Publications

Elberling, B, Kuhl, M, Glud, RN, Jorgensen, CJ, Askaer, L, Rickelt, LF, Joensen, HP, Larsen, M & Liengaard, L 2013, 'Methods to assess high-resolution subsurface gas concentrations and gas fluxes in wetland ecosystems' in DeLaune, RD, Reddy, KR, Richardson, CJ & Megonigal, JP (eds), Methods in Biogeochemistry of Wetlands, Soil Science Society of America, Madison, pp. 949-966.

Hall, CC, Cruz, J, Wood, M, Zegarac, R, DeMars, D, Carpenter, J, Kanazawa, A & Kramer, D 2013, 'Photosynthetic measurements with the idea spec: An integrated diode emitter array spectrophotometer/fluorometer' in Advanced Topics in Science and Technology in China, pp. 184-188.
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© Zhejiang University Press, Hangzhou and Springer-Verlag Berlin Heidelberg 2013. In vivo spectrophotometry, a non-invasive, nondestructive technique that relies on the leaf’s endogenous chromophores, has become an essential tool for understanding the photosynthetic response of plants to environmental stresses. Based on the pulsed-light spectrophotometer approach, and capitalizing on recent advances in optics and light emitting diode (LED) technology, we have developed an in vivo spectrophotometer capable of measuring absorbance changes of less than 3 × 10 −5 absorption units and microsecond time resolution. The instrument can also simultaneously measure chlorophyll (or other) fluorescence signals with background or saturating actinic light, e.g. PAM fluorometry or induction curves, to give measurements of antenna and photosystem II efficiencies. We use a solid-state light source containing multiple LEDs for both measuring and actinic stimulation and direct the light to the leaf through non-focusing optics, allowing near-simultaneous multi-wavelength measurements useful for signal deconvolution.

Kumari, P, Kumar, M, Reddy, CRK & Jha, B 2013, 'Algal lipids, fatty acids and sterols' in Functional Ingredients from Algae for Foods and Nutraceuticals, Woodhead Publishing Limited, USA, pp. 87-134.
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Algae are photosynthetic organisms with ubiquitous distribution and contain varied forms of lipids owing to their extreme habitat diversity. This chapter presents detailed information on the structure and distribution of lipids, fatty acids and sterols in algae together with the genes and enzymes involved in their metabolism. The developments in acclimatory roles of lipids, fatty acids and sterols in response to changes in environmental factors such as nutrients, light, temperature and salinity have been discussed. Further, the current status of lipidomics in algae has also been discussed presuming its promising implications in elucidation of novel lipids and understanding of complex metabolic pathways. © 2013 Woodhead Publishing Limited All rights reserved.

Larkum, AWD 2013, 'The golden apples of the sun: The history of photosynthesis—So far' in Advanced Topics in Science and Technology in China, pp. 834-839.
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© Zhejiang University Press, Hangzhou and Springer-Verlag Berlin Heidelberg 2013. This article reviews the start of life and of photosynthesis on the Earth. A pivotal evolutionary event in photosynthesis was the ability to use water as the source of hydrogen in the photosynthetic reaction, which occurred about 2.35 billion years ago. This opened up the possibility for photosynthetic organisms to live anywhere on the surface of the Earth where light and water occurred—and secondarily allowed the build-up of oxygen in the biosphere and atmosphere. The accumulation of molecular oxygen allowed the evolution of aerobic respiratory systems with much greater efficiency in output of organically-derived energy. In turn this allowed the evolution of large complex eukaryotic cells by endosymbiosis. The chloroplast was the result of one endosymbiotic development, now found in many phyla of photosynthetic protists (algae) and in land plants. The multicellular land plants, which evolved from streptophyte green algae, now account for a major part of the total bioenergy production from photosynthesis on the Earth. However, the basic mechanism of photosynthesis has changed very little in the last 2 billion years. In the future, radical changes will be necessary to make bioenergy production from algae and plants more efficient and more competitive with other methods of solar energy conversion.

Li, Y, Larkum, A, Schliep, MT, Kuhl, M, Neilan, B & Chen, M 2013, 'Newly isolated Chl d-containing cyanobacteria' in Kuang, T, Lu, C & Zhang, L (eds), Photosynthesis Research for Food, Fuel and the Future - 15th International Conference on Photosynthesis, Springer-Verlag GmbH, Beijing, pp. 686-690.
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Stromatolites are sedimentary structures formed by microbial mats that are typically found in limestone-or dolostone-rich environments. Shark Bay, Australia, has abundant examples of living marine stromatolites. Although the stromatolites from Shark Bay are only about 20003000 years old, they are similar to fossilized evidence of life found on Earth up to 3.5 billion years ago. Using infra-red light centred at 720 nm, new chlorophyll d-containing microorganisms were isolated from the living stromatolites (collected from Shark Bay, Western Australia) and red algae on mangrove pneumatophores (collected from the Georges River, Sydney, Australia) and enriched in KES+ seawater medium. Microscopic examination of the red-light enriched cultures confirmed that they are Acaryochloris-like cyanobacteria. Using cyanobacterial-specific 16S rRNA gene primers, we obtained almost full length sequences of 16S rDNA from the newly isolated Chl d-containing cyanobacteria. The sequences shared 98% identity with Acaryochloris marina MBIC11017. Interestingly, the strain isolated from stromatolites (designated as ssball1 strain) was more similar to Acaryochloris sp CR111A while the strain isolated from Georges River (designated as Mangrove1 strain) was more closely related to Acaryochloris sp CCMEE 5401, which was isolated from an inland lake, Salton Sea in California,. Pigment composition of the newly isolated strains were determined using HPLC, However, no obvious differences were noted. Chl d was the major photopigment while Chl a was present as a minor photopigment, about 2%3.5 % of the total chlorophyll.

McCauley, JI, Zivanovic, A & Skropeta, D 2013, 'Bioassays for Anticancer Activities' in Metabolomics Tools for Natural Product Discovery, Springer.
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Ajani, P, Brett, S, Krogh, M, Scanes, P, Webster, G & Armand, L 2013, 'The risk of harmful algal blooms (HABs) in the oyster-growing estuaries of New South Wales, Australia', ENVIRONMENTAL MONITORING AND ASSESSMENT, vol. 185, no. 6, pp. 5295-5316.
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Ajani, P, Murray, SA, Hallegraeff, G, Brett, S & Armand, L 2013, 'First reports of Pseudo-nitzschia micropora and P. hasleana (Bacillariaceae) from the Southern Hemisphere: Morphological, molecular and toxicological characterization', Phycological Research, vol. 61, no. 3, pp. 237-248.
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Pseudo-nitzschia H. Peragallo is a marine diatom genus found worldwide in polar, temperate, subtropical and tropical waters. It includes toxigenic representatives that produce domoic acid (DA), a neurotoxin responsible for Amnesic Shellfish Poisoning. In this study we characterized two species of Pseudo-nitzschia collected from Port Stephens and the Hawkesbury River (south eastern Australia) previously unreported from Australian waters. Clonal isolates were sub-sampled for (i) light and transmission electron microscopy; (ii) DNA sequencing, based on the nuclear-encoded partial large subunit ribosomal RNA gene and internal transcribed spacer (ITS)-ITS1, 5.8S and ITS2 rDNA regions and, (iii) DA production as measured by liquid chromatography-mass spectrometry. Morphological and molecular data unambiguously revealed the species to be Pseudo-nitzschia micropora Priisholm, Moestrup & Lundholm (Port Stephens) and Pseudo-nitzschia hasleana Lundholm (Hawkesbury River). This is the first report of the occurrence of these species from the Southern Hemisphere and the first report of P.?micropora in warm-temperate waters. Cultures of P.?micropora, tested for DA production for the first time, proved to be non-toxic. Similarly, no detectable toxin concentrations were observed for P.?hasleana. Species resolution and knowledge on the toxicity of local Pseudo-nitzschia species has important implications for harmful algal bloom monitoring and management.

Ajani, P, Murray, SA, Hallegraeff, G, Lundholm, N, Gillings, M, Brett, S & Armand, L 2013, 'The diatom genus Pseudo-nitzschia (Bacillariophyceae) in New South Wales, Australia: morphotaxonomy, molecular phylogeny, toxicity, and distribution', Journal of Phycology, vol. 49, no. 4, pp. 765-785.
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Species belonging to the potentially harmful diatom genus Pseudo-nitzschia, isolated from 16 localities (31 sampling events) in the coastal waters of south-eastern Australia, were examined. Clonal isolates were characterized by (i) light and transmission electron microscopy; (ii) phylogenies, based on sequencing of nuclear-encoded ribosomal deoxyribonucleic acid (rDNA) regions and, (iii) domoic acid (DA) production as measured by liquid chromatographymass spectrometry (LC-MS/MS). Ten taxa were unequivocally confirmed as Pseudo-nitzschia americana, P. arenysensis, P. calliantha, P. cuspidata, P. fraudulenta, P. hasleana, P. micropora, P. multiseries, P. multistriata, and P. pungens. An updated taxonomic key for south-eastern Australian Pseudo-nitzschia is presented. The occurrence of two toxigenic species, P. multistriata (maximum concentration 11 pg DA per cell) and P. cuspidata (25.4 pg DA per cell), was documented for the first time in Australia. The Australian strains of P. multiseries, a consistent producer of DA in strains throughout the world, were nontoxic. Data from 5,888 water samples, collected from 31 oyster-growing estuaries (2,000 km coastline) from 2005 to 2009, revealed 310 regulatory exceedances for Total Pseudo-nitzschia, resulting in six toxic episodes. Further examination of high-risk estuaries revealed that the P. seriata group had highest cell densities in the austral summer, autumn, or spring (species dependent), and lowest cell densities in the austral winter, while the P. delicatissima group had highest in winter and spring

Andrews, M, Raven, JA & Lea, PJ 2013, 'Do plants need nitrate? The mechanisms by which nitrogen form affects plants', ANNALS OF APPLIED BIOLOGY, vol. 163, no. 2, pp. 174-199.
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Ashworth, J, Coesel, S, Lee, A, Armbrust, EV, Orellana, MV & Baliga, NS 2013, 'Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 110, no. 18, pp. 7518-7523.
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Baird, ME, Ralph, PJ, Rizwi, F, Wild-Allen, K & Steven, A 2013, 'A dynamic model of the cellular carbon to chlorophyll ratio applied to a batch culture and a continental shelf ecosystem', Limnology and Oceanography, vol. 58, no. 4, pp. 1215-1226.
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A novel parameterization of the dynamical relationship between cellular carbon (C) and chlorophyll (Chl) is developed using a Chl synthesis term that includes the physiological status of the cell and the effect of packaging of pigments within cells. The geometric derivation highlights the non-linear relationship between Chl content and absorption due to the package effect. When parameterized for a generic 3 mm radius phytoplankton cell, the model reproduces the magnitude and daily variations of C: Chl and C: nitrogen ratios of the diatom Skeletonema costatum in published laboratory experiments. The parameterization is then applied in a three-dimensional biogeochemical model containing three phytoplankton classes in the coastal waters off southeast Tasmania, Australia, which demonstrates the behavior of the dynamic Chl parameterization over a range of light- and nutrient-limiting environments for phytoplankton of different sizes and growth rates. The model produces C: Chl ratios of , 1220 (weight : weight) and , 6080 for phytoplankton communities dominated by fast-growing small and fast-growing large cells, respectively, close to the ratios of 17 and 76 observed at two sampling stations during periods with diatom- and flagellate-dominated communities. Throughout the simulation, community C: Chl ratios generally vary between 12 and 200, which is similar to the range observed globally. In the new parameterization, C: Chl ratios are most influenced by the package effect for light-limited, slow-growing large microalgae, with physiological processes becoming important for smaller, nutrient-limited, fast-growing microalgae.

Baker, IT, Harper, AB, Rocha, HR, Denning, AS, Araujo, AC, Borma, LS, Freitas, HC, Goulden, ML, Manzi, AO, Miller, SD, Nobre, AD, Restrepo Coupe, N, Saleska, SR, Stockli, R, von Randow, C & Wofsy, SC 2013, 'Surface ecophysiological behavior across vegetation and moisture gradients in tropical South America', Agricultural and Forest Meteorology, vol. 182-183, pp. 177-188.
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Surface ecophysiology at five sites in tropical South America across vegetation and moisture gradients is investigated. From the moist northwest (Manaus) to the relatively dry southeast (Pé de Gigante, state of São Paulo) simulated seasonal cycles of latent and sensible heat, and carbon flux produced with the Simple Biosphere Model (SiB3) are confronted with observational data. In the northwest, abundant moisture is available, suggesting that the ecosystem is light-limited. In these wettest regions, Bowen ratio is consistently low, with little or no annual cycle. Carbon flux shows little or no annual cycle as well; efflux and uptake are determined by high-frequency variability in light and moisture availability. Moving downgradient in annual precipitation amount, dry season length is more clearly defined. In these regions, a dry season sink of carbon is observed and simulated. This sink is the result of the combination of increased photosynthetic production due to higher light levels, and decreased respiratory efflux due to soil drying. The differential response time of photosynthetic and respiratory processes produce observed annual cycles of net carbon flux. In drier regions, moisture and carbon fluxes are in-phase; there is carbon uptake during seasonal rains and efflux during the dry season. At the driest site, there is also a large annual cycle in latent and sensible heat flux

Beardall, J & Raven, JA 2013, 'Calcification and ocean acidification: new insights from the coccolithophore Emiliania huxleyi', NEW PHYTOLOGIST, vol. 199, no. 1, pp. 1-3.
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Behrendt, L, Staal, M, Cristescu, SM, Harren, FJ, Schliep, M, Larkum, AW & Kühl, M 2013, 'Reactive oxygen production induced by near-infrared radiation in three strains of the Chl d-containing cyanobacterium Acaryochloris marina.', F1000Research, vol. 2, pp. 44-44.
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Cyanobacteria in the genus Acaryochloris have largely exchanged Chl a with Chl d, enabling them to harvest near-infrared-radiation (NIR) for oxygenic photosynthesis, a biochemical pathway prone to generate reactive oxygen species (ROS). In this study, ROS production under different light conditions was quantified in three Acaryochloris strains (MBIC11017, HICR111A and the novel strain CRS) using a real-time ethylene detector in conjunction with addition of 2-keto-4-thiomethylbutyric acid, a substrate that is converted to ethylene when reacting with certain types of ROS. In all strains, NIR was found to generate less ROS than visible light (VIS). More ROS was generated if strains MBIC11017 and HICR111A were adapted to NIR and then exposed to VIS, while strain CRS demonstrated the opposite behavior. This is the very first study of ROS generation and suggests that Acaryochloris can avoid a considerable amount of light-induced stress by using NIR instead of VIS for its photosynthesis, adding further evolutionary arguments to their widespread appearance.

Bjarnsholt, T, Alhede, M, Alhede, M, Eickhardt-Sørensen, S, Moser, C, Kuhl, M, Østrup Jensen, P & Høiby, N 2013, 'The in vivo biofilm', Trends In Microbiology, vol. 21, no. 9, pp. 466-474.
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Bacteria can grow and proliferate either as single, independent cells or organized in aggregates commonly referred to as biofilms. When bacteria succeed in forming a biofilm within the human host, the infection often becomes very resistant to treatment and can develop into a chronic state. Biofilms have been studied for decades using various in vitro models, but it remains debatable whether such in vitro biofilms actually resemble in vivo biofilms in chronic infections. In vivo biofilms share several structural characteristics that differ from most in vitro biofilms. Additionally, the in vivo experimental time span and presence of host defenses differ from chronic infections and the chemical microenvironment of both in vivo and in vitro biofilms is seldom taken into account. In this review, we discuss why the current in vitro models of biofilms might be limited for describing infectious biofilms, and we suggest new strategies for improving this discrepancy.

Brading, P, Warner, ME, Smith, DJ & Suggett, DJ 2013, 'Contrasting modes of inorganic carbon acquisition amongst Symbiodinium (Dinophyceae) phylotypes', New Phytologist, vol. 200, no. 2, pp. 432-442.
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Growing concerns over ocean acidification have highlighted the need to critically understand inorganic carbon acquisition and utilization in marine microalgae. Here, we contrast these characteristics for the first time between two genetically distinct di

Bramucci, A, Han, S, Beckers, J, Haas, C & Lanoil, B 2013, 'Composition, diversity, and stability of microbial assemblages in seasonal lake ice, Miquelon Lake, Central Alberta', Biology, vol. 2, no. 2, pp. 514-532.
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The most familiar icy environments, seasonal lake and stream ice, have received little microbiological study. Bacteria and Eukarya dominated the microbial assemblage within the seasonal ice of Miquelon Lake, a shallow saline lake in Alberta, Canada. The bacterial assemblages were moderately diverse and did not vary with either ice depth or time. The closest relatives of the bacterial sequences from the ice included Actinobacteria, Bacteroidetes, Proteobacteria, Verrucomicrobia, and Cyanobacteria. The eukaryotic assemblages were less conserved and had very low diversity. Green algae relatives dominated the eukaryotic gene sequences; however, a copepod and cercozoan were also identified, possibly indicating the presence of complete microbial loop. The persistence of a chlorophyll a peak at 25-30 cm below the ice surface, despite ice migration and brine flushing, indicated possible biological activity within the ice. This is the first study of the composition, diversity, and stability of seasonal lake ice. © 2013 by the authors; licensee MDPI, Basel, Switzerland.

Camp, EF, Lohr, KE, Barry, SC, Bush, PG, Jacoby, CA & Manfrino, C 2013, 'MICROHABITAT ASSOCIATIONS OF LATE JUVENILE NASSAU GROUPER (EPINEPHELUS STRIATUS) OFF LITTLE CAYMAN, BWI', BULLETIN OF MARINE SCIENCE, vol. 89, no. 2, pp. 571-581.
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Carrillo, MC, Rowe, CC, Szoeke, C, Masters, CL, Ames, D, O’Meara, T, Macaulay, SL, Milner, A, Ellis, KA, Maruff, P, Rainey-Smith, SR, Martins, RN, Bain, LJ & Head, RJ 2013, 'Research and standardization in Alzheimer's trials: Reaching international consensus', Alzheimer's & Dementia, vol. 9, no. 2, pp. 160-168.
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Ceh, J, Kilburn, MR, Cliff, JB, Raina, J, van Keulen, M & Bourne, DG 2013, 'Nutrient cycling in early coral life stages: Pocillopora damicornis larvae provide their algal symbiont (Symbiodinium) with nitrogen acquired from bacterial associates', Ecology and Evolution, vol. 3, no. 8, pp. 2393-2400.
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Clark, J, Poore, AG, Ralph, PJ & Doblin, MA 2013, 'Potential for adaptation in response to thermal stress in an intertidal macroalga', Journal of Phycology, vol. 49, no. 4, pp. 630-639.
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Understanding responses of marine algae to changing ocean temperatures requires knowledge of the impacts of elevated temperatures and the likelihood of adaptation to thermal stress. The potential for rapid evolution of thermal tolerance is dependent on the levels of heritable genetic variation in response to thermal stress within a population. Here, we use a quantitative genetic breeding design to establish whether there is a heritable variation in thermal sensitivity in two populations of a habitat-forming intertidal macroalga, Hormosira banksii (Turner) Descaisne. Gametes from multiple parents were mixed and growth and photosynthetic performance were measured in the resulting embryos, which were incubated under control and elevated temperature (20°C and 28°C). Embryo growth was reduced at 28°C, but significant interactions between male genotype and temperature in one population indicated the presence of genetic variation in thermal sensitivity. Selection for more tolerant genotypes thus has the ability to result in the evolution of increased thermal tolerance. Furthermore, genetic correlations between embryos grown in the two temperatures were positive, indicating that those genotypes that performed well in elevated temperature also performed well in control temperature. Chlorophyll a fluorescence measurements showed a marked decrease in maximum quantum yield of photosystem II (PSII) under elevated temperature. There was an increase in the proportion of energy directed to photoinhibition (nonregulated nonphotochemical quenching) and a concomitant decrease in energy used to drive photochemistry and xanthophyll cycling (regulated nonphotochemical quenching). However, PSII performance between genotypes was similar, suggesting that thermal sensitivity is related to processes other than photosynthesis.

Commault, AS, Lear, G, Packer, MA & Weld, RJ 2013, 'Influence of anode potentials on selection of Geobacter strains in microbial electrolysis cells', Bioresource Technology, vol. 139, pp. 226-234.
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Through their ability to directly transfer electrons to electrodes, Geobacter sp. are key organisms for microbial fuel cell technology. This study presents a simple method to reproducibly select Geobacter-dominated anode biofilms from a mixed inoculum of bacteria using graphite electrodes initially poised at −0.25, −0.36 and −0.42 V vs. Ag/AgCl. The biofilms all produced maximum power density of approximately 270 mW m−2 (projected anode surface area). Analysis of 16S rRNA genes and intergenic spacer (ITS) sequences found that the biofilm communities were all dominated by bacteria closely related to Geobacter psychrophilus. Anodes initially poised at −0.25 V reproducibly selected biofilms that were dominated by a strain of G. psychrophilus that was genetically distinct from the strain that dominated the −0.36 and −0.42 V biofilms. This work demonstrates for the first time that closely related strains of Geobacter can have very different competitive advantages at different anode potentials.

Dafforn, KA, Kelaher, BP, Simpson, SL, Coleman, MA, Hutchings, PA, Clark, GF, Knott, NA, Doblin, MA & Johnston, EL 2013, 'Polychaete richness and abundance enhanced in anthropogenically modified estuaries despite high concentrations of toxic contaminants', PLoS One, vol. 8, no. 9, pp. 1-10.
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Ecological communities are increasingly exposed to multiple chemical and physical stressors, but distinguishing anthropogenic impacts from other environmental drivers remains challenging. Rarely are multiple stressors investigated in replicated studies over large spatial scales (.1000 kms) or supported with manipulations that are necessary to interpret ecological patterns. We measured the composition of sediment infaunal communities in relation to anthropogenic and natural stressors at multiple sites within seven estuaries. We observed increases in the richness and abundance of polychaete worms in heavily modified estuaries with severe metal contamination, but no changes in the diversity or abundance of other taxa. Estuaries in which toxic contaminants were elevated also showed evidence of organic enrichment. We hypothesised that the observed response of polychaetes was not a `positive response to toxic contamination or a reduction in biotic competition, but due to high levels of nutrients in heavily modified estuaries driving productivity in the water column and enriching the sediment over large spatial scales. We deployed defaunated field-collected sediments from the surveyed estuaries in a small scale experiment, but observed no effects of sediment characteristics (toxic or enriching). Furthermore, invertebrate recruitment instead reflected the low diversity and abundance observed during field surveys of this relatively `pristine estuary. This suggests that differences observed in the survey are not a direct consequence of sediment characteristics (even severe metal contamination) but are related to parameters that covary with estuary modification such as enhanced productivity from nutrient inputs and the diversity of the local species pool. This has implications for the interpretation of diversity measures in large-scale monitoring studies in which the observed patterns may be strongly influenced by many factors that covary with anthropogenic modification.

de Gonç, LG, Borak, JS, Costa, MH, Saleska, SR, Baker, I, Restrepo Coupe, N, Muza, MN, Poulter, B, Verbeeck, H, Fisher, JB, Arain, MA, Arkin, P, Cestaro, BP, Christoffersen, B, Galbraith, D, Guan, X, van den Hurk, BJ, Ichii, K, Imbuzeiro, HM, Jain, AK, Levine, N, Lu, C, Miguez-Macho, G, Roberti, DR, Sahoo, A, Sakaguchi, K, Schaefer, K, Shi, M, Shuttleworth, WJ, Tian, W, Yang, Z & Zeng, X 2013, 'Overview of the Large-Scale Biosphere-Atmosphere experiment in Amazonia Data Model Intercomparison Project (LBA-DMIP)', Agricultural and Forest Meteorology, vol. 182-183, pp. 111-127.
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A fundamental question connecting terrestrial ecology and global climate change is the sensitivity of key terrestrial biomes to climatic variability and change. The Amazon region is such a key biome: it contains unparalleled biological diversity, a globally significant store of organic carbon, and it is a potent engine driving global cycles of water and energy. The importance of understanding how land surface dynamics of the Amazon region respond to climatic variability and change is widely appreciated, but despite significant recent advances, large gaps in our understanding remain. Understanding of energy and carbon exchange between terrestrial ecosystems and the atmosphere can be improved through direct observations and experiments, as well as through modeling activities. Land surface/ecosystem models have become important tools for extrapolating local observations and understanding to much larger terrestrial regions. They are also valuable tools to test hypothesis on ecosystem functioning. Funded by NASA under the auspices of the LBA (the Large-Scale BiosphereAtmosphere Experiment in Amazonia), the LBA Data Model Intercomparison Project (LBA-DMIP) uses a comprehensive data set from an observational network of flux towers across the Amazon, and an ecosystem modeling community engaged in ongoing studies using a suite of different land surface and terrestrial ecosystem models to understand Amazon forest function. Here an overview of this project is presented accompanied by a description of the measurement sites, data, models and protocol.

Dennis, PG, Seymour, JR, Kumbun, K & Tyson, G 2013, 'Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients', ISME Journal, vol. 7, no. 8, pp. 1661-1664.
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Chemotaxis allows microorganisms to rapidly respond to different environmental stimuli; however, understanding of this process is limited by conventional assays, which typically focus on the response of single axenic cultures to given compounds. In this study, we used a modified capillary assay coupled with flow cytometry and 16S rRNA gene amplicon pyrosequencing to enumerate and identify populations within a lake water microbial community that exhibited chemotaxis towards ammonium, nitrate and phosphate. All compounds elicited chemotactic responses from populations within the lake water, with members of Sphingobacteriales exhibiting the strongest responses to nitrate and phosphate, and representatives of the Variovorax, Actinobacteria ACK-M1 and Methylophilaceae exhibiting the strongest responses to ammonium. Our results suggest that chemotaxis towards inorganic substrates may influence the rates of biogeochemical processes.

Exton, DA, Suggett, DJ, McGenity, TJ & Steinke, M 2013, 'Chlorophyll-normalized isoprene production in laboratory cultures of marine microalgae and implications for global models', Limnology and Oceanography, vol. 58, no. 4, pp. 1301-1311.
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We used laboratory cultures of marine microalgae to investigate the effects of growth conditions and their taxonomic position on the production of isoprene, a gas that has major effects on atmospheric chemistry and provides stress tolerance to many primary producers. Isoprene was quantified from 21 microalgal strains sampled during exponential growth, using purge-and-trap pre-concentration and gas chromatography with flameionization detection. Isoprene production rates varied by two orders of magnitude between strains (0.03 1.34 mmol [g chlorophyll a]21 h21), and were positively correlated with temperature (r2 5 0.52, p , 0.001, n 5 59). Three distinct sea surface temperature (SST)dependent relationships were found between isoprene and chlorophyll a (mmol [g chlorophyll a]21 h21), an improvement in resolution over the single relationship used in previous models: for three polar strains grown at 21uC (slope 5 0.03, R2 5 0.76, p , 0.05, n 5 9), nine strains grown at 16uC (slope 5 0.24, R2 5 0.43, p , 0.05, n 5 27 with Dunaliella tertiolecta excluded), and eight strains grown at 26uC (slope 5 0.39, R2 5 0.15, p , 0.05, n 5 24). We then used a simple model that applied the SSTdependent nature of isoprene production to three representative bioregions for the growth temperatures used in this study. This approach yielded an estimate of global marine isoprene production that was 51% higher than previous attempts using an SST-independent single relationship. Taking into account the effect of temperature therefore potentially allows more precise modeling of marine isoprene production, and suggests that increasing the SST-based resolution of data beyond the three groups used here could further improve future modeling simulations.

Farrell, H, Brett, S, Ajani, P & Murray, SA 2013, 'Distribution of the genus Alexandrium (Halim) and paralytic shellfish toxins along the coastline of New South Wales, Australia', Marine Pollution Bulletin, vol. 72, no. 1, pp. 133-145.
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Blooms of Alexandrium species, in particular the species Alexandrium catenella, accounted for more than 50% of algal related, shellfish aquaculture harvest zone closures in New South Wales (NSW) Australia since 2005. While there are indications that species of Alexandrium are more abundant than they were formerly, there is little data available on the spatial and temporal distribution and abundance of the genus in NSW. A six and a half year dataset comprising a total of 8649 fortnightly samples from 31 estuaries spread over 2000 km of NSW coastline was analysed. The greatest abundances of Alexandrium spp. were observed during the austral Spring and Summer, in estuaries in the mid and southern latitudes of the state. In identifying these high risk zones, we propose variables such as season, temperature, rainfall and estuarine flushing to be targeted in intensive site specific studies, to support the development of predictive tools for resource managers.

Flynn, KJ, Stoecker, DK, Mitra, A, Raven, JA, Glibert, PM, Hansen, PJ, Graneli, E & Burkholder, JM 2013, 'Misuse of the phytoplanktonzooplankton dichotomy: the need to assign organisms as mixotrophs within plankton functional types', JOURNAL OF PLANKTON RESEARCH, vol. 35, no. 1, pp. 3-11.
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Fowler, D, Pyle, JA, Raven, JA & Sutton, MA 2013, 'The global nitrogen cycle in the twenty-first century: introduction', PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 368, no. 1621.
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Garby, T, Walter, M, Larkum, A & Neilan, BA 2013, 'Diversity Of Cyanobacterial Biomarker Genes From The Stromatolites Of Shark Bay, Western Australia', Environmental Microbiology, vol. 15, no. 5, pp. 1464-1475.
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Families of closely related chemical compounds, which are relatively resistant to degradation, are often used as biomarkers to help trace the evolutionary history of early groups of organisms and the environments in which they lived. Biomarkers derived from hopanoid variations are particularly useful in determining bacterial community compositions. 2-Methylhopananoids have been thought to be diagnostic for cyanobacteria, and 2-methylhopanes in the geological record are taken as evidence for the presence of cyanobacteria-containing communities at the time of sediment deposition. Recently, however, doubt has been cast on the validity of 2-methylhopanes as cyanobacterial biomarkers, since non-cyanobacterial species have been shown to produce significant amounts of 2-methylhopanoids. This study examines the diversity of hpnP, the hopanoid biosynthesis gene coding for the enzyme that methylates hopanoids at the C2 position. Genomic DNA isolated from stromatolite-associated pustular and smooth microbial mat samples from Shark Bay, Western Australia, was analysed for bacterial diversity, and used to construct an hpnP clone library. A total of 117 partial hpnP clones were sequenced, representing 12 operational taxonomic units (OTUs). Phylogenetic analysis showed that 11 of these OTUs, representing 115 sequences, cluster within the cyanobacterial clade. We conclude that the dominant types of microorganisms with the detected capability of producing 2-methylhopanoids within pustular and smooth microbial mats in Shark Bay are cyanobacteria.

Gleason, FH, van Ogtrop, F, Lilje, O & Larkum, A 2013, 'Ecological roles of zoosporic parasites in blue carbon ecosystems', Fungal Ecology, vol. 6, no. 5, pp. 319-327.
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Pathosystems describe the relationships between parasites, hosts and the environment. Generally these systems remain in a dynamic equilibrium over time. In this review we examine some of the evidence for the potential impacts of change in dynamic equilibrium in blue carbon ecosystems and the relationships to the amount of stored carbon. Blue carbon ecosystems are marine and estuarine ecosystems along the coasts. Virulent pathogens can be introduced into ecosystems along with non-native hosts. Alteration of environmental conditions, such as temperature, pH and salinity, may cause parasites to dominate the pathosystems resulting in significant decreases in productivity and population sizes of producer hosts and in changes in the overall species composition and function in these ecosystems. Such changes in blue carbon ecosystems may result in accelerated release of carbon dioxide back into the ocean and atmosphere, which could then drive further changes in the global climate. The resiliency of these ecosystems is not known. However, recent evidence suggests that significant proportions of blue carbon ecosystems have already disappeared.

Gobler, CJ, Lobanov, AV, Tang, Y, Turanov, AA, Zhang, Y, Doblin, MA, Taylor, GT, Sanudo-Wilhelm, SA, Grigoriev, IV & Gladyshev, VN 2013, 'The central role of selenium in the biochemistry and ecology of the harmful pelagophyte, Aureococcus anophagefferens', The ISME Journal, vol. 7, no. 7, pp. 1333-1343.
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The trace element selenium (Se) is required for the biosynthesis of selenocysteine (Sec), the 21st amino acid in the genetic code, but its role in the ecology of harmful algal blooms (HABs) is unknown. Here, we examined the role of Se in the biology and ecology of the harmful pelagophyte, Aureococcus anophagefferens, through cell culture, genomic analyses and ecosystem studies. This organism has the largest and the most diverse selenoproteome identified to date that consisted of at least 59 selenoproteins, including known eukaryotic selenoproteins, selenoproteins previously only detected in bacteria, and novel selenoproteins. The A. anophagefferens selenoproteome was dominated by the thioredoxin fold proteins and oxidoreductase functions were assigned to the majority of detected selenoproteins. Insertion of Sec in these proteins was supported by a unique Sec insertion sequence. Se was required for the growth of A. anophagefferens as cultures grew maximally at nanomolar Se concentrations. In a coastal ecosystem, dissolved Se concentrations were elevated before and after A. anophagefferens blooms, but were reduced by 495% during the peak of blooms to 0.05 nM. Consistent with this pattern, enrichment of seawater with selenite before and after a bloom did not affect the growth of A. anophagefferens, but enrichment during the peak of the bloom significantly increased population growth rates. These findings demonstrate that Se inventories, which can be anthropogenically enriched, can support proliferation of HABs, such as A. anophagefferens through its synthesis of a large arsenal of Se-dependent oxidoreductases that fine-tune cellular redox homeostasis.

Grob, C, Ostrowski, M, Holland, RJ, Heldal, M, Norland, S, Erichsen, ES, Blindauer, C, Martin, AP, Zubkov, MV & Scanlan, DJ 2013, 'Elemental composition of natural populations of key microbial groups in Atlantic waters', ENVIRONMENTAL MICROBIOLOGY, vol. 15, no. 11, pp. 3054-3064.
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Gupta, V, Trivedi, N, Kumar, M, Reddy, CRK & Jha, B 2013, 'Purification and characterization of exo-beta-agarase from an endophytic marine bacterium and its catalytic potential in bioconversion of red algal cell wall polysaccharides into galactans', BIOMASS & BIOENERGY, vol. 49, pp. 290-298.
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Gustafsson, MS, Baird, ME & Ralph, PJ 2013, 'The interchangeability of autotrophic and heterotrophic nitrogen sources in Scleractinian coral symbiotic relationships: A numerical study', Ecological Modelling, vol. 250, pp. 183-194.
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The success of corals in tropical oligotrophic waters depends largely on their symbiotic relationship with the dinoflagellate algae residing in their tissues. Understanding the dynamics of this symbiosis is essential to predict how corals respond to environmental stressors, such as changes in nutrients availability, water temperatures and irradiance. This study presents a numerical model of the symbiotic relationship between a heterotrophic coral (cnidarian) host and autotrophic symbiotic dinoflagellates, including the major metabolic and physical functions of the system, under non-bleaching conditions. The coral acquires nitrogen (N) through two processes, uptake of dissolved inorganic nitrogen (VH DIN) and heterotrophic feeding (ZN). Numerical experiments were used to highlight the importance of these different sources of N for coral survival and growth. The model was analyzed for four external nutrient supply scenarios, using combinations of two VH DIN rates (high and low) and two ZN rates (high and low), and for a range of light levels. The model outputs showed the importance of the algae symbionts to the coral host as a source of both N and C when the feeding rate was limited, with heterotrophic feeding providing only 14% of the N needed to sustain the host biomass for the low ZN + high VH DIN scenario. In contrast, with no light or low light, conditions under which the symbiont population dies, the host was able to survive if ZN was high. Living inside the host the symbiont population thrived as long as there was enough light, as well as, DIN and DIC in the host tissues, independent of whether N was supplied as ZN or VH DIN. Translocation and recycling of nutrient were two of the most important features of this model, emphasizing why it is essential to resolve host and symbiont in a coral model. The model highlights that the interchangeability of N sources, and the ability to exchange and recycle nutrients in the host-symbiont system, is the key to coral su...

Hildebrand, M, Abbriano, RM, Polle, JE, Traller, JC, Trentacoste, EM, Smith, SR & Davis, AK 2013, 'Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production', CURRENT OPINION IN CHEMICAL BIOLOGY, vol. 17, no. 3, pp. 506-514.
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Hong, Y, Burford, MA, Ralph, PJ, Udy, JW & Doblin, MA 2013, 'The cyanobacterium Cylindrospermopsis raciborskii is facilitated by copepod selective grazing', Harmful Algae, vol. 29, no. 1, pp. 14-21.
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Blooms of the toxin-producing cyanobacterium Cylindrospermopsis raciborskii occur in tropical and subtropical lakes during spring-summer but the mechanisms behind bloom formation are unclear. This study tests the hypothesis that C. raciborskii accumulations in freshwater systems are facilitated by selective copepod grazing. Prey selection was examined in a series of experiments with C. raciborskii and the green alga, Chlamydomonas reinhardtii, as well as within natural phytoplankton assemblages. Clearance rates of the copepod Boeckella sp. on a C. raciborskii diet were 24 times lower than that of a common cladoceran Ceriodaphnia sp. when both grazers had prey choice. More C. raciborskii was cleared by Boeckella sp. when in mixed natural phytoplankton assemblages, but the clearance rate declined when nutrient replete C. reinhardtii was added, demonstrating that when alternate high quality algae were present, so did C. raciborskii consumption. The clearance rates of Boeckella sp. on two toxic C. raciborskii strains were significantly lower than on a non-toxic strain, and on C. raciborskii with low cellular P content. When we tested the grazing preference of a copepod dominated mixed zooplankton community on C. raciborskii during the early bloom period, clearance rates were relatively low (0.050.20 ml individual-1 h-1), and decreased significantly as the proportion of C. raciborskii increased above 5%. These results suggest that C. raciborskii persistence could be promoted by copepods preferentially grazing on other algae, with significant loss of top-down control as C. raciborskii abundance increases.

Hoppenrath, M, Chomerat, N, Horiguchi, T, Schweikert, M, Nagahama, Y & Murray, SA 2013, 'Taxonomy and phylogeny of the benthic Prorocentrum species (Dinophyceae) - A proposal and review', Harmful Algae, vol. 27, no. 1, pp. 1-28.
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Based on a literature review and new morphological and molecular phylogenetic data, a summary of all described benthic Prorocentrum species is presented. Short descriptions of the 29 species are provided including information and illustrations of platelet pattern. Increasing morphological data of the same taxon from different sites has revealed unexpected morphological variability. The variability of characters used for taxonomy is discussed. Many of these may be more variable than previously thought or phenotypically plastic. We conclude that the following features are constant within a species: (1) asymmetry or symmetry of the theca in combination with (2) the shape of the periflagellar area visible on the right thecal plate, (a) arc-shaped, (b) wide or simply V-shaped, (c) narrow and deep V-shaped, and (d) linear. At the same time, we are now beginning to understand that the cell shape of some species is more variable than thought and not in others. The stability of pore patterns is not known to date nor is it known whether the presence of a starch sheath is a reliable taxonomic character. The morphology of the periflagellar area might be a very useful character. The unstable terminology to describe similar or identical structures has made it difficult to interpret the literature on these features.

Jakobsen, TH, Hansen, MA, Jensen, PO, Hansen, L, Riber, L, Cockburn, A, Kolpen, M, Hansen, CR, Ridderberg, W, Eickhardt, S, Hansen, M, Kerpedjiev, P, Alhede, M, Qvortrup, K, Burmolle, M, Moser, C, Kuhl, M, Ciofu, O, Givskov, M, Sorensen, SJ, Hoiby, N & Bjarnsholt, T 2013, 'Complete Genome Sequence of the Cystic Fibrosis Pathogen Achromobacter xylosoxidans NH44784-1996 Complies with Important Pathogenic Phenotypes', PLOS ONE, vol. 8, no. 7.
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Klatt, CG, Liu, Z, Ludwig, M, Kuhl, M, Jensen, SI, Bryant, DA & Ward, DM 2013, 'Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring', ISME Journal, vol. 7, no. 1, pp. 1775-1789.
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Filamentous anoxygenic phototrophs (FAPs) are abundant members of microbial mat communities inhabiting neutral and alkaline geothermal springs. Natural populations of FAPs related to Chloroflexus spp. and Roseiflexus spp. have been well characterized in Mushroom Spring, where they occur with unicellular cyanobacteria related to Synechococcus spp. strains A and B0. Metatranscriptomic sequencing was applied to the microbial community to determine how FAPs regulate their gene expression in response to fluctuating environmental conditions and resource availability over a diel period. Transcripts for genes involved in the biosynthesis of bacteriochlorophylls (BChls) and photosynthetic reaction centers were much more abundant at night. Both Roseiflexus spp. and Chloroflexus spp. expressed key genes involved in the 3-hydroxypropionate (3-OHP) carbon dioxide fixation bi-cycle during the day, when these FAPs have been thought to perform primarily photoheterotrophic and/or aerobic chemoorganotrophic metabolism. The expression of genes for the synthesis and degradation of storage polymers, including glycogen, polyhydroxyalkanoates and wax esters, suggests that FAPs produce and utilize these compounds at different times during the diel cycle. We summarize these results in a proposed conceptual model for temporal changes in central carbon metabolism and energy production of FAPs living in a natural environment. The model proposes that, at night, Chloroflexus spp. and Roseiflexus spp. synthesize BChl, components of the photosynthetic apparatus, polyhydroxyalkanoates and wax esters in concert with fermentation of glycogen. It further proposes that, in daytime, polyhydroxyalkanoates and wax esters are degraded and used as carbon and electron reserves to support photomixotrophy via the 3-OHP bi-cycle.

Kolpen, M, Bjarnsholt, T, Hansen, CR, Dalboge, CS, Kuhl, M, Hoiby, N & Jensen, PO 2013, 'DENITRIFICATION BY CYSTIC FIBROSIS PATHOGENS', PEDIATRIC PULMONOLOGY, vol. 48, pp. 316-316.

Kopp, C, Pernice, M, Domart-Coulon, I, Djediat, C, Spangenberg, JE, Alexander, DTL, Hignette, M, Meziane, T & Meibom, A 2013, 'Highly Dynamic Cellular-Level Response of Symbiotic Coral to a Sudden Increase in Environmental Nitrogen', MBIO, vol. 4, no. 3.
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Kramer, W, Schrameyer, V, Hill, R, Ralph, PJ & Bischof, K 2013, 'PSII Activity And Pigment Dynamics Of Symbiodinium In Two Indo-pacific Corals Exposed To Short-term High-light Stress', Marine Biology, vol. 160, no. 3, pp. 563-577.
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This study examined the capacity for photoprotection and repair of photo-inactivated photosystem II in the same Symbiodinium clade associated with two coexisting coral species during high-light stress in order to test for the modulation of the symbionts photobiological response by the coral host. After 4 days exposure to in situ irradiance, symbionts of the bleaching-sensitive Pocillopora damicornis showed rapid synthesis of photoprotective pigments (by 44 %) and strongly enhanced rates of xanthophyll cycling (by 446 %) while being insufficient to prevent photoinhibition (sustained loss in F v/F m at night) and loss of symbionts after 4 days. By contrast, Pavona decussata showed no significant changes in F v/F m, symbiont density or xanthophyll cycling. Given the association with the same Symbiodinium clade in both coral species, our findings suggest that symbionts in the two species examined may experience different in hospite light conditions as a result of different biometric properties of the coral host.

Krug, LA, Gherardi, DF, Stech, JL, Leão, ZM, Kikuchi, RK, Junior, ER & Suggett, DJ 2013, 'The construction of causal networks to estimate coral bleaching intensity', Environmental Modelling & Software, vol. 42, no. 1, pp. 157-167.
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Current metrics for predicting bleaching episodes, e.g. NOAA's Coral Reef Watch Program, do not seem to apply well to Brazil's marginal reefs located in Bahia state and alternative predictive approaches must be sought for effective long term management.

Kumar, M, Reddy, CRK & Jha, B 2013, 'The ameliorating effect of Acadian marine plant extract against ionic liquids-induced oxidative stress and DNA damage in marine macroalga Ulva lactuca.', Journal of Applied Phycology, vol. 25, no. 2, pp. 369-378.
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Ionic liquids (ILs) are generally considered as the green replacement for conventional volatile organic solvents. Nonetheless, their high solubility in water with proven toxic effects on aquatic biota has questioned their green credentials. In the present study, the detoxification potential of Acadian marine plant extract powder (AMPEP) prepared from the brown alga Ascophyllum nodosum was investigated against the 1-alkyl-3-methylimidazolium bromide [C12mim]Br ionic liquid-induced toxicity and oxidative stress in marine macroalga Ulva lactuca. The IL ([C12mim]Br) at LC50 (70 μM) exposure triggered the generation of reactive oxygen species (ROS) such as O 2 ·− , H2O2 and OH· causing membrane and DNA damage together with inhibition of antioxidant systems in the alga. The supplementation of AMPEP (150 μg mL−1) to the culture medium significantly reduced the accumulation of ROS and lipid peroxidation together with the inhibition of lipoxygenase (LOX) activity specially LOX-2 and LOX-3 isoforms. This is for the first time wherein comet assay was performed to ascertain the protective role of AMPEP against DNA damage in algal tissue grown in medium supplemented with IL and AMPEP. The AMPEP showed protective role against DNA damage (5–45 % tail DNA) when compared to those of grown in IL alone (45–70 % tail DNA). Further, specific isomorphs of different antioxidant enzymes such as superoxide dismutase (Mn-SOD-1, ~150 kDa), ascorbate peroxidase (APX-4, ~55 kDa), glutathione peroxidase (GSH-Px-2, ~55 kDa) and glutathione reductase (GR-1, ~180 kDa) responded specifically to AMPEP supplementation. It is evident from these findings that AMPEP could possibly be used for circumventing the negative effects arising from ILs-induced toxicity in marine ecosystem.

Kuzhiumparambil, U & Fu, S 2013, 'Effect of hydrogen peroxide oxidation systems on human urinary steroid profiles', Analytical Methods, vol. 5, no. 17, pp. 4402-4408.
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In sports drug testing the steroid profile is the most versatile and informative screening tool for the detection of steroid abuse. Despite the introduction of observed urine collection procedures by the World Anti-Doping Agency (WADA), chemical manipulation of urine specimens by athletes to conceal drug use still occurs and poses an ongoing challenge for doping control laboratories worldwide. In vitro urine adulteration using highly oxidative chemicals have been reported several times in the past. In this study we report the effect of two oxidising agents, Fenton's reagent and peroxidaseperoxide system on the human urinary steroid profile. Varying concentrations of these oxidants were reacted with urine and the reactions monitored by gas chromatography-mass spectrometry. A significant decrease in the absolute concentrations of androsterone, etiocholanolone, 5a-androstane-3a,17ß-diol, 5ß-androstane-3a,17ß-diol and epitestosterone was observed with consequent alteration of the steroid profile ratios. Adulteration of urine sample with these oxidants can thus mask the abnormality in a steroidal profile following steroid abuse. Drug testing authorities should take into account the effects of these oxidizing adulterants while interpreting the steroid profile data for doping control purposes.

Kuzhiumparambil, U & Fu, S 2013, 'Effect of oxidizing adulterants on human urinary steroid profiles', Steroids, vol. 78, no. 2, pp. 288-296.
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Steroid profiling is the most versatile and informative technique adapted by doping control laboratories for detection of steroid abuse. The absolute concentrations and ratios of endogenous steroids including testosterone, epitestosterone, androsterone, etiocholanolone, 5a-androstane-3a,17ß-diol and 5ß-androstane-3a,17ß-diol constitute the significant characteristics of a steroid profile. In the present study we report the influence of various oxidizing adulterants on the steroid profile of human urine. Gas chromatographymass spectrometry analysis was carried out to develop the steroid profile of human male and female urine. Oxidants potassium nitrite, sodium hypochlorite, potassium permanganate, cerium ammonium nitrate, sodium metaperiodate, pyridinium chlorochromate, potassium dichromate and potassium perchlorate were reacted with urine at various concentrations and conditions and the effect of these oxidants on the steroid profile were analyzed. Most of the oxidizing chemicals led to significant changes in endogenous steroid profile parameters which were considered stable under normal conditions. These oxidizing chemicals can cause serious problems regarding the interpretation of steroid profiles and have the potential to act as masking agents that can complicate or prevent the detection of the steroid abuse

Lane, N, Martin, WF, Raven, JA & Allen, JF 2013, 'Energy, genes and evolution: introduction to an evolutionary synthesis', PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 368, no. 1622.
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Lawrenz, E, Silsbe, G, Capuzzo, E, Ylostalo, P, Forster, RM, Simis, SG, Prasil, O, Kromkamp, JC, Hickman, AE, Moore, CM, Forget, M, Geider, RJ & Suggett, DJ 2013, 'Predicting the electron requirement for carbon fixation in seas and oceans', Plos One, vol. 8, no. 3, pp. 0-0.
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Marine phytoplankton account for about 50% of all global net primary productivity (NPP). Active fluorometry, mainly Fast Repetition Rate fluorometry (FRRf), has been advocated as means of providing high resolution estimates of NPP. However, not measuring

Lee, LK, Bryant, KJ, Bouveret, R, Lei, P-W, Duff, AP, Harrop, SJ, Huang, EP, Harvey, RP, Gelb, MH, Gray, PP, Curmi, PM, Cunningham, AM, Church, WB & Scott, KF 2013, 'Selective Inhibition of Human Group IIA-secreted Phospholipase A2(hGIIA) Signaling Reveals Arachidonic Acid Metabolism Is Associated with Colocalization of hGIIA to Vimentin in Rheumatoid Synoviocytes', Journal of Biological Chemistry, vol. 288, no. 21, pp. 15269-15279.
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Lefay, C, Guillaneuf, Y, Moreira, G, Thevarajah, JJ, Castignolles, P, Ziarelli, F, Bloch, E, Major, M, Charles, L, Gaborieau, M, Bertina, D & Gigmes, D 2013, 'Heterogeneous modification of chitosan via nitroxide-mediated polymerization', POLYMER CHEMISTRY, vol. 4, no. 2, pp. 322-328.
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Liengaard, L, Nielsen, LP, Revsbech, NP, Prieme, A, Elberling, B, Enrich-Prast, A & Kuhl, M 2013, 'Extreme emission of N2O from tropical wetland soil (Pantanal, South America)', Frontiers in Microbiology, vol. Jan, pp. 1-13.
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Nitrous oxide (N2O) is an important greenhouse gas and ozone depleter, but the global budget of N2O remains unbalanced. Currently, ~25% of the global N2O emission is ascribed to uncultivated tropical soils, but the exact locations and controlling mechanisms are not clear. Here we present the first study of soil N2O emission from the Pantanal indicating that this South American wetland may be a significant natural source of N2O. At three sites, we repeatedly measured in situ fluxes of N2O and sampled porewater nitrate (NO3-) during the low water season in 2008 and 2009. In 2010, 10 sites were screened for in situ fluxes of N2O and soil NO3- content. The in situ fluxes of N2O were comparable to fluxes from heavily fertilized forests or agricultural soils.

Ma, X, Huete, A, Yu, Q, Restrepo Coupe, N, Davies, KP, Broich, M, Ratana, P, Beringer, J, Hutley, LB, Cleverly, J, Boulain, NP & Eamus, D 2013, 'Spatial patterns and temporal dynamics in savanna vegetation phenology across the North Australian Tropical Transect', Remote Sensing of Environment, vol. 139, no. 1, pp. 97-115.
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The phenology of a landscape is a key parameter in climate and biogeochemical cycle models and its correct representation is central to the accurate simulation of carbon, water and energy exchange between the land surface and the atmosphere. Whereas biogeographic phenological patterns and shifts have received much attention in temperate ecosystems, much less is known about the phenology of savannas, despite their sensitivity to climate change and their coverage of approximately one eighth of the global land surface. Savannas are complex assemblages of multiple tree, shrub, and grass vegetation strata, each with variable phenological responses to seasonal climate and environmental variables. The objectives of this study were to investigate biogeographical and inter-annual patterns in savanna phenology along a 1100 km ecological rainfall gradient, known as North Australian Tropical Transect (NATT), encompassing humid coastal Eucalyptus forests and woodlands to xeric inland Acacia woodlands and shrublands. Key phenology transition dates (start, peak, end, and length of seasonal greening periods) were extracted from13 years (20002012) of Moderate Resolution Imaging Spectroradiometer (MODIS) Enhanced Vegetation Index (EVI) data using Singular Spectrum Analysis (SSA). Two distinct biogeographical patterns in phenology were observed, controlled by different climate systems. The northern (mesic) portion of the transect, from 12°S, to around 17.7°S, was influenced by the Inter-Tropical Convergence Zone (ITCZ) seasonal monsoon climate system, resulting in strong latitudinal shifts in phenology patterns, primarily associated with the functional response of the C4 grass layer.

Manfrino, C, Jacoby, CA, Camp, E & Frazer, TK 2013, 'A positive trajectory for corals at Little Cayman Island.', PLoS ONE, vol. 8, no. 10, pp. e75432-e75432.
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Coral reefs are damaged by natural disturbances and local and global anthropogenic stresses. As stresses intensify, so do debates about whether reefs will recover after significant damage. True headway in this debate requires documented temporal trajectories for coral assemblages subjected to various combinations of stresses; therefore, we report relevant changes in coral assemblages at Little Cayman Island. Between 1999 and 2012, spatiotemporal patterns in cover, densities of juveniles and size structure of assemblages were documented inside and outside marine protected areas using transects, quadrats and measurements of maximum diameters. Over five years, bleaching and disease caused live cover to decrease from 26% to 14%, with full recovery seven years later. Juvenile densities varied, reaching a maximum in 2010. Both patterns were consistent within and outside protected areas. In addition, dominant coral species persisted within and outside protected areas although their size frequency distributions varied temporally and spatially. The health of the coral assemblage and the similarity of responses across levels of protection suggested that negligible anthropogenic disturbance at the local scale was a key factor underlying the observed resilience.

McGinley, MP, Suggett, DJ & Warner, ME 2013, 'Transcript patterns of chloroplast-encoded genes in cultured Symbiodinium spp. (Dinophyceae): testing the influence of a light shift and diel periodicity', Journal of Phycology, vol. 49, no. 4, pp. 709-718.
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Microalgae possess numerous cellular mechanisms specifically employed for acclimating the photosynthetic pathways to changes in the physical environment. Despite the importance of coral-dinoflagellate symbioses, little focus has been given as to how the symbiotic algae (Symbiodinium spp.) regulate the expression of their photosynthetic genes. This study used real-time PCR to investigate the transcript abundance of the plastid-encoded genes, psbA (encoding the D1 protein of photosystem II) and psaA (encoding the P700 protein in photosystem I), within the cultured Symbiodinium ITS-2 (internal transcribed spacer region) types A20 and A13. Transcript abundance was monitored during a low to high-light shift, as well as over a full diel light cycle. In addition, psaA was characterized in three isolates (A20, A13, and D4-5) and noted as another example of a dinoflagellate plastid gene encoded on a minicircle. In general, the overall incongruence of transcript patterns for both psbA and psaA between the Symbiodinium isolates and other models of transcriptionally controlled chloroplast gene expression (e.g., Pisum sativum [pea], Sinapis alba [mustard seedling], and Synechocystis sp. PCC 6803 [cyanobacteria]) suggests that Symbiodinium is reliant on posttranscriptional mechanisms for homeostatic regulation of its photosynthetic proteins.

Mitchell, J, Seuront, L, Doubell, M, Losic, D, Voelcker, N, Seymour, JR & Lal, R 2013, 'The Role Of Diatom Nanostructures In Biasing Diffusion To Improve Uptake In A Patchy Nutrient Environment', PLoS One, vol. 8, no. 5, pp. 1-9.
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Background Diatoms are important single-celled autotrophs that dominate most lit aquatic environments and are distinguished by surficial frustules with intricate designs of unknown function. Principal Findings We show that some frustule designs constrain diffusion to positively alter nutrient uptake. In nutrient gradients of 4 to 160 times over <5 cm, the screened-chambered morphology of Coscincodiscus sp. biases the nutrient diffusion towards the cell by at least 3.8 times the diffusion to the seawater. In contrast, the open-chambers of Thalassiosira eccentrica produce at least a 1.3 times diffusion advantage to the membrane over Coscincodiscus sp. when nutrients are homogeneous. Significance Diffusion constraint explains the success of particular diatom species at given times and the overall success of diatoms. The results help answer the unresolved question of how adjacent microplankton compete. Furthermore, diffusion constraint by supramembrane nanostructures to alter molecular diffusion suggests that microbes compete via supramembrane topology, a competitive mechanism not considered by the standard smooth-surface equations used for nutrient uptake nor in microbial ecology and cell physiology.

Mnatsakanyan, M, Thevarajah, JJ, Roi, RS, Lauto, A, Gaborieau, M & Castignolles, P 2013, 'Separation of chitosan by degree of acetylation using simple free solution capillary electrophoresis', ANALYTICAL AND BIOANALYTICAL CHEMISTRY, vol. 405, no. 21, pp. 6873-6877.
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O'Brien, CJ, Peloquin, JA, Vogt, M, Heinle, M, Gruber, N, Ajani, P, Andruleit, H, Aristegui, J, Beaufort, L, Estrada, M, Karentz, D, Kopczynska, E, Lee, R, Poulton, AJ, Pritchard, T & Widdicombe, C 2013, 'Global marine plankton functional type biomass distributions: coccolithophores', EARTH SYSTEM SCIENCE DATA, vol. 5, no. 2, pp. 259-276.
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O'Malley-James, JT, Greaves, JS, Raven, JA & Cockell, CS 2013, 'Swansong biospheres: Refuges for life and novel microbial biospheres on terrestrial planets near the end of their habitable lifetimes', International Journal of Astrobiology, vol. 12, no. 2, pp. 99-112.
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The future biosphere on Earth (as with its past) will be made up predominantly of unicellular micro-organisms. Unicellular life was probably present for at least 2.5 Gyr before multicellular life appeared and will likely be the only form of life capable of surviving on the planet in the far future, when the ageing Sun causes environmental conditions to become more hostile to more complex forms of life. Therefore, it is statistically more likely that habitable Earth-like exoplanets we discover will be at a stage in their habitable lifetime more conducive to supporting unicellular, rather than multicellular life. The end stage of habitability on Earth is the focus of this work. A simple, latitude-based climate model incorporating eccentricity and obliquity variations is used as a guide to the temperature evolution of the Earth over the next 3 Gyr. This allows inferences to be made about potential refuges for life, particularly in mountains and cold-trap (ice) caves and what forms of life could live in these environments. Results suggest that in high latitude regions, unicellular life could persist for up to 2.8 Gyr from present. This begins to answer the question of how the habitability of Earth will evolve at local scales alongside the Sun's main sequence evolution and, by extension, how the habitability of Earth-like planets would evolve over time with their own host stars

Orr, RJ, Stuken, A, Murray, SA & Jakobsen, KS 2013, 'Evolutionary acquisition and loss of saxitoxin biosynthesis in dinoflagellates: the second "core" gene, sxtG', Applied and Environmental Microbiology, vol. 79, no. 7, pp. 2128-2136.
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Saxitoxin and its derivatives are potent neurotoxins produced by several cyanobacteria and dinoflagellate species. SxtA is the initial enzyme in the biosynthesis of saxitoxin. The dinoflagellate full mRNA and partial genomic sequences have previously been characterized, and it appears that sxtA originated in dinoflagellates through a horizontal gene transfer from a bacterium. So far, little is known about the remaining genes involved in this pathway in dinoflagellates. Here we characterize sxtG, an amidinotransferase enzyme gene that putatively encodes the second step in saxitoxin biosynthesis. In this study, the entire sxtG transcripts from Alexandrium fundyense CCMP1719 and Alexandrium minutum CCMP113 were amplified and sequenced. The transcripts contained typical dinoflagellate spliced leader sequences and eukaryotic poly(A) tails. In addition, partial sxtG transcript fragments were amplified from four additional Alexandrium species and Gymnodinium catenatum. The phylogenetic inference of dinoflagellate sxtG, congruent with sxtA, revealed a bacterial origin. However, it is not known if sxtG was acquired independently of sxtA. Amplification and sequencing of the corresponding genomic sxtG region revealed noncanonical introns. These introns show a high interspecies and low intraspecies variance, suggesting multiple independent acquisitions and losses. Unlike sxtA, sxtG was also amplified from Alexandrium species not known to synthesize saxitoxin. However, amplification was not observed for 22 non-saxitoxin-producing dinoflagellate species other than those of the genus Alexandrium or G. catenatum. This result strengthens our hypothesis that saxitoxin synthesis has been secondarily lost in conjunction with sxtA for some descendant species.

Orr, RJ, Stüken, A, Murray, SA & Jakobsen, KS 2013, 'Evolution and distribution of saxitoxin biosynthesis in dinoflagellates', Marine Drugs, vol. 11, no. 8, pp. 2814-2828.
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Numerous species of marine dinoflagellates synthesize the potent environmental neurotoxic alkaloid, saxitoxin, the agent of the human illness, paralytic shellfish poisoning. In addition, certain freshwater species of cyanobacteria also synthesize the same toxic compound, with the biosynthetic pathway and genes responsible being recently reported. Three theories have been postulated to explain the origin of saxitoxin in dinoflagellates: The production of saxitoxin by co-cultured bacteria rather than the dinoflagellates themselves, convergent evolution within both dinoflagellates and bacteria and horizontal gene transfer between dinoflagellates and bacteria. The discovery of cyanobacterial saxitoxin homologs in dinoflagellates has enabled us for the first time to evaluate these theories. Here, we review the distribution of saxitoxin within the dinoflagellates and our knowledge of its genetic basis to determine the likely evolutionary origins of this potent neurotoxin

Petrou, K, Jimenez-denness, I, Chartrand, KM, Mccormack, C, Rasheed, M & Ralph, PJ 2013, 'Seasonal heterogeneity in the photophysiological response to air exposure in two tropical intertidal seagrass species', Marine Ecology Progress Series, vol. 482, pp. 93-106.
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Photosynthesis, chlorophyll a fluorescence, leaf bio-optical properties and pigments were measured in 2 tropical intertidal seagrass species, Zostera muelleri ssp. capricorni and Halophila ovalis before, during and after air-exposure over a tidal cycle. Data were collected across 4 seasons (October and January-growing seasons; May and July-senescent seasons) to determine seasonal dynamics in physiological responses to air exposure. Both species showed clear light-dependent responses with a decline in photosynthetic efficiency and increased photoprotection during periods of combined maximum daily irradiance and air exposure for all seasons. In Z. muelleri ssp. capricorni there was a negative correlation between air-exposed effective quan - tum yield and light intensity, suggesting exposure was driving this decline. Conversely, sensitivity (decline in effective quantum yield of photosystem II) to increased irradiance dominated the response in H. ovalis, with no change in the magnitude of this response between air-exposed and submerged blades. The response to air exposure observed in Z. muelleri ssp. capricorni showed seasonal variation, with a greater decline in photosynthesis during the spring (October). Tidal exposure did not provide intertidal seagrasses a 'window' of photosynthetic respite (increase in photosynthesis) from high natural or anthropogenic turbidity. However, the periods immediately prior to and after exposure were important for providing an optimum period for net photosynthetic gain.

Raina, J, Tapiolas, DM, Foret, S, Lutz, A, Abrego, D, Ceh, J, Seneca, FO, Clode, PL, Bourne, DG, Willis, BL & Motti, CA 2013, 'DMSP biosynthesis by an animal and its role in coral thermal stress response', Nature, vol. 502, pp. 677-680.
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Globally, reef-building corals are the most prolific producers of dimethylsulphoniopropionate (DMSP)1,2, a central molecule in the marine sulphur cycle and precursor of the climate-active gas dimethylsulphide3,4. At present, DMSP production by corals is attributed entirely to their algal endosymbiont, Symbiodinium2. Combining chemical, genomic and molecular approaches, we show that coral juveniles produce DMSP in the absence of algal symbionts. DMSP levels increased up to 54% over time in newly settled coral juveniles lacking algal endosymbionts, and further increases, up to 76%, were recorded when juveniles were subjected to thermal stress. We uncovered coral orthologues of two algal genes recently identified in DMSP biosynthesis, strongly indicating that corals possess the enzymatic machinery necessary for DMSP production. Our results overturn the paradigm that photosynthetic organisms are the sole biological source of DMSP, and highlight the double jeopardy represented by worldwide declining coral cover, as the potential to alleviate thermal stress through coral-produced DMSP declines correspondingly.

Raven, J 2013, 'Polar auxin transport in relation to long-distance transport of nutrients in the Charales', Journal Of Experimental Botany, vol. 64, no. 1, pp. 1-9.
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This paper examines the significance of the recent demonstration of polar auxin transport (PAT) in the green macroalga Chara (Charophyceae: Charales) and, especially, options for explaining some features of PAT in the Charales. The occurrence of PAT in the Charales shows that PAT originated in the algal ancestors of the embryophytes (liverworts, mosses, hornworts, and vascular plants), although it is not yet known if PAT occurs elsewhere in the Charophyceae or in other algae. While in the embryophytes PAT occurs in parenchymatously constructed structures which commonly also have xylem and phloem (or their bryophyte analogues) as long-distance transport processes in parallel to PAT, in Chara corallina PAT shares the pathway for long-distance transport of nutrients though the parenchymatously constructed nodal complexes and the single giant cells of the internode. The speed of auxin movement of PAT is much more rapid than that attributable to diffusion and of the same order as the rate of cytoplasmic streaming in the giant internodal cells, yet complete inhibition of streaming by the inhibitor cytochalasin H does not slow down auxin transport. Explanations for this phenomenon are sought in the operation of other mechanochemical motors, dyneinâtubulin and kinesinâtubulin, as alternatives to the myosinâactin system which powers cytoplasmic streaming. Experiments in which microtubules are disrupted, for example by colchicine, could show if one of the tubulin-based motors is involved. If these motors are involved, some mechanism is needed to amplify the speeds known for the motors to explain the order of magnitude higher speeds seen for auxin transport.

Raven, J, Beardall, J, Larkum, A & Sanchez-baracaldo, P 2013, 'Interactions of photosynthesis with genome size and function', Philosophical Transactions of the Royal Society B, vol. 368, no. 1622, pp. 1-11.
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Photolithotrophs are divided between those that use water as their electron donor (Cyanobacteria and the photosynthetic eukaryotes) and those that use a different electron donor (the anoxygenic photolithotrophs, all of them Bacteria). Photolithotrophs wi

Raven, JA 2013, 'Cells inside Cells: Symbiosis and Continuing Phagotrophy', CURRENT BIOLOGY, vol. 23, no. 12, pp. R530-R531.
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Raven, JA 2013, 'Iron acquisition and allocation in stramenopile algae', JOURNAL OF EXPERIMENTAL BOTANY, vol. 64, no. 8, pp. 2119-2127.
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Raven, JA 2013, 'RNA function and phosphorus use by photosynthetic organisms', FRONTIERS IN PLANT SCIENCE, vol. 4.
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Raven, JA 2013, 'Rubisco: still the most abundant protein of Earth?', NEW PHYTOLOGIST, vol. 198, no. 1, pp. 1-3.
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Raven, JA 2013, 'Rubisco: still the most abundant protein of Earth? (vol 198, pg 1, 2013)', NEW PHYTOLOGIST, vol. 198, no. 3, pp. 970-970.
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Raven, JA 2013, 'The evolution of autotrophy in relation to phosphorus requirement', JOURNAL OF EXPERIMENTAL BOTANY, vol. 64, no. 13, pp. 4023-4046.
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Restrepo Coupe, N, Rocha, HR, Hutyra, LR, Araujo, AC, Borma, LS, Christoffersen, B, Cabral, OM, de Camargo, PB, Cardoso, FL, Costa, AC, Fitzjarrald, DR, Goulden, ML, Kruijt, B, Maia, JM, Malhi, YS, Manzi, AO, Miller, SD, Nobre, AD, von Randow, C, Sa, LD, Sakai, RK, Tota, J, Wofsy, SC, Zanchi, FB & Saleska, SR 2013, 'What drives the seasonality of photosynthesis across the Amazon basin? A cross-site analysis of eddy flux tower measurements from the Brasil flux network', Agricultural and Forest Meteorology, vol. 182-183, pp. 128-144.
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We investigated the seasonal patterns of Amazonian forest photosynthetic activity, and the effects thereon of variations in climate and land-use, by integrating data from a network of ground-based eddy flux towers in Brazil established as part of the `Large-Scale Biosphere Atmosphere Experiment in Amazonia project. We found that degree of water limitation, as indicated by the seasonality of the ratio of sensible to latent heat flux (Bowen ratio) predicts seasonal patterns of photosynthesis. In equatorial Amazonian forests (5° N5° S), water limitation is absent, and photosynthetic fluxes (or gross ecosystem productivity, GEP) exhibit high or increasing levels of photosynthetic activity as the dry season progresses, likely a consequence of allocation to growth of new leaves. In contrast, forests along the southern flank of the Amazon, pastures converted from forest, and mixed forest-grass savanna, exhibit dry-season declines in GEP, consistent with increasing degrees of water limitation. Although previous work showed tropical ecosystem evapotranspiration (ET) is driven by incoming radiation, GEP observations reported here surprisingly show no or negative relationships with photosynthetically active radiation (PAR). Instead, GEP fluxes largely followed the phenology of canopy photosynthetic capacity (Pc), with only deviations from this primary pattern driven by variations in PAR. Estimates of leaf flush at three non-water limited equatorial forest sites peak in the dry season, in correlation with high dry season light levels.

Rickelt, LF, Askaer, L, Walpersdorf, E, Elberling, B, Glud, RN & Kuhl, M 2013, 'An optode sensor array for long-term in situ oxygen measurements in soil and sediment', Journal Of Environmental Quality, vol. 42, no. 4, pp. 1267-1273.
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Long-term measurements of molecular oxygen (O2) dynamics in wetlands are highly relevant for understanding the eff ects of water level changes on net greenhouse gas budgets in these ecosystems. However, such measurements have been limited due to a lack of suitable measuring equipment. We constructed an O2 optode sensor array for long-term in situ measurements in soil and sediment. Th e new device consists of a 1.3-m-long, cylindrical, spear-shaped rod equipped with 10 sensor spots along the shaft . Each spot contains a thermocouple fi xed with a robust fi beroptic O2 optode made by immobilizing a layer of Pt(II) meso-tetra(pentafl uorophenyl) porphine in polystyrene at the end of a 2-mm polymethyl methacrylate plastic fi ber. Temperature and O2 optode readings are collected continuously by a data logger and a multichannel fi beroptic O2 meter. Th e construction and measuring characteristics of the sensor array system are presented along with a novel approach for temperature compensation of O2 optodes. During in situ application over several months in a peat bog, we used the new device to document pronounced variations in O2 distribution aft er marked shift s in water level. Th e measurements showed anoxic conditions below the water level but also diel variations in O2 concentrations in the upper layer presumably due to rhizospheric oxidation by the main vegetation Phalaris arundinacea. Th e new fi eld instrument thus enables new and more detailed insights to the in situ O2 dynamics in wetlands.

Roudnew, B, Lavery, T, Seymour, JR, Smith, R & Mitchell, J 2013, 'Spatially Varying Complexity Of Bacterial And Virus-like Particle Communities Within An Aquifer System', Aquatic Microbial Ecology, vol. 68, no. 3, pp. 259-266.
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Hydrological and geological heterogeneity in the subsurface can isolate groundwater bodies in an aquifer system and create hydrologically distinct aquifers overlying each other with varying amounts of water exchange and unknown amounts of biological exchange. The heterogeneous nature of these subsurface waters likely drives changes in groundwater microbiological parameters. In the present study, flow cytometry was used to examine the abundance and cytometrically defined subpopulation structure of bacteria and virus-like particles (VLPs) in 3 distinct, vertically stratified aquifer layers consisting of an unconfined aquifer, a confining layer and a confined aquifer. Despite total microbial abundances remaining constant, the composition of bacterial and VLP communities varied among the aquifer layers. Cytometrically defined subpopulations were defined by nucleic acid content and size and ranged from 1 bacterial and VLP subpopulation in the unconfined aquifer to 4 bacterial and 3 VLP subpopulations in the confined aquifer. This variability in the subpopulation assemblages is likely driven by a combination of hydrological heterogeneity and biological interactions. The results presented here indicate complexity in microbial communities in discrete aquifer layers that may be overlooked when reporting general abundances. Groundwater bacteria and VLPs appear to be a sensitive indicator of the biological dynamics of aquifer systems and may be used to identify heterogeneous water bodies and help distinguish individual aquifer layers in an aquifer system.

Rowe, CC, Bourgeat, P, Ellis, KA, Brown, B, Lim, YY, Mulligan, R, Jones, G, Maruff, P, Woodward, M, Price, R, Robins, P, Tochon-Danguy, H, O'Keefe, G, Pike, KE, Yates, P, Szoeke, C, Salvado, O, Macaulay, SL, O'Meara, T, Head, R, Cobiac, L, Savage, G, Martins, R, Masters, CL, Ames, D & Villemagne, VL 2013, 'Predicting Alzheimer disease with β-amyloid imaging: Results from the Australian imaging, biomarkers, and lifestyle study of ageing', Annals of Neurology, vol. 74, no. 6, pp. 905-913.
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Sackett, O, Petrou, K, Reedy, B, De Grazia, A, Hill, R, Doblin, M, Beardall, J, Ralph, P & Heraud, P 2013, 'Phenotypic Plasticity of Southern Ocean Diatoms: Key to Success in the Sea Ice Habitat?', PLOS ONE, vol. 8, no. 11.
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Schliep, MT, Cavigliasso, G, Quinnell, RG, Stranger, R & Larkum, A 2013, 'Formyl group modification of chlorophyll a: a major evolutionary mechanism in oxygenic photosynthesis', Plant Cell and Environment, vol. 36, pp. 521-527.
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We discuss recent advances in chlorophyll research in the context of chlorophyll evolution and conclude that some derivations of the formyl side chain arrangement of the porphyrin ring from that of the Chl a macrocycle can extend the photosynthetic active radiation (PAR) of these molecules, for example, Chl d and Chl f absorb light in the near-infrared region, up to ~750 nm. Derivations such as this confer a selective advantage in particular niches and may, therefore, be beneficial for photosynthetic organisms thriving in light environments with particular light signatures, such as red- and near-far-red light-enriched niches. Modelling of formyl side chain substitutions of Chl a revealed yet unidentified but theoretically possible Chls with a distinct shift of light absorption properties when compared to Chl a.

Schmidt, S, Raven, JA & Paungfoo-Lonhienne, C 2013, 'The mixotrophic nature of photosynthetic plants', FUNCTIONAL PLANT BIOLOGY, vol. 40, no. 5, pp. 425-438.
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Sinutok, S, Hill, R, Doblin, MA & Ralph, PJ 2013, 'Diurnal photosynthetic response of the motile symbiotic benthic foraminiferan Marginopora vertebralis', Marine Ecology Progress Series, vol. 478, pp. 127-138.
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Movement of the symbiont-bearing foraminiferan Marginopora vertebralis and photo physiological response to diurnal fluctuations in irradiance were investigated in field and laboratory experiments. The abundance of M. vertebralis from both light-exposed and sheltered habitats was determined 5 times during the day, from pre-dawn to post-dusk. M. vertebralis abundance was significantly higher in sheltered compared to exposed habitats at midday under high irradiance, and this movement enabled the algal symbionts to avoid excessive photoinhibition. The diurnal changes in photosynthetic efficiency were not consistent with the typical midday solar maximum downregulation of photosystem II observed in other photoautotrophs and was likely due to the negatively phototactic capacity of the foraminifera. To confirm the light-dependent movement of foraminifera, individuals in exposed and sheltered habitats were exposed to the photosynthetic inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) in the laboratory. The lack of movement in DCMU-exposed specimens confirmed light-dependent movement and subsequent disruption of signalling between the host foraminiferan and the algal symbionts. Analysis of chlorophyll and xanthophyll pigments, as well as symbiont density, indicated that under high irradiance, foraminiferal symbionts have the capacity to reduce light stress by activating photo-protective mechanisms. The negatively phototactic behaviour prevented chlorophyll degradation, symbiont loss and bleaching, suggesting that it is the primary mechanism for controlling light exposure in these foraminifera. This behaviour provides a competitive advantage over other sessile organisms in avoiding photoinhibition and bleaching by moving away from over-saturating irradiance, towards less damaging light fields.

Smith, R, Jeffries, TC, Roudnew, B, Seymour, JR, Fitch, AJ, Simons, KL, Speck, PG, Newton, K, Brown, MH & Mitchell, JG 2013, 'Confined aquifers as viral reservoirs', Environmental Microbiology Reports, vol. 5, no. 5, pp. 725-730.
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Knowledge about viral diversity and abundance in deep groundwater reserves is limited. We found that the viral community inhabiting a deep confined aquifer in South Australia was more similar to reclaimed water communities than to the viral communities in the overlying unconfined aquifer community. This similarity was driven by high relative occurrence of the single-stranded DNA viral groups Circoviridae, Geminiviridae and Microviridae, which include many known plant and animal pathogens. These groups were present in a 1500-year-old water situated 80?m below the surface, which suggests the potential for long-term survival and spread of potentially pathogenic viruses in deep, confined groundwater. Obtaining a broader understanding of potentially pathogenic viral communities within aquifers is particularly important given the ability of viruses to spread within groundwater ecosystems.

Suggett, DJ, Dong, LF, Lawson, T, Lawrenz, E, Torres, L & Smith, DJ 2013, 'Light availability determines susceptibility of reef building corals to ocean acidification', Coral Reefs, vol. 32, no. 2, pp. 327-337.
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Elevated seawater pCO(2), and in turn ocean acidification (OA), is now widely acknowledged to reduce calcification and growth of reef building corals. As with other environmental factors (e.g., temperature and nutrients), light availability fundamentally

Tamburic, B, Dechatiwongse, P, Zemichael, FW, Maitland, GC & Hellgardt, K 2013, 'Process and reactor design for biophotolytic hydrogen production', Physical Chemistry Chemical Physics, vol. 15, no. 26, pp. 10783-10794.
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The green alga Chlamydomonas reinhardtii has the ability to produce molecular hydrogen (H2), a clean and renewable fuel, through the biophotolysis of water under sulphur-deprived anaerobic conditions. The aim of this study was to advance the development of a practical and scalable biophotolytic H2 production process. Experiments were carried out using a purpose-built flat-plate photobioreactor, designed to facilitate green algal H2 production at the laboratory scale and equipped with a membrane-inlet mass spectrometry system to accurately measure H2 production rates in real time. The nutrient control method of sulphur deprivation was used to achieve spontaneous H2 production following algal growth. Sulphur dilution and sulphur feed techniques were used to extend algal lifetime in order to increase the duration of H2 production. The sulphur dilution technique proved effective at encouraging cyclic H2 production, resulting in alternating Chlamydomonas reinhardtii recovery and H2 production stages. The sulphur feed technique enabled photobioreactor operation in chemostat mode, resulting in a small improvement in H2 production duration. A conceptual design for a large-scale photobioreactor was proposed based on these experimental results. This photobioreactor has the capacity to enable continuous and economical H2 and biomass production using green algae. The success of these complementary approaches demonstrate that engineering advances can lead to improvements in the scalability and affordability of biophotolytic H2 production, giving increased confidence that H2 can fulfil its potential as a sustainable fuel of the future.

Tapiolas, DM, Raina, J, Lutz, A, Willis, BL & Motti, CA 2013, 'Direct measurement of dimethylsulfoniopropionate (DMSP) in reef-building corals using quantitative nuclear magnetic resonance (qNMR) spectroscopy', Journal of Experimental Marine Biology and Ecology, vol. 443, pp. 85-89.
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Reef building corals are among the largest producers of dimethylsulfoniopropionate (DMSP), a sulfur molecule synthesized by their endosymbiotic dinoflagellates in the genus Symbiodinium. DMSP is potentially involved in important physiological and ecological processes in corals, but investigating the functional role of this molecule requires rapid and accurate quantification techniques. Here we introduce a simple method enabling direct quantification of DMSP and one of its breakdown products acrylate using quantitative nuclear magnetic resonance (qNMR) spectroscopy. The method was tested on a range of coral genera and presents a number of advantages over currently used quantification techniques, including simultaneous and direct quantification of multiple molecules from the same extract, and rapid processing with high reproducibility enabling analyses of large numbers of samples in short time periods. The method was successfully applied to environmental samples and provides the first baseline information on diel variation of DMSP and acrylate concentrations in the coral Acropora millepora.

Tetu, SG, Johnson, DA, Varkey, D, Phillippy, K, Stuart, RK, Dupont, CL, Hassan, KA, Palenik, B & Paulsen, IT 2013, 'Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species', FRONTIERS IN MICROBIOLOGY, vol. 4.
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Van Moerkercke, A, Fabris, M, Pollier, J, Baart, GJE, Rombauts, S, Hasnain, G, Rischer, H, Memelink, J, Oksman-Caldentey, K-M & Goossens, A 2013, 'CathaCyc, a Metabolic Pathway Database Built from Catharanthus roseus RNA-Seq Data', PLANT AND CELL PHYSIOLOGY, vol. 54, no. 5, pp. 673-685.
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von Randow, C, Zeri, M, Restrepo Coupe, N, Muza, MN, de Goncalves, LG, Costa, MH, Araujo, AC, Manzi, AO, Rocha, HR, Saleska, SR, Arain, MA, Baker, IT, Cestaro, BP, Christoffersen, B, Ciais, P, Fisher, JB, Galbraith, D, Guan, X, van den Hurk, B, Ichii, K, Imbuzeiro, H, Jain, A, Levine, N, Miguez-Macho, G, Poulter, B, Roberti, DR, Sahoo, A, Schaefer, K, Shi, M, Tian, W, Verbeeck, H & Yang, Z 2013, 'Inter-annual variability of carbon and water fluxes in Amazonian forest, Cerrado and pasture sites, as simulated by terrestrial biosphere models', Agricultural and Forest Meteorology, vol. 182-183, no. 1, pp. 145-155.
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This study analyzes the inter-annual variability (IAV) of simulations of 21 different land surface model formulations, driven by meteorological conditions measured at 8 flux towers, located in rain forest, forest-savanna ecotone and pasture sites in Amazonia, and one in savanna site in Southeastern Brazil. Annual totals of net ecosystem exchange (NEE) of carbon and evapotranspiration (ET), measured and simulated by each model for each site-year, were compared in terms of year-to-year variability and possible relation to climate drivers. Results have shown that most of models simulations for annual totals of NEE and ET, and IAV of these fluxes, are frequently different from measurements. The average of the model simulations of annual fluxes tend to respond to climatic drivers similarly to the observations, but with noticeable discrepancies. Annual measurements of NEE are negatively correlated to annual rainfall in the forest sites group. Although the ensemble of all models yields a similar result, only three model formulations reproduce a significant negative correlation of simulated NEE with rainfall. For the IAV of ET, tower measurements are controlled by annual variations of radiation and this feature is captured by the ensemble of the models, both at individual sites and when all forest sites are grouped. However, simulated ET values are also significantly correlated to the amount of precipitation in many models and in the model ensemble, while there is no significant correlation in the observations. In general, the surface models are able to reproduce the responses of fluxes to climatic drivers, but improvements are still needed to better capture their inter-annual variability

Wang, X-L, Ye, J, Gonzalez Perez, P, Tang, D-M & Huang, D-F 2013, 'The impact of organic farming on the soluble organic nitrogen pool in horticultural soil under open field and greenhouse conditions: a case study', SOIL SCIENCE AND PLANT NUTRITION, vol. 59, no. 2, pp. 237-248.
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Ye, Z, Robakowski, P & Suggett, DJ 2013, 'A mechanistic model for the light response of photosynthetic electron transport rate based on light harvesting properties of photosynthetic pigment molecules', Planta, vol. 237, no. 3, pp. 837-847.
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Models describing the light response of photosynthetic electron transport rate (ETR) are routinely used to determine how light absorption influences energy, reducing power and yields of primary productivity; however, no single model is currently able to

Ye, Z, Suggett, DJ, Robakowski, P & Kang, H 2013, 'A mechanistic model for the photosynthesis-light response based on the photosynthetic electron transport of photosystem II in C3 and C4 species', New Phytologist, vol. 199, no. 1, pp. 110-120.
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A new mechanistic model of the photosynthesis-light response is developed based on photosynthetic electron transport via photosystem II (PSII) to specifically describe light-harvesting characteristics and associated biophysical parameters of photosynthet

York, PH, Gruber, RK, Hill, R, Ralph, PJ, Booth, DJ & Macreadie, PI 2013, 'Physiological and Morphological Responses of the Temperate Seagrass Zostera muelleri to Multiple Stressors: Investigating the Interactive Effects of Light and Temperature', PLOS ONE, vol. 8, no. 10.
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Ajani, P 2013, 'Algal Blooms: the good, the bad and the downright toxic!', Diverse Depths: Sea Beneath the Shallows Forum, Sydney Coastal Council Group.
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Invited Oral presentation

Ajani, P, Allen, AP & Ingleton, T 2013, 'A decadal decline in abundance and a shift in microphytoplankton composition at a long-term coastal station off southeast Australia', Australian Marine Science Association Conference, Gold Coast, QLD, Australia.
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Poster Presentation, Winner Photographic Award

Ajani, P, Armand, L, Murray, S, Brett, S & Hallegraeff, G 2013, 'Morphological, molecular and toxicological characterization of the diatom genus Pseudo-nitzschia in south eastern Australian coastal waters', 9th International Conference on Molluscan Shellfish Safety 2013, International Conference on Molluscan Shellfish Safety, Sydney 2013. Morphological, molecular and toxicological characterization of the diatom genus Pseudo-nitzschia in south eastern Australian coastal waters. P, Sydney, Australia.
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Oral Presentation, Runner Up Best Student Presentation (Oral Presentation - Runner Up Best Student Presentation),

Bretherton, L, Lawson, T, Moore, CM, Poulton, A, Geider, R & Suggett, D 2013, 'LIGHT AVAILABILITY AFFECTS THE OCEAN ACIDIFCATION RESPONSE IN COCCOLITHOPHORES', PHYCOLOGIA, INT PHYCOLOGICAL SOC, pp. 13-13.

Devlin, M, Debose, J, Ajani, P & Brodie, J 2013, 'Chlorophyll biomass and phytoplankton community measures in flood plumes increasing the evidence base between degraded water quality and Crown of Thorns', Australian Marine Science Association Conference, Gold Coast, QLD, Australia.
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Oral Presentation

Howes, JM, Stuart, BH & Ralph, PJ 2013, 'Assessing metabolic variation of endosymbiotic and cultured Symbiodinium microadriaticum using synchrotron imaging FTIR spectroscopy', 7th International Workshop on Infrared Microscopy and Spectroscopy with Accelerator-Based Sources Abstracts, 7th International Workshop on Infrared Microscopy and Spectroscopy with Accelerator-Based Sources.

Howes, JM, Stuart, BH & Ralph, PJ 2013, 'Macromolecular composition varies significantly between genetic clades of Symbiodinium microadriaticum', 10th International Phycological Congress Abstracts, 10th International Phycological Congress.

Lawrenz, E, Huete-Ortega, M, Suggett, DJ & Geider, RJ 2013, 'ASSESSING THE RELATIONSHIPS BETWEEN ELECTRON TRANSFER AND CARBON FIXATION IN NITROGEN LIMITED MARINE PHYTOPLANKTON', PHYCOLOGIA, INT PHYCOLOGICAL SOC, pp. 59-59.

O'Malley-James, JT, Greaves, JS, Raven, JA & Cockell, CS 2013, 'Swansong biospheres: The biosignatures of inhabited earth-like planets nearing the end of their habitable lifetimes', Proceedings of the International Astronomical Union, IAUS 299: Exploring the formation and evolution of planetary systems, pp. 378-379.
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The biosignatures of life on Earth are not fixed, but change with time as environmental conditions change and life living within those environments adapts to the new conditions. A latitude-based climate model, incorporating orbital parameter variations, was used to simulate conditions on the far-future Earth as the Sun enters the late main sequence. Over time, conditions increasingly favour a unicellular microbial biosphere, which can persist for a maximum of 2.8 Gyr from present. The biosignature changes associated with the likely biosphere changes are evaluated using a biosphere-atmosphere gas exchange model and their detectability is discussed. As future Earth-like exoplanet discoveries could be habitable planets nearing the end of their habitable lifetimes, this helps inform the search for the signatures of life beyond Earth Copyright © 2013, International Astronomical Union.

Sutherland, DL, Howard-Williams, C, Turnbull, M, Broady, P & Craggs, R 1970, 'Mixing it up – is more better? Effects of mixing frequency on microalgae in a wastewater high rate algal pond', Annual Biological School Conference, Christchurch, NZ.

Blount, C, Alderson, B, Roberts, C, Cummings, D, Pernice, M & Neilson, J 2013, Bimonthly Coral Monitoring Report: Dredging Baseline Report − Ichthys Nearshore Environmental Monitoring Program, pp. 1-258, Sydney.
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Blount, C, Roberts, C, Cummings, D, Pernice, M, Neilson, J & Nicastro, A 2013, Bimonthly Coral Monitoring Report: Dredging Report 2 − Ichthys Nearshore Environmental Monitoring Program, no. 2, pp. 1-126, Sydney.
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Clayton, J & Sutherland, DL 2013, Waitaki Weeds Surveillance Plan, Hamilton, NZ.

de Winton, M, Sutherland, DL & Clayton, J 2013, Kākahi (freshwater mussel) survey of the Ō Tū Wharekai Lakes, Hamilton, NZ.

Devlin, M, Debose, J, Ajani, PA & Brodie, J TropWATER 2013, Chapter 8: Analysis of phytoplankton community structure in flood events in the Great Barrier Reef, Assessment of the relative risk of water quality to ecosystems of the Great Barrier Reef: Supporting Studies. A report to the Department of the Environment and Heritage Protection, Queensland Government, Brisbane, no. 13/30, Townsville, Australia.

Pernice, M, Roberts, C & Nicastro, A 2013, Bimonthly Coral Monitoring Report: Dredging Report 5 − Ichthys Nearshore Environmental Monitoring Program., no. 5, pp. 1-204, Sydney.
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Ralph, PJ & Sinutok, S AccessUTS Pty Limited 2013, Vallisneria and submerged macrophyte management in Penrith Lakes, Sydney.

Ralph, PJ, Skilbeck, G & Sinutok, S AccessUTS Pty Limited 2013, Vallisneria and submerged macrophyte management in the Penrith Lakes Scheme, Sydney.

Roberts, C, Pernice, M & Nicastro, A 2013, Bimonthly Coral Monitoring Report: Dredging Report 3 − Ichthys Nearshore Environmental Monitoring Program., no. 3, pp. 1-154, Sydney.
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Roberts, C, Pernice, M & Nicastro, A 2013, Bimonthly Coral Monitoring Report: Dredging Report 4 − Ichthys Nearshore Environmental Monitoring Program., no. 4, pp. 1-177, Sydney.
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Sutherland, D 2013, Risk posed by aquatic weed species to the Waitaki Catchment, Christchurch.

Sutherland, D & Taumoepaeu, A 2013, Lake Hood Aquatic Weed Survey, Christchurch.

Sutherland, D & Taumoepeau, A 2013, Macrophyte monitoring in Waituna Lagoon - February 2013, Christchurch.

Sutherland, D, Edwards, T, Wells, R & Kelly, G 2013, Assessment of the ecological condition of 8 Canterbury lakes using LakeSPI - and weed surveillance in 12 lakes, Christchurch.

Sutherland, D, Inder, F, Molineux, M, Kelly, G & Wells, R 2013, Monitoring the potential effects of MTAD on the Waiau Arm water quality and macrophytes: year one, Chritchurch.

Waterhouse, J TropWATER 2013, Assessment of the relative risk ofdegraded water quality to ecosystems ofthe Great Barrier Reef:Supporting Studies, no. 13/30.