M, Doblin, MA, Brown, MV & Seymour, JR 2016, 'High levels of heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation', ISME JOURNAL, vol. 10, no. 6, pp. 1499-1513.
View/Download from: Publisher's site
View description>>

© 2016 International Society for Microbial Ecology. Australia's tropical waters represent predicted 'hotspots' for nitrogen (N 2) fixation based on empirical and modelled data. However, the identity, activity and ecology of diazotrophs within this region are virtually unknown. By coupling DNA and cDNA sequencing of nitrogenase genes (nifH) with size-fractionated N 2 fixation rate measurements, we elucidated diazotroph dynamics across the shelf region of the Arafura and Timor Seas (ATS) and oceanic Coral Sea during Austral spring and winter. During spring, Trichodesmium dominated ATS assemblages, comprising 60% of nifH DNA sequences, while Candidatus Atelocyanobacterium thalassa (UCYN-A) comprised 42% in the Coral Sea. In contrast, during winter the relative abundance of heterotrophic unicellular diazotrophs (δ-proteobacteria and γ-24774A11) increased in both regions, concomitant with a marked decline in UCYN-A sequences, whereby this clade effectively disappeared in the Coral Sea. Conservative estimates of N 2 fixation rates ranged from <1 to 91 nmol l -1 day -1, and size fractionation indicated that unicellular organisms dominated N 2 fixation during both spring and winter, but average unicellular rates were up to 10-fold higher in winter than in spring. Relative abundances of UCYN-A1 and γ-24774A11 nifH transcripts negatively correlated to silicate and phosphate, suggesting an affinity for oligotrophy. Our results indicate that Australia's tropical waters are indeed hotspots for N 2 fixation and that regional physicochemical characteristics drive differential contributions of cyanobacterial and heterotrophic phylotypes to N 2 fixation.

Mondal, AK, Liu, H, Li, Z-F & Wang, G 2016, 'Multiwall carbon nanotube-nickel cobalt oxide hybrid structure as high performance electrodes for supercapacitors and lithium ion batteries', ELECTROCHIMICA ACTA, vol. 190, pp. 346-353.
View/Download from: Publisher's site
View description>>

© 2015 Elsevier Ltd. All rights reserved. We developed a simple strategy to prepare a multiwall carbon nanotube-nickel cobalt oxide nanosheet hybrid structure by using a microwave method followed by subsequent calcination in air. The structure and morphology of the material are characterized by X-ray diffraction, scanning electron microscopy and transmission electron microscopy. When applied as electrode material in 2 M KOH electrolyte for supercapacitors, the multiwall carbon nanotube-nickel cobalt oxide nanosheet structure shows a high specific capacitance of 1395 F g-1 at a current density of 1 A g-1 and excellent cycling stability over 5000 cycles. As an anode material for lithium ion battery applications, the hybrid material presents a high reversible capacity of 904 mA h g-1, good rate capability and better cycling performance than nickel cobalt oxide nanosheets and pristine multiwall carbon nanotube. The improved performances of supercapacitors and lithium ion batteries could be accredited to the unique structural features, which support high electron conductivity and rapid ion/electron transport within the electrode and at the electrode/electrolyte interface, and also accommodate volume variation during charge-discharge cycling.

Mondal, AK, Liu, H, Xie, X, Kretschmer, K & Wang, G 2016, 'Hydrothermal Synthesis of Multiwalled Carbon Nanotube-Zinc Manganate Nanoparticles as Anode Materials for Lithium Ion Batteries', CHEMPLUSCHEM, vol. 81, no. 4, pp. 399-405.
View/Download from: Publisher's site

Mongin, M, Baird, ME, Tilbrook, B, Matear, RJ, Lenton, A, Herzfeld, M, Wild-Allen, K, Skerratt, J, Margvelashvili, N, Robson, BJ, Duarte, CM, Gustafsson, MSM, Ralph, PJ & Steven, ADL 2016, 'The exposure of the Great Barrier Reef to ocean acidification', Nature Communications, vol. 7, no. 1, pp. 1-8.
View/Download from: Publisher's site
View description>>

AbstractThe Great Barrier Reef (GBR) is founded on reef-building corals. Corals build their exoskeleton with aragonite, but ocean acidification is lowering the aragonite saturation state of seawater (Ωa). The downscaling of ocean acidification projections from global to GBR scales requires the set of regional drivers controlling Ωa to be resolved. Here we use a regional coupled circulation–biogeochemical model and observations to estimate the Ωa experienced by the 3,581 reefs of the GBR, and to apportion the contributions of the hydrological cycle, regional hydrodynamics and metabolism on Ωa variability. We find more detail, and a greater range (1.43), than previously compiled coarse maps of Ωa of the region (0.4), or in observations (1.0). Most of the variability in Ωa is due to processes upstream of the reef in question. As a result, future decline in Ωa is likely to be steeper on the GBR than currently projected by the IPCC assessment report.

Murray, SA, Suggett, DJ, Doblin, MA, Kohli, GS, Seymour, JR, Fabris, M & Ralph, PJ 2016, 'Unravelling the functional genetics of dinoflagellates: a review of approaches and opportunities', Perspectives in Phycology, vol. 3, no. 1, pp. 37-52.
View/Download from: Publisher's site
View description>>

Dinoflagellates occupy an extraordinarily diverse array of ecological niches. Their success stems from a suite of functional and ecological strategies, including the production of secondary metabolites with anti-predator or allelopathic impacts, nutritional flexibility, and the ability to form symbiotic relationships. Despite their ecological importance, we currently have a poor understanding of the genetic basis for many of these strategies, due to the complex genomes of dinoflagellates. Genomics and transcriptomic sequencing approaches are now providing the first insights into the genetic basis of some dinoflagellate functional traits, providing the opportunity for novel ecological experiments, novel methods for monitoring of harmful biotoxins, and allowing us to investigate the production of ecologically and economically important compounds such as the long chain polyunsaturated fatty acid, docosahexanoic acid and the climatically important metabolite, dimethylsulfoniopropionate. Despite these advances, we still generally lack the ability to genetically manipulate species, which would enable the confirmation of biosynthetic pathways and the development of novel bio-engineering applications. Here, we describe advances in understanding the genetic basis of dinoflagellate ecology, and propose biotechnological approaches that could be applied to further transform our understanding of this unique group of eukaryotes.

Pernice, M, Sinutok, S, Sablok, G, Commault, AS, Schliep, M, Macreadie, PI, Rasheed, MA & Ralph, PJ 2016, 'Molecular physiology reveals ammonium uptake and related gene expression in the seagrass Zostera muelleri', Marine Environmental Research, vol. 122, pp. 126-134.
View/Download from: Publisher's site
View description>>

© 2016 Elsevier Ltd Seagrasses are important marine foundation species, which are presently threatened by coastal development and global change worldwide. The molecular mechanisms that drive seagrass responses to anthropogenic stresses, including elevated levels of nutrients such as ammonium, remains poorly understood. Despite the evidence that seagrasses can assimilate ammonium by using glutamine synthetase (GS)/glutamate synthase (glutamine-oxoglutarate amidotransferase or GOGAT) cycle, the regulation of this fundamental metabolic pathway has never been studied at the gene expression level in seagrasses so far. Here, we combine (i) reverse transcription quantitative real-time PCR (RT-qPCR) to measure expression of key genes involved in the GS/GOGAT cycle, and (ii) stable isotope labelling and mass spectrometry to investigate 15N-ammonium assimilation in the widespread Australian species Zostera muelleri subsp. capricorni (Z. muelleri). We demonstrate that exposure to a pulse of ammonium in seawater can induce changes in GS gene expression of Z. muelleri, and further correlate these changes in gene expression with 15N-ammonium uptake rate in above- and below-ground tissue.

Petrou, K, Kranz, SA, Trimborn, S, Hassler, CS, Ameijeiras, SB, Sackett, O, Ralph, PJ & Davidson, AT 2016, 'Southern Ocean phytoplankton physiology in a changing climate', JOURNAL OF PLANT PHYSIOLOGY, vol. 203, pp. 135-150.
View/Download from: Publisher's site
View description>>

© 2016 Elsevier GmbH The Southern Ocean (SO) is a major sink for anthropogenic atmospheric carbon dioxide (CO2), potentially harbouring even greater potential for additional sequestration of CO2 through enhanced phytoplankton productivity. In the SO, primary productivity is primarily driven by bottom up processes (physical and chemical conditions) which are spatially and temporally heterogeneous. Due to a paucity of trace metals (such as iron) and high variability in light, much of the SO is characterised by an ecological paradox of high macronutrient concentrations yet uncharacteristically low chlorophyll concentrations. It is expected that with increased anthropogenic CO2 emissions and the coincident warming, the major physical and chemical process that govern the SO will alter, influencing the biological capacity and functioning of the ecosystem. This review focuses on the SO primary producers and the bottom up processes that underpin their health and productivity. It looks at the major physico-chemical drivers of change in the SO, and based on current physiological knowledge, explores how these changes will likely manifest in phytoplankton, specifically, what are the physiological changes and floristic shifts that are likely to ensue and how this may translate into changes in the carbon sink capacity, net primary productivity and functionality of the SO.

Phong, VHN, Koottatep, T, Chapagain, SK, Panuvatvanich, A, Polprasert, C & Ahn, K-H 2016, 'Removal of acetaminophen from wastewater by constructed wetlands with Scirpus validus', Environmental Engineering Research, vol. 21, no. 2, pp. 164-170.
View/Download from: Publisher's site

Pitt, FD, Millard, A, Ostrowski, M, Dervish, S, Mazard, S, Paulsen, IT, Zubkov, MV & Scanlan, DJ 2016, 'A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus', Frontiers in Microbiology, vol. 7, no. OCT, p. 1592.
View/Download from: Publisher's site
View description>>

Recent studies using whole community metagenomic and metatranscriptomic approaches are revealing important new insights into the functional potential and activity of natural marine microbial communities. Here, we complement these approaches by describing a complete ocean sample-to-sequence protocol, specifically designed to target a single bacterial genus for purposes of both DNA and RNA profiling using fluorescence activated cell sorting (FACS). The importance of defining and understanding the effects of a sampling protocol are critical if we are to gain meaningful data from environmental surveys. Rigorous pipeline trials with a cultured isolate, Synechococcus sp. BL107 demonstrate that water filtration has a well-defined but limited impact on the transcriptomic profile of this organism, whilst sample storage and multiple rounds of cell sorting have almost no effect on the resulting RNA sequence profile. Attractively, the means to replicate the sampling strategy is within the budget and expertise of most researchers.

R. Marcelino, V, Cremen, MCM, Jackson, CJ, Larkum, AAW & Verbruggen, H 2016, 'Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green Alga Ostreobium quekettii', Genome Biology and Evolution, vol. 8, no. 9, pp. 2939-2951.
View/Download from: Publisher's site
View description>>

Abstract Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species’ genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints reflected in the chloroplast genome architecture. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. We expected the ability of Ostreobium to perform photosynthesis in very low light to be associated with positive selection in genes related to the photosynthetic machinery, but instead, we observed that these genes may be under stronger purifying selection. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the diversity of genome architectures observed in nature.

Raina, J-B, Tapiolas, D, Motti, CA, Foret, S, Seemann, T, Tebben, J, Willis, BL & Bourne, DG 2016, 'Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals', PeerJ, vol. 4, no. 8, pp. e2275-e2275.
View/Download from: Publisher's site
View description>>

Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced byPseudovibriosp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities byPseudovibriosp., and prevented the growth of two previously identified coral pathogens,Vibrio coralliilyticusandV. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing ofPseudovibriosp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention.

Rehman, AU, Szabó, M, Deák, Z, Sass, L, Larkum, A, Ralph, P & Vass, I 2016, 'Symbiodinium sp. cells produce light‐induced intra‐ and extracellular singlet oxygen, which mediates photodamage of the photosynthetic apparatus and has the potential to interact with the animal host in coral symbiosis', New Phytologist, vol. 212, no. 2, pp. 472-484.
View/Download from: Publisher's site
View description>>

SummaryCoral bleaching is an important environmental phenomenon, whose mechanism has not yet been clarified. The involvement of reactive oxygen species (ROS) has been implicated, but direct evidence of what species are involved, their location and their mechanisms of production remains unknown.Histidine‐mediated chemical trapping and singlet oxygen sensor green (SOSG) were used to detect intra‐ and extracellular singlet oxygen (1O2) in Symbiodinium cultures.Inhibition of the Calvin–Benson cycle by thermal stress or high light promotes intracellular 1O2 formation. Histidine addition, which decreases the amount of intracellular 1O2, provides partial protection against photosystem II photoinactivation and chlorophyll (Chl) bleaching. 1O2 production also occurs in cell‐free medium of Symbiodinium cultures, an effect that is enhanced under heat and light stress and can be attributed to the excretion of 1O2‐sensitizing metabolites from the cells. Confocal microscopy imaging using SOSG showed most extracellular 1O2 around the cell surface, but it is also produced across the medium distant from the cells.We demonstrate, for the first time, both intra‐ and extracellular

Rinke, C, Low, S, Woodcroft, BJ, Raina, J-B, Skarshewski, A, Le, XH, Butler, MK, Stocker, R, Seymour, J, Tyson, GW & Hugenholtz, P 2016, 'Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics', PeerJ, vol. 4, no. 9, pp. e2486-e2486.
View/Download from: Publisher's site
View description>>

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.

Ros, M, Pernice, M, Le Guillou, S, Doblin, MA, Schrameyer, V & Laczka, O 2016, 'Colorimetric Detection of Caspase 3 Activity and Reactive Oxygen Derivatives: Potential Early Indicators of Thermal Stress in Corals', Journal of Marine Biology, vol. 2016, pp. 1-11.
View/Download from: Publisher's site
View description>>

There is an urgent need to develop and implement rapid assessments of coral health to allow effective adaptive management in response to coastal development and global change. There is now increasing evidence that activation of caspase-dependent apoptosis plays a key role during coral bleaching and subsequent mortality. In this study, a “clinical” approach was used to assess coral health by measuring the activity of caspase 3 using a commercial kit. This method was first applied while inducing thermal bleaching in two coral species,Acropora milleporaandPocillopora damicornis. The latter species was then chosen to undergo further studies combining the detection of oxidative stress-related compounds (catalase activity and glutathione concentrations) as well as caspase activity during both stress and recovery phases. Zooxanthellae photosystem II (PSII) efficiency and cell density were measured in parallel to assess symbiont health. Our results demonstrate that the increased caspase 3 activity in the coral host could be detected before observing any significant decrease in the photochemical efficiency of PSII in the algal symbionts and/or their expulsion from the host. This study highlights the potential of host caspase 3 and reactive oxygen species scavenging activities as early indicators of stress in individual coral colonies.

Sablok, G, Mudunuri, SB, Edwards, D & Ralph, PJ 2016, 'Chloroplast genomics: Expanding resources for an evolutionary conserved miniature molecule with enigmatic applications', Current Plant Biology, vol. 7-8, pp. 34-38.
View/Download from: Publisher's site
View description>>

© 2016 The Authors Chloroplast, methylation depreived uniparental organelle genome is the most studied organelle genome from the perspective of evolution and functional omics. Recent advances in organelle genome sequencing both in terms of genome or transcriptome sequencing has opened a wide range of opportunities to understand the transcriptional and translational role of the genes mainly involved in the light harvesting apparatus and the evolution of the inverted repeats across the lineage. However, as compared to the nuclear genome, limited resources are available in case of organelle genome. In this review, we discuss the recent advances in the chloroplast genomics and the resources that have been developed for understanding the evolution, repeat patterns, functional genomics of this miniature molecule with enigmatic applications.

Sablok, G, Pérez-Pulido, AJ, Do, T, Seong, TY, Casimiro-Soriguer, CS, La Porta, N, Ralph, PJ, Squartini, A, Muñoz-Merida, A & Harikrishna, JA 2016, 'PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers', Frontiers in Plant Science, vol. 7, pp. 1-9.
View/Download from: Publisher's site
View description>>

© 2016 Sablok, Pérez-Pulido, Do, Seong, Casimiro-Soriguer, La Porta, Ralph, Squartini, Muñoz-Merida and Harikrishna. Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intrageneric differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www. bioinfocabd.upo.es/plantssr.

Sackett, O, Petrou, K, Reedy, B, Hill, R, Doblin, M, Beardall, J, Ralph, P & Heraud, P 2016, 'Snapshot prediction of carbon productivity, carbon and protein content in a Southern Ocean diatom using FTIR spectroscopy', ISME JOURNAL, vol. 10, no. 2, pp. 416-426.
View/Download from: Publisher's site
View description>>

© 2016 International Society for Microbial Ecology All rights reserved. Diatoms, an important group of phytoplankton, bloom annually in the Southern Ocean, covering thousands of square kilometers and dominating the region's phytoplankton communities. In their role as the major food source to marine grazers, diatoms supply carbon, nutrients and energy to the Southern Ocean food web. Prevailing environmental conditions influence diatom phenotypic traits (for example, photophysiology, macromolecular composition and morphology), which in turn affect the transfer of energy, carbon and nutrients to grazers and higher trophic levels, as well as oceanic biogeochemical cycles. The paucity of phenotypic data on Southern Ocean phytoplankton limits our understanding of the ecosystem and how it may respond to future environmental change. Here we used a novel approach to create a 'snapshot' of cell phenotype. Using mass spectrometry, we measured nitrogen (a proxy for protein), total carbon and carbon-13 enrichment (carbon productivity), then used this data to build spectroscopy-based predictive models. The models were used to provide phenotypic data for samples from a third sample set. Importantly, this approach enabled the first ever rate determination of carbon productivity from a single time point, circumventing the need for time-series measurements. This study showed that Chaetoceros simplex was less productive and had lower protein and carbon content during short-term periods of high salinity. Applying this new phenomics approach to natural phytoplankton samples could provide valuable insight into understanding phytoplankton productivity and function in the marine system.

Scanes, E, Johnston, E, Cole, V, O’Connor, W, Parker, L & Ross, P 2016, 'Quantifying abundance and distribution of native and invasive oysters in an urbanised estuary', Aquatic Invasions, vol. 11, no. 4, pp. 425-436.
View/Download from: Publisher's site
View description>>

Human activities have modified the chemical, physical and biological attributes of many of the world’s estuaries. Natural foreshores have been replaced by artificial habitats and non-indigenous species have been introduced by shipping, aquaculture, and as ornamental pets. In south east Australia, the native Sydney rock oyster Saccostrea glomerata is threatened by pollution, disease and competition from the invasive Pacific oyster Crassostrea gigas. This study assessed the abundance (as number m-2), size, and distribution of both invasive and native oyster species at 32 sites in the heavily urbanised Port Jackson Estuary, Australia. We tested the hypotheses that there would be: (1) a difference in the proportion of C. gigas and S. glomerata among locations; (2) a greater proportion of C. gigas on artificial compared to natural substrates; (3) a greater numbers of all oysters, with differing size characteristics, on artificial compared to natural substrates; and (4) that the abundance and size of all oysters would vary among locations along an environmental gradient. Environmental variables included distance from the estuary mouth and salinity. We found the abundance and size of all oysters differed among locations; smaller oysters occurred at greater abundances near the mouth of the estuary. Abundance was also higher on artificial, than on natural substrate. Habitat type, however, had no effect on which species of oyster was present. In contrast, distance from the estuary mouth strongly influenced the relative proportion of the two species. The invasive C. gigas comprised 16% of the oysters sampled, and up to 85% at some of the upper estuary sites. As predicted, C. gigas was more abundant at locations in the bay ends and upper channel of the estuary; it was also larger in size than the native S. glomerata. This is the first assessment of oyster distribution in Port Jackson and provides a solid base for monitoring changes in the estuarine distribution of ...

Schrameyer, V, Krämer, W, Hill, R, Jeans, J, Larkum, AWD, Bischof, K, Campbell, DA & Ralph, PJ 2016, 'Under high light stress two Indo-Pacific coral species display differential photodamage and photorepair dynamics', Marine Biology, vol. 163, no. 8.
View/Download from: Publisher's site

Siboni, N, Balaraju, V, Carney, R, Labbate, M & Seymour, JR 2016, 'Spatiotemporal Dynamics of Vibrio spp. within the Sydny harbour Estuary', FRONTIERS IN MICROBIOLOGY, vol. 7, no. APR.
View/Download from: Publisher's site
View description>>

© 2016 Siboni, Balaraju, Carney, Labbate and Seymour. Vibrio are a genus of marine bacteria that have substantial environmental and human health importance, and there is evidence that their impact may be increasing as a consequence of changing environmental conditions. We investigated the abundance and composition of the Vibrio community within the Sydney Harbour estuary, one of the most densely populated coastal areas in Australia, and a region currently experiencing rapidly changing environmental conditions. Using quantitative PCR (qPCR) and Vibrio-specific 16S rRNA amplicon sequencing approaches we observed significant spatial and seasonal variation in the abundance and composition of the Vibrio community. Total Vibrio spp. abundance, derived from qPCR analysis, was higher during the late summer than winter and within locations with mid-range salinity (5-26 ppt). In addition we targeted three clinically important pathogens: Vibrio cholerae, V. Vulnificus, and V. parahaemolyticus. While toxigenic strains of V. cholerae were not detected in any samples, non-toxigenic strains were detected in 71% of samples, spanning a salinity range of 0-37 ppt and were observed during both late summer and winter. In contrast, pathogenic V. vulnificus was only detected in 14% of samples, with its occurrence restricted to the late summer and a salinity range of 5-26 ppt. V. parahaemolyticus was not observed at any site or time point. A Vibrio-specific 16S rRNA amplicon sequencing approach revealed clear shifts in Vibrio community composition across sites and between seasons, with several Vibrio operational taxonomic units (OTUs) displaying marked spatial patterns and seasonal trends. Shifts in the composition of the Vibrio community between seasons were primarily driven by changes in temperature, salinity and NO2, while a range of factors including pH, salinity, dissolved oxygen (DO) and NOx (Nitrogen Oxides) explained the observed spatial variation. Our evidence for th...

Slavov, C, Schrameyer, V, Reus, M, Ralph, PJ, Hill, R, Büchel, C, Larkum, AWD & Holzwarth, AR 2016, '“Super-quenching” state protects Symbiodinium from thermal stress — Implications for coral bleaching', Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1857, no. 6, pp. 840-847.
View/Download from: Publisher's site
View description>>

The global rise in sea surface temperatures causes regular exposure of corals to high temperature and high light stress, leading to worldwide disastrous coral bleaching events (loss of symbiotic dinoflagellates (Symbiodinium) from reef-building corals). Our picosecond chlorophyll fluorescence experiments on cultured Symbiodinium clade C cells exposed to coral bleaching conditions uncovered the transformations of the alga's photosynthetic apparatus (PSA) that activate an extremely efficient non-photochemical 'super-quenching' mechanism. The mechanism is associated with a transition from an initially heterogeneous photosystem II (PSII) pool to a homogeneous 'spillover' pool, where nearly all excitation energy is transferred to photosystem I (PSI). There, the inherently higher stability of PSI and high quenching efficiency of P(700)(+) allow dumping of PSII excess excitation energy into heat, resulting in almost complete cessation of photosynthetic electron transport (PET). This potentially reversible 'super-quenching' mechanism protects the PSA against destruction at the cost of a loss of photosynthetic activity. We suggest that the inhibition of PET and the consequent inhibition of organic carbon production (e.g. sugars) in the symbiotic Symbiodinium provide a trigger for the symbiont expulsion, i.e. bleaching.

Tran, N-AT, Padula, MP, Evenhuis, CR, Commault, AS, Ralph, PJ & Tamburic, B 2016, 'Proteomic and biophysical analyses reveal a metabolic shift in nitrogen deprived Nannochloropsis oculata', Algal Research, vol. 19, pp. 1-11.
View/Download from: Publisher's site
View description>>

© 2016. The microalga Nannochloropsis oculata is a model organism for understanding intracellular lipid production, with potential benefits to the biofuel, aquaculture and nutraceutical industries. It is well known that nitrogen deprivation increases lipid accumulation in microalgae but the underlying processes are not fully understood. In this study, detailed proteomic and biophysical analyses were used to describe mechanisms that regulate carbon partitioning in nitrogen-deplete N. oculata. The alga selectively up- or down-regulated proteins to shift its metabolic flux in order to compensate for deficits in nitrate availability. Under nitrogen deprivation, proteins involved in photosynthesis, carbon fixation and chlorophyll biosynthesis were all down-regulated, and this was reflected in reduced cell growth and chlorophyll content. Protein content was reduced 4.9-fold in nitrogen-deplete conditions while fatty acid methyl esters increased by 60%. Proteomic analysis revealed that organic carbon and nitrogen from the breakdown of proteins and pigments is channeled primarily into fatty acid synthesis. As a result, the fatty acid concentration increased and the fatty acid profile became more favorable for algal biodiesel production. This advancement in microalgal proteomic analysis will help inform lipid accumulation strategies and optimum cultivation conditions for overproduction of fatty acids in N. oculata.

Varkey, D, Mazard, S, Ostrowski, M, Tetu, SG, Haynes, P & Paulsen, IT 2016, 'Effects of low temperature on tropical and temperate isolates of marine Synechococcus', The ISME Journal, vol. 10, no. 5, pp. 1252-1263.
View/Download from: Publisher's site
View description>>

Abstract Temperature is an important factor influencing the distribution of marine picocyanobacteria. However, molecular responses contributing to temperature preferences are poorly understood in these important primary producers. We compared the temperature acclimation of a tropical Synechococcus strain WH8102 with temperate strain BL107 at 18 °C relative to 22 °C and examined their global protein expression, growth patterns, photosynthetic efficiency and lipid composition. Global protein expression profiles demonstrate the partitioning of the proteome into major categories: photosynthesis (&gt;40%), translation (10–15%) and membrane transport (2–8%) with distinct differences between and within strains grown at different temperatures. At low temperature, growth and photosynthesis of strain WH8102 was significantly decreased, while BL107 was largely unaffected. There was an increased abundance of proteins involved in protein biosynthesis at 18 °C for BL107. Each strain showed distinct differences in lipid composition with higher unsaturation in strain BL107. We hypothesize that differences in membrane fluidity, abundance of protein biosynthesis machinery and the maintenance of photosynthesis efficiency contribute to the acclimation of strain BL107 to low temperature. Additional proteins unique to BL107 may also contribute to this strain’s improved fitness at low temperature. Such adaptive capacities are likely important factors favoring growth of temperate strains over tropical strains in high latitude niches.

Wang, Y, Kretschmer, K, Zhang, J, Mondal, AK, Guo, X & Wang, G 2016, 'Organic sodium terephthalate@graphene hybrid anode materials for sodium-ion batteries', RSC ADVANCES, vol. 6, no. 62, pp. S7098-S7102.
View/Download from: Publisher's site
View description>>

© The Royal Society of Chemistry 2016. In the search for high-performance electrodes for sodium-ion battery applications, there is a high demand for organic materials with satisfactory electrochemical performances, especially high rate capabilities. Herein, we report an organic based composite, sodium terephthalate@graphene (Na2TP@GE) hybrid synthesized via freeze-drying technique. This material shows an interconnected, multi-channelled monolith structure, which resulted in outstanding rate capability for sodium storage. This hybrid material demonstrated a high reversible capacity of 268.9 mA h g-1 and prolonged cyclability with capacity retention of 77.3% over 500 cycles.

Wangpraseurt, D, Pernice, M, Guagliardo, P, Kilburn, MR, Clode, PL, Polerecky, L & Kuehl, M 2016, 'Light microenvironment and single-cell gradients of carbon fixation in tissues of symbiont-bearing corals', ISME JOURNAL, vol. 10, no. 3, pp. 788-792.
View/Download from: Publisher's site
View description>>

© 2016 International Society for Microbial Ecology. Recent coral optics studies have revealed the presence of steep light gradients and optical microniches in tissues of symbiont-bearing corals. Yet, it is unknown whether such resource stratification allows for physiological differences of Symbiodinium within coral tissues. Using a combination of stable isotope labelling and nanoscale secondary ion mass spectrometry, we investigated in hospite carbon fixation of individual Symbiodinium as a function of the local O 2 and light microenvironment within the coral host determined with microsensors. We found that net carbon fixation rates of individual Symbiodinium cells differed on average about sixfold between upper and lower tissue layers of single coral polyps, whereas the light and O 2 microenvironments differed ∼15- and 2.5-fold, respectively, indicating differences in light utilisation efficiency along the light microgradient within the coral tissue. Our study suggests that the structure of coral tissues might be conceptually similar to photosynthetic biofilms, where steep physico-chemical gradients define form and function of the local microbial community.

Watanabe, S, Kuzhiumparambil, U, Winiarski, Z & Fu, S 2016, 'Biotransformation of synthetic cannabinoids JWH-018, JWH-073 and AM2201 by Cunninghamella elegans', FORENSIC SCIENCE INTERNATIONAL, vol. 261, pp. 33-42.
View/Download from: Publisher's site
View description>>

© 2015 Elsevier Ireland Ltd. Being marketed as 'legal' smoking blends or mixtures, synthetic cannabinoids are abused widely owing to its cannabis-like effect. Due to the rapid introduction of new generation analogues of synthetic cannabinoids to escape from legislative/judicial control, the investigation of the metabolic pathways of these substances is of particular importance for drug control, abstinence and forensic toxicology purposes. In this study, the in vitro metabolism of JWH-018, JWH-073 and AM2201 by the fungus Cunninghamella elagans has been investigated with the purpose of validating its potential as a complementary model for investigating synthetic cannabinoid metabolism. JWH-018, JWH-073 and AM2201 were incubated for 72 h with C. elegans. Detection of metabolites was based on liquid chromatography-tandem mass spectrometry and high resolution mass spectrometry analysis. C. elegans was found capable of producing the majority of the phase I metabolites observed in earlier in vitro and in vivo mammalian studies as a result of monohydroxylation, dihydroxylation, carboxylation, dehydrogenation, ketone formation, dihydrodiol formation, dihydrodiol formation with N-dealkylation and combinations thereof. C. elegans can thus be a useful and economic model for studying synthetic cannabinoid metabolism.

Watanabe, S, Kuzhiumparambil, U, Winiarski, Z & Fu, S 2016, 'Data on individual metabolites of synthetic cannabinoids JWH-018, JWH-073 and AM2201 by Cunninghamella elegans', Data in Brief, vol. 7, pp. 332-340.
View/Download from: Publisher's site
View description>>

Synthetic cannabinoids JWH-018, JWH-073 and AM2201 were metabolised by the fungus Cunninghamella elegans. In this article, data on individual metabolites of their retention times, mass accuracies, major product ions and structures indicated by product ions are presented. The data in this article is related to “Biotransformation of synthetic cannabinoids JWH-018, JWH-073 and AM2201 by Cunninghamella elegans”

Zavřel, T, Červený, J, Knoop, H & Steuer, R 2016, 'Optimizing cyanobacterial product synthesis: Meeting the challenges', Bioengineered, vol. 7, no. 6, pp. 490-496.
View/Download from: Publisher's site

Zavřel, T, Knoop, H, Steuer, R, Jones, PR, Červený, J & Trtílek, M 2016, 'A quantitative evaluation of ethylene production in the recombinant cyanobacterium Synechocystis sp. PCC 6803 harboring the ethylene-forming enzyme by membrane inlet mass spectrometry', Bioresource Technology, vol. 202, pp. 142-151.
View/Download from: Publisher's site

Zhu, Y, Ishizaka, J, Tripathy, SC, Wang, S, Mino, Y, Matsuno, T & Suggett, DJ 2016, 'Variation of the photosynthetic electron transfer rate and electron requirement for daily net carbon fixation in Ariake Bay, Japan', Journal of Oceanography, vol. 72, no. 5, pp. 761-776.
View/Download from: Publisher's site
View description>>

© 2016, The Oceanographic Society of Japan and Springer Japan. Fast repetition rate fluorometry (FRRf) provides a potential means to examine marine primary productivity; however, FRRf-based productivity estimations require knowledge of the electron requirement (K) for carbon (C) uptake (KC) to scale an electron transfer rate (ETR) to the CO2 uptake rate. Most previous studies have derived KC from parallel measurements of ETR and CO2 uptake over relatively short incubations, with few from longer-term daily-integrated periods. Here we determined KC by comparing depth-specific, daily ETRs and CO2-uptake rates obtained from 24-h on-deck incubation experiments undertaken on seven cruises in Ariake Bay, Japan, from 2008 to 2010. The purpose of this study was to determine the extent of variability of KC and to what extent this variability could be reconciled with the prevailing environmental conditions and ultimately to develop a method for determining net primary productivity (NPP) based on FRRf measurements. Both daily ETR and KC of the upper layer varied considerably, from 0.5 to 115.7 mmol e− mg Chl-a−1 day−1 and 4.1–26.6 mol e− (mol C)−1, respectively, throughout the entire data set. Multivariate analysis revealed a strong correlation between daily photosynthetically active radiation (PAR) and KC (r2 = 0.94). A simple PAR-dependent relationship derived from the data set was used for generating KC, and this relationship was validated by comparing the FRRf-predicted NPP with the 13C uptake measured in 2007. These new observations demonstrate the potential application of FRRf for estimating regional NPP from ETR.

Troják, M, Šafránek, D, Hrabec, J, Šalagovič, J, Romanovská, F & Červený, J 1970, 'E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria', COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY (CMSB 2016), 14th International Conference on Computational Methods in Systems Biology (CMSB), Springer International Publishing, Univ Cambridge, Comp Lab, Cambridge, ENGLAND, pp. 316-322.
View/Download from: Publisher's site

Vlachynska, A, Cerveny, J, Cmiel, V & Turecek, T 1970, 'Automatic Image-Based Method for Quantitative Analysis of Photosynthetic Cell Cultures', Hybrid Artificial Intelligent Systems, 11th International Conference on Hybrid Artificial Intelligence Systems (HAIS), Springer International Publishing, Seville, SPAIN, pp. 402-413.
View/Download from: Publisher's site

Wilkinson, SJ, Stoller, P, Ralph, P & Hamdorf, B UTS 2016, Feasibility of Algae Building Technology in Sydney, Feasibility of Algae Building Technology in Sydney, no. 1, pp. 1-56, Sydney Australia.

Doblin, MA, Petrou, K, Sinutok, S, Seymour, JR, Messer, LF, Brown, MV, Norman, L, Everett, JD, McInnes, AS, Ralph, PJ, Thompson, PA & Hassler, CS 2016, 'Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current', PeerJ.
View/Download from: Publisher's site

Doblin, MA, Petrou, K, Sinutok, S, Seymour, JR, Messer, LF, Brown, MV, Norman, L, Everett, JD, McInnes, AS, Ralph, PJ, Thompson, PA & Hassler, CS 2016, 'Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current', PeerJ.
View/Download from: Publisher's site

Labbate, M, Seymour, JR, Lauro, F & Brown, MV 2016, 'Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments', Frontiers Media SA, Lausanne, Switzerland.
View/Download from: Publisher's site
View description>>

Aquatic ecosystems are currently experiencing unprecedented levels of impact from human activities including over-exploitation of resources, habitat destruction, pollution and the influence of climate change. The impacts of these activities on the microbial ecology of aquatic environments are only now beginning to be defined. One of the many implications of environmental degradation and climate change is the geographical expansion of disease- causing microbes such as those from the Vibrio genus. Elevating sea surface temperatures correlate with increasing Vibrio numbers and disease in marine animals (e.g. corals) and humans. Contamination of aquatic environments with heavy metals and other pollutants affects microbial ecology with downstream effects on biogeochemical cycles and nutrient turnover. Also of importance is the pollution of aquatic environments with antibiotics, resistance genes and the mobile genetic elements that house resistance genes from human and animal waste. Such contaminated environments act as a source of resistance genes long after an antibiotic has ceased being used in the community. Environments contaminated with mobile genetic elements that are adapted to human commensals and pathogens function to capture new resistance genes for potential reintroduction back into clinical environments. This research topic encompasses these diverse topics and describes the affect(s) of human activity on the microbial ecology and function in aquatic environments and, describes methods of restoration and for modelling disturbances.

Marcelino, VR, Cremen, MCM, Jackson, CJ, Larkum, AWD & Verbruggen, H 2016, 'Evolutionary dynamics of chloroplast genomes in low light: a case study of the endolithic green algaOstreobium quekettii', Cold Spring Harbor Laboratory.
View/Download from: Publisher's site

McInnes, AS, Messer, LF, Laiolo, L, Laverock, B, Laczka, O, Brown, M, Seymour, JR & Doblin, MA 2016, 'Microbial utilization of nitrogen in cold core eddies: size does matter'.
View description>>

As the base of the marine food web, and the first step in the biological carbon pump, understanding changes in microbial community composition is essential for predicting changes in the marine nitrogen (N) cycle. Climate change projections suggest that oligotrophic waters will become more stratified with a concomitant shift in microbial community composition based on changes in N supply. In regions of strong boundary currents, eddies could reduce this limitation through nutrient uplift and other forms of eddy mixing. Understanding the preference for different forms of N by microbes is essential for understanding and predicting shifts in the microbial community. This study aims to understand the utilization of different N species within different microbial size fractions as well as understand the preferred source of N to these groups across varying mesoscale and sub-mesoscale features in the East Australian Current (EAC). In June 2015 we sampled microbial communities from three depths (surface, chlorophyll-a maximum and below the mixed layer), in three mesoscale and sub-mesoscale eddy features, as well as two end-point water masses (coastal and oligotrophic EAC water). Particulate matter was analysed for stable C and N isotopes, and seawater incubations with trace amounts of 15NO3, 15NH4, 15N2, 15Urea and 13C were undertaken. All samples were size fractionated into 0.3-2.0 µm, 2.0-10 µm, and >10 µm size classes, encompassing the majority of microbes in these waters. Microbial community composition was also assessed (pigments, flow cytometry, DNA), as well as physical and chemical parameters, to better understand the drivers of carbon fixation and nitrogen utilization across a diversity of water masses and microbial size classes. We observed that small, young features have a greater abundance of larger size classes. We therefore predict that these microbes will preferentially draw down the recently pulsed NO3. Ultimately, the size and age of a feature wil...