Publications

Contreras-Porcia, L, López-Cristoffanini, C, Meynard, A & Kumar, M 2017, 'Tolerance Pathways to Desiccation Stress in Seaweeds' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 13-33.
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© Springer International Publishing AG 2017. Seaweeds are sessile organisms that inhabit coastal benthic systems and are key species for the equilibrium of marine communities. Rocky intertidal zone seaweeds are distributed in marked patterns determined by interactions between biotic and abiotic factors influenced by tide levels. It has been proposed that the distribution and abundance of organisms in the upper intertidal zones, with longer emersions, are mostly regulated by abiotic factors. Desiccation is a particularly noteworthy abiotic factor since, during low tide, algae of the upper intertidal zones can lose more than 90% of cellular water content, which can ultimately induce oxidative stress. Considering the necessary activation of several desiccation tolerance mechanisms, these algal species are ideal research models in ecophysiology. In fact, several studies using physiological, transcriptomic, and proteomic approaches have determined that desiccation tolerance mechanisms are expressed within a well-coordinated network that includes morphological and cell wall changes, photosynthetic activity diminishment, increased expression of desiccation-associated proteins, hormone accumulation, ROS scavenging by antioxidant enzymes and compounds, and osmolyte and protein synthesis. These mechanisms explain the permanence of tolerant algae species in the upper intertidal zone in comparison with lower intertidal species. Therefore, this chapter focuses on identifying tolerant algal species, and explaining the mechanisms underlying the high capacity of these species to cope with desiccation- induced oxidative stress.

Contreras-Porcia, L, Meynard, A, López-Cristoffanini, C, Latorre, N & Kumar, M 2017, 'Marine Metal Pollution and Effects on Seaweed Species' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 35-48.
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© Springer International Publishing AG 2017. Heavy metals are significant pollutants continuously released into the biosphere, both naturally and anthropogenically. Conceptually, metal speciation, bioavailability, and associated toxicity in marine organisms depend on a wide array of abiotic and biotic factors. Among these, pH variation is one of the most important environmental factors influencing metal speciation and toxicity. Due to this, ocean acidification is expected to modify metal speciation, altering the effects these nondegradable contaminants have on marine organisms, such as seaweeds. One clear effect of heavy metals on seaweeds is the rapid formation of reactive oxygen species (ROS). The production of ROS beyond the physiological tolerance threshold causes an oxidative stress condition that, if not attenuated, can irreversibly damage cellular constituents such as DNA/RNA, proteins, and lipids. To cope with heavy metal excess, several mechanisms exist in tolerant seaweed species, including the activation of an efficient ROS-scavenging system constituted by metal-binding compounds, antioxidant enzymes, and oxygenated polyunsaturated fatty acids, among others. Another adaptive mechanism involves the participation of ATP-binding cassette (ABC) transporter proteins in translocating a wide variety of compounds across cell membranes, including heavy metals. In contrast, an excessive heavy metal presence can inhibit photosynthesis, reduce pigment concentration and growth, induce cation losses, and disrupt gametophyte development in non-tolerant seaweed species. In a scenario of lowered ocean pH and increased heavy metal toxicity, the important roles played by non-tolerant seaweed species in structuring communities could be severely compromised, with unknown consequences for associated organisms. Therefore, in the upcoming decades, marine pollution could majorly shift and rearrange community compositions and the distributional ranges of species.

Gupta, V, Jain, M & Reddy, CRK 2017, 'Macroalgal Functional Genomics: A Missing Area' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 3-12.
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Kumar, M, Kuzhiumparambil, U, Ralph, PJ & Contreras-Porcia, L 2017, 'Polyamines' in Algal Green Chemistry, Elsevier, pp. 243-255.
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© 2017 Elsevier B.V. All rights reserved. Marine macrophytes including seaweeds and sea grasses are the ecosystem engineers and experience constant threats from a wide range of anthropogenic stressors and climate fluctuations in their ecological niche. Marine macrophytes acclimate and/or tolerate these external perturbations by reprogramming their metabolite networks. Among the various metabolites that contribute to alleviate the stress, polyamines (PAs) are the nitrogenous metabolites that play a key role in plant growth, development, and biotic/abiotic stress protection in land plants. Their mode of action, signaling, and cross talk with diverse metabolic networks have been well studied in land plants; however, their functionality in marine macrophytes has merely scratched the window. In this brief chapter we attempt to summarize PA research in marine macrophytes in response to abiotic stress conditions. We emphasize to undertake futuristic efforts to explore PA involvement in stress response and to identify novel stress tolerance mechanism in marine macrophytes.

Kuzhiumparambil, U, Kumar, M & Ralph, P 2017, 'Gas and Liquid Chromatography-Mass Spectrometry-Based Metabolic Profiling of Marine Angiosperm Zostera muelleri (Alismatales, Zosteraceae)' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 189-203.
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© Springer International Publishing AG 2017. Seagrasses are monocotyledonous marine flowering plants that are considered lungs of the sea and are the most intense carbon sinks on the planet, delivering a range of ecologically and economically valuable biological services. In this study, we report the chemical fingerprint of Zostera muelleri using an untargeted metabolomic approach. High-performance liquid chromatography-mass spectrometry (HPLC-MS) and gas chromatography-mass spectrometry (GC-MS) were performed to study the metabolic profile of Z. muelleri. A total of 98 metabolites belonging to various chemical classes including flavonoids, phenolics, lipids, fatty acids, sugar alcohols and amino acids were identified, including two characteristic marker compounds of the genus, zosteric acid and rosmarinic acid. Chromatographic profiling yield a comprehensive map for the chemical constituents of Z. muelleri, and this method can be used as an effective and convenient approach to gain insights into the chemical composition of other seagrasses.

Shahid, A, Zafar Khan, A, Liu, T, Malik, S, Afzal, I & Mehmood, MA 2017, 'Production and Processing of Algal Biomass' in Algae Based Polymers, Blends, and Composites, Elsevier, pp. 273-299.
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Microalgae are considered as a promising biological resource for biotechnological applications ranging from biofuels to pigments and metabolites of industrial and pharmaceutical importance. Unfortunately, their full potential could not be harnessed for several technical hindrances from biomass cultivation to processing. Selection of potential strains, optimizing the mass cultivation conditions, cultivation without contamination risks, easy harvesting, and extraction are the key aspects in algal research. Several cultivation and harvesting methods have been established to date, where each has its own advantages and disadvantages. This chapter discusses some most common methods to cultivate, harvest, and process the algal biomass for various applications. The bottleneck issues of these methods and opportunities have also been discussed.

Varkey, DR & Doblin, MA 2017, 'Application of ‘Omics’ Approaches to Microbial Oceanography' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 223-233.
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Viruses, bacteria, archaea and single celled eukaryotes, collectively known as microbes, dominate the biomass and metabolism of ocean ecosystems. Marine microbes are highly abundant and critical to human survival, but the vast majority of taxa have not yet been cultured. The use of environmental nucleic acid sequencing as a cultivation-independent approach to microbial oceanography has therefore significantly expanded our understanding of the diversity, evolution, biogeography and important biogeochemical roles of marine microorganisms. Here we provide illustrative examples of how genomic, transcriptomic and proteomic approaches have been applied to marine microbes to advance our understanding of their ecology. A remaining challenge is the need to link phenotypes to their environment, requiring a better understanding of genomic features that influence transcription (e.g. promoters and methylation) as well as post-translational modifications, and how such regulatory processes are impacted by extracellular abiotic and biotic processes. In addition, the expansion of available protein and taxonomic databases will greatly increase our capacity to link microbial function to specific taxa.

Aguilar, C, Raina, J-B, Motti, CA, Fôret, S, Hayward, DC, Lapeyre, B, Bourne, DG & Miller, DJ 2017, 'Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals', BMC Genomics, vol. 18, no. 1, pp. 1-14.
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© 2017 The Author(s). Background: Dimethylsulfoniopropionate (DMSP) is a small sulphur compound which is produced in prodigious amounts in the oceans and plays a pivotal role in the marine sulfur cycle. Until recently, DMSP was believed to be synthesized exclusively by photosynthetic organisms; however we now know that corals and specific bacteria can also produce this compound. Corals are major sources of DMSP, but the molecular basis for its biosynthesis is unknown in these organisms. Results: Here we used salinity stress, which is known to trigger DMSP production in other organisms, in conjunction with transcriptomics to identify coral genes likely to be involved in DMSP biosynthesis. We focused specifically on both adults and juveniles of the coral Acropora millepora: after 24 h of exposure to hyposaline conditions, DMSP concentrations increased significantly by 2.6 fold in adult corals and 1.2 fold in juveniles. Concomitantly, candidate genes enabling each of the necessary steps leading to DMSP production were up-regulated. Conclusions: The data presented strongly suggest that corals use an algal-like pathway to generate DMSP from methionine, and are able to rapidly change expression of the corresponding genes in response to environmental stress. However, our data also indicate that DMSP is unlikely to function primarily as an osmolyte in corals, instead potentially serving as a scavenger of ROS and as a molecular sink for excess methionine produced as a consequence of proteolysis and osmolyte catabolism in corals under hypo-osmotic conditions.

Anthony, K, Bay, LK, Costanza, R, Firn, J, Gunn, J, Harrison, P, Heyward, A, Lundgren, P, Mead, D, Moore, T, Mumby, PJ, van Oppen, MJH, Robertson, J, Runge, MC, Suggett, DJ, Schaffelke, B, Wachenfeld, D & Walshe, T 2017, 'New interventions are needed to save coral reefs', Nature Ecology & Evolution, vol. 1, no. 10, pp. 1420-1422.
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Bellgrove, A, van Rooyen, A, Weeks, AR, Clark, JS, Doblin, MA & Miller, AD 2017, 'New resource for population genetics studies on the Australasian intertidal brown alga, Hormosira banksii: isolation and characterization of 15 polymorphic microsatellite loci through next generation DNA sequencing', Journal of Applied Phycology, vol. 29, no. 3, pp. 1721-1727.
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© 2016, Springer Science+Business Media Dordrecht. The Australasian fucoid, Hormosira banksii, commonly known as ‘Neptune’s necklace’ or ‘bubbleweed’ is regarded as an autogenic ecosystem engineer with no functional equivalents. Population declines resulting from climate change and other anthropogenic disturbances pose significant threats to intertidal biodiversity. For effective conservation strategies, patterns of gene flow and population genetic structure across the species distribution need to be clearly understood. We developed a suite of 15 polymorphic microsatellite markers using next generation sequencing of 53–55 individuals from two sites (south-western Victoria and central New South Wales, Australia) and a replicated spatially hierarchical sampling design. We observed low to moderate genetic variation across most loci (mean number of alleles per locus =3.26; mean expected heterozygosity =0.38) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Independent spatial autocorrelation analyses were performed for each site using multilocus genotypes and different relatedness measures. Both analyses indicated no significant patterns between relatedness and geographic distance, complemented by non-significant Hardy-Weinberg estimates (P  <  0.05), suggesting that individuals from each site represent a randomly mating, outcrossing population. A preliminary investigation of population structure indicates that gene flow among sites is limited (F ST  = 0.49), however more comprehensive sampling is needed to determine the extent of population structure across the species range ( > 10,000 km). The genetic markers described provide a valuable resource for future population genetic assessments that will help guide conservation planning for H. banksii and the associated intertidal communities.

Brodersen, KE, Hammer, KJ, Schrameyer, V, Floytrup, A, Rasheed, MA, Ralph, PJ, Kühl, M & Pedersen, O 2017, 'Sediment Resuspension and Deposition on Seagrass Leaves Impedes Internal Plant Aeration and Promotes Phytotoxic H2S Intrusion', Frontiers in Plant Science, vol. 8, pp. 1-13.
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© 2017 Brodersen, Hammer, Schrameyer, Floytrup, Rasheed, Ralph, Kühl and Pedersen. Anthropogenic activities leading to sediment re-suspension can have adverse effects on adjacent seagrass meadows, owing to reduced light availability and the settling of suspended particles onto seagrass leaves potentially impeding gas exchange with the surrounding water. We used microsensors to determine O2 fluxes and diffusive boundary layer (DBL) thickness on leaves of the seagrass Zostera muelleri with and without fine sediment particles, and combined these laboratory measurements with in situ microsensor measurements of tissue O2 and H2 S concentrations. Net photosynthesis rates in leaves with fine sediment particles were down to ∼20% of controls without particles, and the compensation photon irradiance increased from a span of 20–53 to 109–145 µmol photons m−2 s−1. An ∼2.5-fold thicker DBL around leaves with fine sediment particles impeded O2 influx into the leaves during darkness. In situ leaf meristematic O2 concentrations of plants exposed to fine sediment particles were lower than in control plants and exhibited long time periods of complete meristematic anoxia during night-time. Insufficient internal aeration resulted in H2 S intrusion into the leaf meristematic tissues when exposed to sediment resuspension even at relatively high night-time water-column O2 concentrations. Fine sediment particles that settle on seagrass leaves thus negatively affect internal tissue aeration and thereby the plants’ resilience against H2 S intrusion.

Brodersen, KE, Koren, K, Moßhammer, M, Ralph, PJ, Kühl, M & Santner, J 2017, 'Seagrass-Mediated Phosphorus and Iron Solubilization in Tropical Sediments', Environmental Science & Technology, vol. 51, no. 24, pp. 14155-14163.
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© 2017 American Chemical Society. Tropical seagrasses are nutrient-limited owing to the strong phosphorus fixation capacity of carbonate-rich sediments, yet they form densely vegetated, multispecies meadows in oligotrophic tropical waters. Using a novel combination of high-resolution, two-dimensional chemical imaging of O2, pH, iron, sulfide, calcium, and phosphorus, we found that tropical seagrasses are able to mobilize the essential nutrients iron and phosphorus in their rhizosphere via multiple biogeochemical pathways. We show that tropical seagrasses mobilize phosphorus and iron within their rhizosphere via plant-induced local acidification, leading to dissolution of carbonates and release of phosphate, and via local stimulation of microbial sulfide production, causing reduction of insoluble Fe(III) oxyhydroxides to dissolved Fe(II) with concomitant phosphate release into the rhizosphere porewater. These nutrient mobilization mechanisms have a direct link to seagrass-derived radial O2 loss and secretion of dissolved organic carbon from the below-ground tissue into the rhizosphere. Our demonstration of seagrass-derived rhizospheric phosphorus and iron mobilization explains why seagrasses are widely distributed in oligotrophic tropical waters.

Camp, EF, Dong, LF, Suggett, DJ, Smith, DJ, Boatman, TG, Crosswell, JR, Evenhuis, C, Scorfield, S, Walinjkar, A, Woods, J & Lawson, T 2017, 'A novel membrane inlet‐infrared gas analysis (MI‐IRGA) system for monitoring of seawater carbonate system', Limnology and Oceanography: Methods, vol. 15, no. 1, pp. 38-53.
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AbstractIncreased atmospheric CO2 concentrations are driving changes in ocean chemistry at unprecedented rates resulting in ocean acidification, which is predicted to impact the functioning of marine biota, in particular of marine calcifiers. However, the precise understanding of such impacts relies on an analytical system that determines the mechanisms and impact of elevated pCO2 on the physiology of organisms at scales from species to entire communities. Recent work has highlighted the need within experiments to control all aspects of the carbonate system to resolve the role of different inorganic carbon species on the physiological responses observed across taxa in real‐time. Presently however, there are limited options available for continuous quantification of physiological responses, coupled with real‐time calculation of the seawater carbonate chemistry system within microcosm environments. Here, we describe and characterise the performance of a novel pCO2 membrane equilibrium system (the Membrane Inlet Infra‐Red Gas Analyser, MI‐IRGA) integrated with a continuous pH and oxygen monitoring platform. The system can detect changes in the seawater carbonate chemistry and determine organism physiological responses, while providing the user with real‐time control over the microcosm system. We evaluate the systems control, response time and associated error, and demonstrate the flexibility of the system to operate under field conditions and within a laboratory. We use the system to measure physiological parameters (photosynthesis and respiration) for the corals Pocillipora damicornis and Porites cylindrica; in doing so we present a novel dataset examining the interactive role of temperature, light and pCO2 ...

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

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

del Campo, J, Pombert, J-F, Šlapeta, J, Larkum, A & Keeling, PJ 2017, 'The ‘other’ coral symbiont: Ostreobium diversity and distribution', The ISME Journal, vol. 11, no. 1, pp. 296-299.
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Abstract Ostreobium is an endolithic algal genus thought to be an early-diverging lineage of the Bryopsidales (Ulvophyceae, Chlorophyta). Ostreobium can live in low-light conditions on calcium carbonate substrata in tropical conditions. It is best known as a symbiont of corals, where it lives deep within the animal skeleton and exchanges nitrogen and carbon, as well as providing nutrients and photoassimilates. In contrast to the relatively well-studied role of the photosynthetic zooxanthellae symbionts in coral (Symbiodinium), Ostreobium phylogeny, diversity and distribution are all poorly understood. Here, we describe the phylogenetic position and diversity of Ostreobium based on plastid 16S ribosomal DNA (rDNA), 18S rDNA and rbcL genes from a nuclear genome survey and complete plastid genome, and determined its environmental diversity and distribution by screening the publicly available environmental data for those genes. The results shed light on the phylogeny and the ecology of the ‘other’ coral symbiont.

Garby, TJ, Matys, ED, Ongley, SE, Salih, A, Larkum, AWD, Walter, MR, Summons, RE & Neilan, BA 2017, 'Lack of Methylated Hopanoids Renders the Cyanobacterium Nostoc punctiforme Sensitive to Osmotic and pH Stress', Applied and Environmental Microbiology, vol. 83, no. 13, pp. 1-15.
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ABSTRACT To investigate the function of 2-methylhopanoids in modern cyanobacteria, the hpnP gene coding for the radical S -adenosyl methionine (SAM) methylase protein that acts on the C-2 position of hopanoids was deleted from the filamentous cyanobacterium Nostoc punctiforme ATCC 29133S. The resulting Δ hpnP mutant lacked all 2-methylhopanoids but was found to produce much higher levels of two bacteriohopanepentol isomers than the wild type. Growth rates of the Δ hpnP mutant cultures were not significantly different from those of the wild type under standard growth conditions. Akinete formation was also not impeded by the absence of 2-methylhopanoids. The relative abundances of the different hopanoid structures in akinete-dominated cultures of the wild-type and Δ hpnP mutant strains were similar to those of vegetative cell-dominated cultures. However, the Δ hpnP mutant was found to have decreased growth rates under both pH and osmotic stress, confirming a role for 2-methylhopanoids in stress tolerance. Evidence of elevated photosystem II yield and NAD(P)H-dependent oxidoreductase activity in the Δ hpnP mutant under stress conditions, compared to the wild type, suggested that the absence of 2-methylhopanoids increases cellular metabolic rates under stress conditions. IMPORTANCE As the first group of organisms to develop oxygenic photosynthesis,

Gardner, SG, Raina, J-B, Nitschke, MR, Nielsen, DA, Stat, M, Motti, CA, Ralph, PJ & Petrou, K 2017, 'A multi-trait systems approach reveals a response cascade to bleaching in corals', BMC Biology, vol. 15, no. 1, p. 117.
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BACKGROUND: Climate change causes the breakdown of the symbiotic relationships between reef-building corals and their photosynthetic symbionts (genus Symbiodinium), with thermal anomalies in 2015-2016 triggering the most widespread mass coral bleaching on record and unprecedented mortality on the Great Barrier Reef. Targeted studies using specific coral stress indicators have highlighted the complexity of the physiological processes occurring during thermal stress, but have been unable to provide a clear mechanistic understanding of coral bleaching.RESULTS: Here, we present an extensive multi-trait-based study in which we compare the thermal stress responses of two phylogenetically distinct and widely distributed coral species, Acropora millepora and Stylophora pistillata, integrating 14 individual stress indicators over time across a simulated thermal anomaly. We found that key stress responses were conserved across both taxa, with the loss of symbionts and the activation of antioxidant mechanisms occurring well before collapse of the physiological parameters, including gross oxygen production and chlorophyll a. Our study also revealed species-specific traits, including differences in the timing of antioxidant regulation, as well as drastic differences in the production of the sulfur compound dimethylsulfoniopropionate during bleaching. Indeed, the concentration of this antioxidant increased two-fold in A. millepora after the corals started to bleach, while it decreased 70% in S. pistillata.CONCLUSIONS: We identify a well-defined cascading response to thermal stress, demarking clear pathophysiological reactions conserved across the two species, which might be central to fully understanding the mechanisms triggering thermally induced coral bleaching. These results highlight that bleaching is a conserved mechanism, but specific adaptations linked to the coral's antioxidant capacity drive differences in the sensitivity and thus tolerance of each coral spe...

Gardner, SG, Raina, J-B, Ralph, PJ & Petrou, K 2017, 'Reactive oxygen species (ROS) and dimethylated sulphur compounds in coral explants under acute thermal stress', Journal of Experimental Biology, vol. 220, no. 10, pp. 1787-1791.
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Coral bleaching is intensifying with global climate change. While the causes for these catastrophic events are well understood, the cellular mechanism that triggers bleaching is not well established. Our understanding of coral bleaching processes is hindered by the lack of robust methods for studying interactions between host and symbiont at the single-cell level. Here we exposed coral explants to acute thermal stress and measured oxidative stress, more specifically, reactive oxygen species (ROS), in individual symbiont cells. Furthermore, we measured concentrations of dimethylsulphoniopropionate (DMSP) and dimethylsulphoxide (DMSO) to elucidate the role of these compounds in coral antioxidant function. This work demonstrates the application of coral explants for investigating coral physiology and biochemistry under thermal stress and delivers a new approach to study host-symbiont interactions at the microscale, allowing us to directly link intracellular ROS with DMSP and DMSO dynamics.

Gleason, FH, Gadd, GM, Pitt, JI & Larkum, AWD 2017, 'The roles of endolithic fungi in bioerosion and disease in marine ecosystems. I. General concepts', Mycology, vol. 8, no. 3, pp. 205-215.
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© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Endolithic true fungi and fungus-like microorganisms penetrate calcareous substrates formed by living organisms, cause significant bioerosion and are involved in diseases of many host animals in marine ecosystems. A theoretical interactive model for the ecology of reef-building corals is proposed in this review. This model includes five principle partners that exist in a dynamic equilibrium: polyps of a colonial coelenterate, endosymbiotic zooxanthellae, endolithic algae (that penetrate coral skeletons), endolithic fungi (that attack the endolithic algae, the zooxanthellae and the polyps) and prokaryotic and eukaryotic microorganisms (which live in the coral mucus). Endolithic fungi and fungus-like boring microorganisms are important components of the marine calcium carbonate cycle because they actively contribute to the biodegradation of shells of animals composed of calcium carbonate and calcareous geological substrates.

Gleason, FH, Gadd, GM, Pitt, JI & Larkum, AWD 2017, 'The roles of endolithic fungi in bioerosion and disease in marine ecosystems. II. Potential facultatively parasitic anamorphic ascomycetes can cause disease in corals and molluscs', Mycology, vol. 8, no. 3, pp. 216-227.
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© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Anamorphic ascomycetes have been implicated as causative agents of diseases in tissues and skeletons of hard corals, in tissues of soft corals (sea fans) and in tissues and shells of molluscs. Opportunist marine fungal pathogens, such as Aspergillus sydowii, are important components of marine mycoplankton and are ubiquitous in the open oceans, intertidal zones and marine sediments. These fungi can cause infection in or at least can be associated with animals which live in these ecosystems. A. sydowii can produce toxins which inhibit photosynthesis in and the growth of coral zooxanthellae. The prevalence of many documented infections has increased in frequency and severity in recent decades with the changing impacts of physical and chemical factors, such as temperature, acidity and eutrophication. Changes in these factors are thought to cause significant loss of biodiversity in marine ecosystems on a global scale in general, and especially in coral reefs and shallow bays.

Goyen, S, Pernice, M, Szabó, M, Warner, ME, Ralph, PJ & Suggett, DJ 2017, 'A molecular physiology basis for functional diversity of hydrogen peroxide production amongst Symbiodinium spp. (Dinophyceae)', Marine Biology, vol. 164, no. 3.
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© 2017, Springer-Verlag Berlin Heidelberg. Hydrogen peroxide (H2O2) production has been demonstrated to play a pivotal role in the photosynthetic stability of higher plants, corals and algae, and considered a primary reactive oxygen species (ROS) associated with the thermal susceptibility of Symbiodinium spp. Here, we simultaneously subjected a large number of Symbiodinium isolates (n = 16) covering broad phylogenetic diversity (clades A, B, D, F) to heat stress and characterized their photosynthetic response via fast repetition rate fluorometry (FRRf) and parallel measurements of H2O2 emissions. Based on their physiological response, isolates clustered into three novel functional groups: (1) thermally tolerant (unchanged photochemical efficiency (Fv/Fm), electron turnover (τQA) or H2O2 emission), or (2) thermally susceptible via decreased Fv/Fm, unchanged τQA, but increased H2O2, indicating energetically uncoupled PSII (thylakoid membrane instability), versus (3) thermally responsive via decreased Fv/Fm, increased τQA and H2O2, indicative of energetically coupled (but downregulated) PSII. There was no correlation between the algal phylogenetic groups and the distribution of isolates amongst these novel functional groups. Two model Symbiodinium isolates for functional groups (1) and (2) (ITS2 type A1, Symbiodinium microadriaticum, and type D1–5, Symbiodinium spp., respectively) were selected to further examine how their different thermal responses corresponded with the expression levels of two genes coding for different metalloforms of superoxide dismutase (MnSOD and NiSOD) that potentially regulate production of H2O2. S. microadriaticum demonstrated the greatest upregulation of MnSOD gene confirming recent suggestions of a role for this metalloform in the antioxidant network associated with thermal stress protection. Assigning Symbiodinium isolates into such functional groups based on coupled molecular-physiological assessment is an important step need...

Gribben, PE, Nielsen, S, Seymour, JR, Bradley, DJ, West, MN & Thomas, T 2017, 'Microbial communities in marine sediments modify success of an invasive macrophyte', Scientific Reports, vol. 7, no. 1, pp. 1-8.
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AbstractInvasive plants have extensive impacts on ecosystem function and biodiversity globally. Our inability to manage invasive species stems in part from a lack of understanding of the processes that control their successful establishment and spread. To date, studies have largely considered how above-ground processes control native/invasive plant interactions. Emerging research from terrestrial and wetland ecosystems demonstrates that below-ground processes under microbial control can determine the outcome of interactions between native and invasive plants. Whether sediment microbes modify the success of invasive macrophytes in marine ecosystems is untested, despite marine sediment microbes controlling many ecological processes (e.g. nutrient cycling) comparable to those in terrestrial ecosystems. We first show that sediment bacterial communities differ between the native seagrass Zostera capricorni and the invasive alga Caulerpa taxifolia and that those differences relate to functional changes in sulfur cycling between the macrophytes. Second, by experimentally manipulating the microbial communities we show that intact microbial communities in Z. capricorni sediments provide biotic resistance by reducing C. taxifolia fragment growth 119% compared to when they are inactive, and intact microbial communities in C. taxifolia sediments have positive feedbacks by increasing fragment growth 200%. Thus, similar to terrestrial ecosystems, microorganisms appear to indirectly control the success of invasive macrophytes in marine ecosystems.

Jiang, Z, Kumar, M, Padula, MP, Pernice, M, Kahlke, T, Kim, M & Ralph, PJ 2017, 'Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis', Frontiers in Plant Science, vol. 8, pp. 1-14.
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© 2017 Jiang, Kumar, Padula, Pernice, Kahlke, Kim and Ralph. The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells. In the present study, three protein extraction methods that are commonly used in plant proteomics i.e., phenol (P); trichloroacetic acid/acetone/SDS/phenol (TASP); and borax/polyvinyl-polypyrrolidone/phenol (BPP) extraction, were evaluated quantitatively and qualitatively based on two dimensional isoelectric focusing (2D-IEF) maps and LC-MS/MS analysis using the two most abundant Australian seagrass species, namely Zostera muelleri and Posidonia australis. All three tested methods produced high quality protein extracts with excellent 2D-IEF maps in P. australis. However, the BPP method produces better results in Z. muelleri compared to TASP and P. Therefore, we further modified the BPP method (M-BPP) by homogenizing the tissue in a modified protein extraction buffer containing both ionic and non-ionic detergents (0.5% SDS; 1.5% Triton X-100), 2%PVPPand protease inhibitors. Further, the extracted proteins were solubilized in 0.5%of zwitterionic detergent (C7BzO) instead of 4%CHAPS. This slight modification to the BPP method resulted in a higher protein yield, and good quality 2-DE maps with a higher number of protein spots in both the tested seagrasses. Further, the M-BPP method was successfully utilized in western-blot analysis of phosphoe...

Jiang, Z, Liu, S, Zhang, J, Zhao, C, Wu, Y, Yu, S, Zhang, X, Huang, C, Huang, X & Kumar, M 2017, 'Newly discovered seagrass beds and their potential for blue carbon in the coastal seas of Hainan Island, South China Sea', Marine Pollution Bulletin, vol. 125, no. 1-2, pp. 513-521.
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© 2017 Elsevier Ltd Eight new seagrass beds were discovered along the coastline of Hainan Island in South China Sea with an area of 203.64 ha. The leaf N content of all seagrasses was above the median value, indicative of N limitation, with their C:N ratio recorded significantly lower than the limiting criteria. This suggested that N is not limiting but in replete status. Further, the lower C content observed in the seagrass leaves was accompanied by higher nutrient concentration. The mean seagrass biomass C was 0.23 ± 0.16 Mg C ha− 1, while the average sediment organic carbon (SOC) stock was 7.02 ± 3.57 Mg C ha− 1. The entire SOC stock of the newly discovered seagrass beds was 1306.45 Mg C, and the overall SOC stock of seagrass bed at Hainan Island was 40858.5 Mg C. These seagrass beds are under constant threats from sea reclamation, nutrient input, aquaculture activities for oyster and snail farming, and fishing activities.

Kelleway, JJ, Saintilan, N, Macreadie, PI, Baldock, JA & Ralph, PJ 2017, 'Sediment and carbon deposition vary among vegetation assemblages in a coastal salt marsh', Biogeosciences, vol. 14, no. 16, pp. 3763-3779.
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Abstract. Coastal salt marshes are dynamic, intertidal ecosystems that are increasingly being recognised for their contributions to ecosystem services, including carbon (C) accumulation and storage. The survival of salt marshes and their capacity to store C under rising sea levels, however, is partially reliant upon sedimentation rates and influenced by a combination of physical and biological factors. In this study, we use several complementary methods to assess short-term (days) deposition and medium-term (months) accretion dynamics within a single marsh that contains three salt marsh vegetation types common throughout southeastern (SE) Australia.We found that surface accretion varies among vegetation assemblages, with medium-term (19 months) bulk accretion rates in the upper marsh rush (Juncus) assemblage (1.74 ± 0.13 mm yr−1) consistently in excess of estimated local sea-level rise (1.15 mm yr−1). Accretion rates were lower and less consistent in both the succulent (Sarcocornia, 0.78 ± 0.18 mm yr−1) and grass (Sporobolus, 0.88 ± 0.22 mm yr−1) assemblages located lower in the tidal frame. Short-term (6 days) experiments showed deposition within Juncus plots to be dominated by autochthonous organic inputs with C deposition rates ranging from 1.14 ± 0.41 mg C cm−2 d−1 (neap tidal period) to 2.37 ± 0.44 mg C cm−2 d−1 (spring tidal period), while minerogenic inputs and lower C deposition dominated Sarcocornia (0.10 ± 0.02 to 0.62 ± 0.08 mg C cm−2 d−1) and Sporobolus (0.17 ± 0.04 to 0.40 ± 0.07 mg C cm−2 d−1) assemblages.Elemental (C : N), isotopic (δ13C), mid-infrared (MIR) and 13C nuclear magnetic resonance (NMR) analyses revealed little difference in either the source or character of materials being deposited among neap versus spring tidal periods. Instead, these analyses point to substantial redistribution of materials within the Sarcocornia and Sporobolus assemblages, compared to high retention and preservation of organic inputs in the Juncus...

Kelleway, JJ, Saintilan, N, Macreadie, PI, Baldock, JA, Heijnis, H, Zawadzki, A, Gadd, P, Jacobsen, G & Ralph, PJ 2017, 'Geochemical analyses reveal the importance of environmental history for blue carbon sequestration', Journal of Geophysical Research: Biogeosciences, vol. 122, no. 7, pp. 1789-1805.
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©2017. American Geophysical Union. All Rights Reserved. Coastal habitats including saltmarshes and mangrove forests can accumulate and store significant blue carbon stocks, which may persist for millennia. Despite this implied stability, the distribution and structure of intertidal-supratidal wetlands are known to respond to changes imposed by geomorphic evolution, climatic, sea level, and anthropogenic influences. In this study, we reconstruct environmental histories and biogeochemical conditions in four wetlands of similar contemporary vegetation in SE Australia. The objective is to assess the importance of historic factors to contemporary organic carbon (C) stocks and accumulation rates. Results from the four cores—two collected from marine-influenced saltmarshes (Wapengo marine site (WAP-M) and Port Stephens marine site (POR-M)) and two from fluvial influenced saltmarshes (Wapengo fluvial site (WAP-F) and Port Stephens fluvial site (POR-F))—highlight different environmental histories and preservation conditions. High C stocks are associated with the presence of a mangrove phase below the contemporary saltmarsh sediments in the POR-M and POR-F cores. 13C nuclear magnetic resonance analyses show this historic mangrove root C to be remarkably stable in its molecular composition despite its age, consistent with its position in deep sediments. WAP-M and WAP-F cores did not contain mangrove root C; however, significant preservation of char C (up to 46% of C in some depths) in WAP-F reveals the importance of historic catchment processes to this site. Together, these results highlight the importance of integrating historic ecosystem and catchment factors into attempts to upscale C accounting to broader spatial scales.

Klein, SG, Pitt, KA, Nitschke, MR, Goyen, S, Welsh, DT, Suggett, DJ & Carroll, AR 2017, 'Symbiodinium mitigate the combined effects of hypoxia and acidification on a noncalcifying cnidarian', Global Change Biology, vol. 23, no. 9, pp. 3690-3703.
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AbstractAnthropogenic nutrient inputs enhance microbial respiration within many coastal ecosystems, driving concurrent hypoxia and acidification. During photosynthesis, Symbiodinium spp., the microalgal endosymbionts of cnidarians and other marine phyla, produce O2 and assimilate CO2 and thus potentially mitigate the exposure of the host to these stresses. However, such a role for Symbiodinium remains untested for noncalcifying cnidarians. We therefore contrasted the fitness of symbiotic and aposymbiotic polyps of a model host jellyfish (Cassiopea sp.) under reduced O2 (~2.09 mg/L) and pH (~ 7.63) scenarios in a full‐factorial experiment. Host fitness was characterized as asexual reproduction and their ability to regulate internal pH and Symbiodinium performance characterized by maximum photochemical efficiency, chla content and cell density. Acidification alone resulted in 58% more asexual reproduction of symbiotic polyps than aposymbiotic polyps (and enhanced Symbiodinium cell density) suggesting Cassiopea sp. fitness was enhanced by CO2‐stimulated Symbiodinium photosynthetic activity. Indeed, greater CO2 drawdown (elevated pH) was observed within host tissues of symbiotic polyps under acidification regardless of O2 co...

Koottatep, T, Phong, VHN, Chapagain, SK, Panuvatvanich, A, Polprasert, C & Ahn, K-H 2017, 'Potential of Laterite Soil Coupling Fenton Reaction in Acetaminophen (ACT) Removal in Constructed Wetlands', Water, Air, & Soil Pollution, vol. 228, no. 8.
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Kumar, M, Padula, MP, Davey, P, Pernice, M, Jiang, Z, Sablok, G, Contreras-Porcia, L & Ralph, PJ 2017, 'Proteome Analysis Reveals Extensive Light Stress-Response Reprogramming in the Seagrass Zostera muelleri (Alismatales, Zosteraceae) Metabolism', Frontiers in Plant Science, vol. 7, pp. 1-19.
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© 2017, Kumar, Padula, Davey, Pernice, Jiang, Sablok, Contreras-Porcia and Ralph. Seagrasses are marine ecosystem engineers that are currently declining in abundance at an alarming rate due to both natural and anthropogenic disturbances in ecological niches. Despite reports on the morphological and physiological adaptations of seagrasses to extreme environments, little is known of the molecular mechanisms underlying photo-acclimation, and/or tolerance in these marine plants. This study applies the two-dimensional isoelectric focusing (2D-IEF) proteomics approach to identify photo-acclimation/tolerance proteins in the marine seagrass Zostera muelleri. For this, Z. muelleri was exposed for 10 days in laboratory mesocosms to saturating (control, 200 µmol photons m−2 s−1), super-saturating (SSL, 600 µmol photons m−2 s−1), and limited light (LL, 20 µmol photons m−2 s−1) irradiance conditions. Using LC-MS/MS analysis, 93 and 40 protein spots were differentially regulated under SSL and LL conditions, respectively, when compared to the control. In contrast to the LL condition, Z. muelleri robustly tolerated super-saturation light than control conditions, evidenced by their higher relative maximum electron transport rate and minimum saturating irradiance values. Proteomic analyses revealed up-regulation and/or appearances of proteins belonging to the Calvin-Benson and Krebs cycle, glycolysis, the glycine cleavage system of photorespiration, and the antioxidant system. These proteins, together with those from the inter-connected glutamate-proline-GABA pathway, shaped Z. muelleri photosynthesis andgrowth under SSL conditions. In contrast, the LL condition negatively impacted the metabolic activities of Z. muelleri by down-regulating key metabolic enzymes for photosynthesis and the metabolism of carbohydrates and amino acids, which is consistent with the observation with lower photosynthetic performance under LL condition. This study provides novel insights into th...

Lambert, BS, Raina, J-B, Fernandez, VI, Rinke, C, Siboni, N, Rubino, F, Hugenholtz, P, Tyson, GW, Seymour, JR & Stocker, R 2017, 'A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities', Nature Microbiology, vol. 2, no. 10, pp. 1344-1349.
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© 2017 The Author(s). Microbial interactions influence the productivity and biogeochemistry of the ocean, yet they occur in miniscule volumes that cannot be sampled by traditional oceanographic techniques. To investigate the behaviours of marine microorganisms at spatially relevant scales, we engineered an in situ chemotaxis assay (ISCA) based on microfluidic technology. Here, we describe the fabrication, testing and first field results of the ISCA, demonstrating its value in accessing the microbial behaviours that shape marine ecosystems.

Larkum, AWD, Davey, PA, Kuo, J, Ralph, PJ & Raven, JA 2017, 'Carbon-concentrating mechanisms in seagrasses', Journal of Experimental Botany, vol. 68, no. 14, pp. 3773-3784.
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Seagrasses are unique angiosperms that carry out growth and reproduction submerged in seawater. They occur in at least three families of the Alismatales. All have chloroplasts mainly in the cells of the epidermis. Living in seawater, the supply of inorganic carbon (Ci) to the chloroplasts is diffusion limited, especially under unstirred conditions. Therefore, the supply of CO2 and bicarbonate across the diffusive boundary layer on the outer side of the epidermis is often a limiting factor. Here we discuss the evidence for mechanisms that enhance the uptake of Ci into the epidermal cells. Since bicarbonate is plentiful in seawater, a bicarbonate pump might be expected; however, the evidence for such a pump is not strongly supported. There is evidence for a carbonic anhydrase outside the outer plasmalemma. This, together with evidence for an outward proton pump, suggests the possibility that local acidification leads to enhanced concentrations of CO2 adjacent to the outer tangential epidermal walls, which enhances the uptake of CO2, and this could be followed by a carbon-concentrating mechanism (CCM) in the cytoplasm and/or chloroplasts. The lines of evidence for such an epidermal CCM are discussed, including evidence for special 'transfer cells' in some but not all seagrass leaves in the tangential inner walls of the epidermal cells. It is concluded that seagrasses have a CCM but that the case for concentration of CO2 at the site of Rubisco carboxylation is not proven.

Larsson, ME, Ajani, PA, Rubio, AM, Guise, K, McPherson, RG, Brett, SJ, Davies, KP & Doblin, MA 2017, 'Long-term perspective on the relationship between phytoplankton and nutrient concentrations in a southeastern Australian estuary', Marine Pollution Bulletin, vol. 114, no. 1, pp. 227-238.
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© 2016 Elsevier Ltd Sixteen years (1997–2013) of physicochemical, nutrient and phytoplankton biomass (Chlorophyll-a (Chl-a)) data and a decade (2003-2013) of phytoplankton composition and abundance data were analyzed to assess how the algal community in a temperate southeastern Australian estuary has responded to decreased chronic point source nitrogen loading following effluent treatment upgrade works in 2003. Nitrogen concentrations were significantly lower (P < 0.05) following enhanced effluent treatment and Chl-a levels decreased (P < 0.05) during the warmer months. Temperature and nutrient concentrations significantly influenced temporal changes of Chl-a (explaining 55% of variability), while salinity, temperature, pH and nutrient concentrations influenced phytoplankton abundance and composition (25% explained). Harmful Algal Bloom (HAB) dynamics differed between sites likely influenced by physical attributes of the estuary. This study demonstrates that enhanced effluent treatment can significantly decrease chronic point source nitrogen loading and that Chl-a concentrations can be lowered during the warmer months when the risk of blooms and HABs is greatest.

Levin, RA, Suggett, DJ, Nitschke, MR, van Oppen, MJH & Steinberg, PD 2017, 'Expanding the Symbiodinium (Dinophyceae, Suessiales) Toolkit Through Protoplast Technology', Journal of Eukaryotic Microbiology, vol. 64, no. 5, pp. 588-597.
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AbstractDinoflagellates within the genus Symbiodinium are photosymbionts of many tropical reef invertebrates, including corals, making them central to the health of coral reefs. Symbiodinium have therefore gained significant research attention, though studies have been constrained by technical limitations. In particular, the generation of viable cells with their cell walls removed (termed protoplasts) has enabled a wide range of experimental techniques for bacteria, fungi, plants, and algae such as ultrastructure studies, virus infection studies, patch clamping, genetic transformation, and protoplast fusion. However, previous studies have struggled to remove the cell walls from armored dinoflagellates, potentially due to the internal placement of their cell walls. Here, we produce the first Symbiodinium protoplasts from three genetically and physiologically distinct strains via incubation with cellulase and osmotic agents. Digestion of the cell walls was verified by a lack of Calcofluor White fluorescence signal and by cell swelling in hypotonic culture medium. Fused protoplasts were also observed, motivating future investigation into intra‐ and inter‐specific somatic hybridization of Symbiodinium. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Generation of Symbiodinium protoplasts opens exciting, new avenues for researching these crucial symbiotic dinoflagellates, including genetic modification.

Levin, RA, Voolstra, CR, Agrawal, S, Steinberg, PD, Suggett, DJ & van Oppen, MJH 2017, 'Engineering Strategies to Decode and Enhance the Genomes of Coral Symbionts', Frontiers in Microbiology, vol. 8, no. JUN, pp. 1220-1220.
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© 2017 Levin, Voolstra, Agrawal, Steinberg, Suggett and van Oppen. Elevated sea surface temperatures from a severe and prolonged El Niño event (2014-2016) fueled by climate change have resulted in mass coral bleaching (loss of dinoflagellate photosymbionts, Symbiodinium spp., from coral tissues) and subsequent coral mortality, devastating reefs worldwide. Genetic variation within and between Symbiodinium species strongly influences the bleaching tolerance of corals, thus recent papers have called for genetic engineering of Symbiodinium to elucidate the genetic basis of bleaching-relevant Symbiodinium traits. However, while Symbiodinium has been intensively studied for over 50 years, genetic transformation of Symbiodinium has seen little success likely due to the large evolutionary divergence between Symbiodinium and other model eukaryotes rendering standard transformation systems incompatible. Here, we integrate the growing wealth of Symbiodinium next-generation sequencing data to design tailored genetic engineering strategies. Specifically, we develop a testable expression construct model that incorporates endogenous Symbiodinium promoters, terminators, and genes of interest, as well as an internal ribosomal entry site from a Symbiodinium virus. Furthermore, we assess the potential for CRISPR/Cas9 genome editing through new analyses of the three currently available Symbiodinium genomes. Finally, we discuss how genetic engineering could be applied to enhance the stress tolerance of Symbiodinium, and in turn, coral reefs.

Lohr, KE, Smith, DJ, Suggett, DJ, Nitschke, MR, Dumbrell, AJ, Woodcock, S & Camp, EF 2017, 'Coral Community Structure and Recruitment in Seagrass Meadows', Frontiers in Marine Science, vol. 4, no. NOV, pp. 1-13.
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© 2017 Lohr, Smith, Suggett, Nitschke, Dumbrell, Woodcock and Camp. Coral communities are increasingly found to populate non-reef habitats prone to high environmental variability. Such sites include seagrass meadows, which are generally not considered optimal habitats for corals as a result of limited suitable substrate for settlement and substantial diel and seasonal fluctuations in physicochemical conditions relative to neighboring reefs. Interest in understanding the ability of corals to persist in non-reef habitats has grown, however little baseline data exists on community structure and recruitment of scleractinian corals in seagrass meadows. To determine how corals populate seagrass meadows, we surveyed the established and recruited coral community over 25 months within seagrass meadows at Little Cayman, Cayman Islands. Simultaneous surveys of established and recruited coral communities at neighboring back-reef sites were conducted for comparison. To fully understand the amount of environmental variability to which corals in each habitat were exposed, we conducted complementary surveys of physicochemical conditions in both seagrass meadows and back-reefs. Despite overall higher variability in physicochemical conditions, particularly pH, compared to the back-reef, 14 coral taxa were capable of inhabiting seagrass meadows, and multiple coral families were also found to recruit to these sites. However, coral cover and species diversity, richness, and evenness were lower at sites within seagrass meadows compared to back-reef sites. Although questions remain regarding the processes governing recruitment, these results provide evidence that seagrass beds can serve as functional habitats for corals despite high levels of environmental variability and suboptimal conditions compared to neighboring reefs.

Macreadie, PI, Nielsen, DA, Kelleway, JJ, Atwood, TB, Seymour, JR, Petrou, K, Connolly, RM, Thomson, ACG, Trevathan‐Tackett, SM & Ralph, PJ 2017, 'Can we manage coastal ecosystems to sequester more blue carbon?', Frontiers in Ecology and the Environment, vol. 15, no. 4, pp. 206-213.
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To promote the sequestration of blue carbon, resource managers rely on best‐management practices that have historically included protecting and restoring vegetated coastal habitats (seagrasses, tidal marshes, and mangroves), but are now beginning to incorporate catchment‐level approaches. Drawing upon knowledge from a broad range of environmental variables that influence blue carbon sequestration, including warming, carbon dioxide levels, water depth, nutrients, runoff, bioturbation, physical disturbances, and tidal exchange, we discuss three potential management strategies that hold promise for optimizing coastal blue carbon sequestration: (1) reducing anthropogenic nutrient inputs, (2) reinstating top‐down control of bioturbator populations, and (3) restoring hydrology. By means of case studies, we explore how these three strategies can minimize blue carbon losses and maximize gains. A key research priority is to more accurately quantify the impacts of these strategies on atmospheric greenhouse‐gas emissions in different settings at landscape scales.

Matthews, JL, Crowder, CM, Oakley, CA, Lutz, A, Roessner, U, Meyer, E, Grossman, AR, Weis, VM & Davy, SK 2017, 'Optimal nutrient exchange and immune responses operate in partner specificity in the cnidarian-dinoflagellate symbiosis', Proceedings of the National Academy of Sciences, vol. 114, no. 50, pp. 13194-13199.
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Significance Flexibility in the endosymbiotic Symbiodinium community could provide reef-building corals with the capacity to survive environmental change, but this may be restricted to compatible host-symbiont combinations. Therefore, determining the underlying molecular, cellular, and physiological processes of symbiont compatibility is of critical importance for elucidating the resilience and adaptability of coral reefs. We coupled gene expression data with high-throughput metabolite profiling to compare the effects on the sea anemone Aiptasia when colonized by the thermally tolerant, opportunistic, but comparatively unproductive Symbiodinium trenchii vs. the regular symbiont species, Symbiodinium minutum . This powerful approach revealed strong evidence that optimal nutritional exchange and the response to intracellular oxidative stress are important determinants in the success of novel cnidarian-dinoflagellate symbioses.

McElroy, DJ, Hochuli, DF, Doblin, MA, Murphy, RJ, Blackburn, RJ & Coleman, RA 2017, 'Effect of copper on multiple successional stages of a marine fouling assemblage', Biofouling, vol. 33, no. 10, pp. 904-916.
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© 2017 Informa UK Limited, trading as Taylor & Francis Group. Copper based paints are used to prevent fouling on the hulls of ships. The widely documented effect of copper on hull assemblages may be primarily due to direct effects on the invertebrates themselves or indirect effects from copper absorbed into the microbial biofilm before settlement has commenced. Artificial units of habitat were exposed to varied regimes of copper to examine (1) the photosynthetic efficiency and pigments of early-colonising biofilms, and (2) subsequent macroinvertebrate assemblage change in response to the different regimes of copper. Macroinvertebrate assemblages were found to be less sensitive to the direct effects of copper than indirect effects as delivered through biofilms that have been historically exposed to copper, with some species more tolerant than others. This raises further concern for the efficacy of copper as a universal antifoulant on the hulls of ships, which may continue to assist the invasion of copper-tolerant invertebrate species.

Mehmood, MA, Ye, G, Luo, H, Liu, C, Malik, S, Afzal, I, Xu, J & Ahmad, MS 2017, 'Pyrolysis and kinetic analyses of Camel grass ( Cymbopogon schoenanthus ) for bioenergy', Bioresource Technology, vol. 228, pp. 18-24.
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The aim of this work was to study the thermal degradation of grass (Cymbopogon schoenanthus) under an inert environment at three heating rates, including 10, 30, and 50°Cmin-1 in order to evaluate its bioenergy potential. Pyrolysis experiments were performed in a simultaneous Thermogravimetry-Differential Scanning Calorimetry analyzer. Thermal data were used to analyze kinetic parameters through isoconversional models of Flynn-Wall-Ozawa (FWO) and Kissenger-Akahira-Sunose (KSA) methods. The pre-exponential factors values have shown the reaction to follow first order kinetics. Activation energy values were shown to be 84-193 and 96-192kJmol-1 as calculated by KSA and FWO methods, respectively. Differences between activation energy and enthalpy of reaction values (∼5 to 6kJmol-1) showed product formation is favorable. The Gibb's free energy (173-177kJmol-1) and High Heating Value (15.00MJkg-1) have shown the considerable bioenergy potential of this low-cost biomass.

Messer, LF, Brown, MV, Furnas, MJ, Carney, RL, McKinnon, AD & Seymour, JR 2017, 'Diversity and Activity of Diazotrophs in Great Barrier Reef Surface Waters', Frontiers in Microbiology, vol. 8, no. JUN, pp. 1-16.
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© 2017 Messer, Brown, Furnas, Carney, McKinnon and Seymour. Discrepancies between bioavailable nitrogen (N) concentrations and phytoplankton growth rates in the oligotrophic waters of the Great Barrier Reef (GBR) suggest that undetermined N sources must play a significant role in supporting primary productivity. One such source could be biological dinitrogen (N2) fixation through the activity of 'diazotrophic' bacterioplankton. Here, we investigated N2 fixation and diazotroph community composition over 10° S of latitude within GBR surface waters. Qualitative N2 fixation rates were found to be variable across the GBR but were relatively high in coastal, inner and outer GBR waters, reaching 68 nmol L-1 d-1. Diazotroph assemblages, identified by amplicon sequencing of the nifH gene, were dominated by the cyanobacterium Trichodesmium erythraeum, γ-proteobacteria from the Gamma A clade, and δ-proteobacterial phylotypes related to sulfate-reducing genera. However, diazotroph communities exhibited significant spatial heterogeneity, correlated with shifts in dissolved inorganic nutrient concentrations. Specifically, heterotrophic diazotrophs generally increased in relative abundance with increasing concentrations of phosphate and N, while Trichodesmium was proportionally more abundant when concentrations of these nutrients were low. This study provides the first in-depth characterization of diazotroph community composition and N2 fixation dynamics within the oligotrophic, N-limited surface waters of the GBR. Our observations highlight the need to re-evaluate N cycling dynamics within oligotrophic coral reef systems, to include diverse N2 fixing assemblages as a potentially significant source of dissolved N within the water column.

Mondal, AK, Kretschmer, K, Zhao, Y, Liu, H, Fan, H & Wang, G 2017, 'Naturally nitrogen doped porous carbon derived from waste shrimp shells for high-performance lithium ion batteries and supercapacitors', Microporous and Mesoporous Materials, vol. 246, pp. 72-80.
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© 2017 Elsevier Inc. Transformation of biomass wastes into sustainable low cost carbon materials is now a topic of great interest. Here, we describe porous carbon from biomass derived waste shrimp shells and its application in two different energy storage systems. The unique porous structure with the presence of heteroatoms (O, N) makes it promising material for both lithium ion batteries and supercapacitors. When applied as anode materials for lithium ion batteries, the as-prepared carbon showed a specific capacity as high as 1507 mA h g−1 and 1014 mA h g−1 at current densities of 0.1 A g−1 and 0.5 A g−1, respectively, good rate performance and superior cycling stability. The porous carbon-based supercapacitor also delivered a specific capacitance of 239 F g−1 at a current density of 0.5 A g−1 in 6 M KOH electrolyte. The specific capacitance retention is 99.4% even after 5000 charge-discharge cycles, indicating excellent cycling stability. The superior electrochemical performances for both lithium ion batteries and supercapacitors could be ascribed to the high specific surface area, porous structure and nitrogen doping effect.

Mondal, AK, Kretschmer, K, Zhao, Y, Liu, H, Wang, C, Sun, B & Wang, G 2017, 'Nitrogen‐Doped Porous Carbon Nanosheets from Eco‐Friendly Eucalyptus Leaves as High Performance Electrode Materials for Supercapacitors and Lithium Ion Batteries', Chemistry – A European Journal, vol. 23, no. 15, pp. 3683-3690.
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AbstractNitrogen‐doped porous carbon nanosheets were prepared from eucalyptus tree leaves by simply mixing the leaf powders with KHCO3 and subsequent carbonisation. Porous carbon nanosheets with a high specific surface area of 2133 m2 g−1 were obtained and applied as electrode materials for supercapacitors and lithium ion batteries. For supercapacitor applications, the porous carbon nanosheet electrode exhibited a supercapacitance of 372 F g−1 at a current density of 500 mA g−1 in 1 m H2SO4 aqueous electrolyte and excellent cycling stability over 15 000 cycles. In organic electrolyte, the nanosheet electrode showed a specific capacitance of 71 F g−1 at a current density of 2 Ag−1 and stable cycling performance. When applied as the anode material for lithium ion batteries, the as‐prepared porous carbon nanosheets also demonstrated a high specific capacity of 819 mA h g−1 at a current density of 100 mA g−1, good rate capability, and stable cycling performance. The outstanding electrochemical performances for both supercapacitors and lithium ion batteries are derived from the large specific surface area, porous nanosheet structure and nitrogen doping effects. The strategy developed in this paper provides a novel route to utilise biomass‐derived materials for low‐cost energy storage systems.

Morelato, M, Barash, M, Blanes, L, Chadwick, S, Dilag, J, Kuzhiumparambil, U, Nizio, KD, Spindler, X & Moret, S 2017, 'Forensic Science: Current State and Perspective by a Group of Early Career Researchers', Foundations of Science, vol. 22, no. 4, pp. 799-825.
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© 2016, Springer Science+Business Media Dordrecht. Forensic science and its influence on policing and the criminal justice system have increased since the beginning of the twentieth century. While the philosophies of the forensic science pioneers remain the pillar of modern practice, rapid advances in technology and the underpinning sciences have seen an explosion in the number of disciplines and tools. Consequently, the way in which we exploit and interpret the remnant of criminal activity are adapting to this changing environment. In order to best exploit the trace, an interdisciplinary approach to both research and investigation is required. In this paper, nine postdoctoral research fellows from a multidisciplinary team discuss their vision for the future of forensic science at the crime scene, in the laboratory and beyond. This paper does not pretend to be exhaustive of all fields of forensic science, but describes a portion of the postdoctoral fellows’ interests and skills.

Munday, R, Murray, S, Rhodes, L, Larsson, M & Harwood, D 2017, 'Ciguatoxins and Maitotoxins in Extracts of Sixteen Gambierdiscus Isolates and One Fukuyoa Isolate from the South Pacific and Their Toxicity to Mice by Intraperitoneal and Oral Administration', Marine Drugs, vol. 15, no. 7, pp. 208-208.
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© 2017 by the authors. Licensee MDPI. Ciguatoxins (CTXs), and possibly maitotoxins (MTXs), are responsible for Ciguatera Fish Poisoning, an important health problem for consumers of reef fish (such as inhabitants of islands in the South Pacific Ocean). The habitational range of the Gambierdiscus species is expanding, and new species are being discovered. In order to provide information on the potential health risk of the Gambierdiscus species, and one Fukuyoa species (found in the Cook Islands, the Kermadec Islands, mainland New Zealand, and New South Wales, Australia), 17 microalgae isolates were collected from these areas. Unialgal cultures were grown and extracts of the culture isolates were analysed for CTXs and MTXs by liquid chromatography tandem mass spectrometry (LC-MS/MS), and their toxicity to mice was determined by intraperitoneal and oral administration. An isolate of G. carpenteri contained neither CTXs nor MTXs, while 15 other isolates (including G. australes, G. cheloniae, G. pacificus, G. honu, and F. paulensis) contained only MTX-1 and/or MTX-3. An isolate of G. polynesiensis contained both CTXs and MTX-3. All the extracts were toxic to mice by intraperitoneal injection, but those containing only MTX-1 and/or -3 were much less toxic by oral administration. The extract of G. polynesiensis was highly toxic by both routes of administration.

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

Najafpour, MM, Heidari, S, Balaghi, SE, Hołyńska, M, Sadr, MH, Soltani, B, Khatamian, M, Larkum, AW & Allakhverdiev, SI 2017, 'Proposed mechanisms for water oxidation by Photosystem II and nanosized manganese oxides', Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1858, no. 2, pp. 156-174.
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Plants, algae and cyanobacteria capture sunlight, extracting electrons from H2O to reduce CO2 into sugars while releasing O2 in the oxygenic photosynthetic process. Because of the important role of water oxidation in artificial photosynthesis and many solar fuel systems, understanding the structure and function of this unique biological catalyst forms a requisite research field. Herein the structure of the water-oxidizing complex and its ligand environment are described with reference to the 1.9Å resolution X-ray-derived crystallographic model of the water-oxidizing complex from the cyanobacterium Thermosynechococcus vulcanus. Proposed mechanisms for water oxidation by Photosystem II and nanosized manganese oxides are also reviewed and discussed in the paper.

Parker, LM, O'Connor, WA, Byrne, M, Coleman, RA, Virtue, P, Dove, M, Gibbs, M, Spohr, L, Scanes, E & Ross, PM 2017, 'Adult exposure to ocean acidification is maladaptive for larvae of the Sydney rock oyster Saccostrea glomerata in the presence of multiple stressors', Biology Letters, vol. 13, no. 2, pp. 20160798-20160798.
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Parental effects passed from adults to their offspring have been identified as a source of rapid acclimation that may allow marine populations to persist as our surface oceans continue to decrease in pH. Little is known, however, whether parental effects are beneficial for offspring in the presence of multiple stressors. We exposed adults of the oyster Saccostrea glomerata to elevated CO 2 and examined the impacts of elevated CO 2 (control = 392; 856 µatm) combined with elevated temperature (control = 24; 28°C), reduced salinity (control = 35; 25) and reduced food concentration (control = full; half diet) on their larvae. Adult exposure to elevated CO 2 had a positive impact on larvae reared at elevated CO 2 as a sole stressor, which were 8% larger and developed faster at elevated CO 2 compared with larvae from adults exposed to ambient CO 2 . These larvae, however, had significantly reduced survival in all multistressor treatments. This was particularly evident for larvae reared at elevated CO 2 combined with elevated temperature or reduced food concentration, with no larvae surviving in some treatment combinations. Larvae from CO 2 -exposed adults had a higher standard metabolic rate. Our results provide evidence that parental exposure to ocean acidification may be maladaptive when larvae experience multiple stressors.

Parker, LM, Scanes, E, O'Connor, WA, Coleman, RA, Byrne, M, Pörtner, H-O & Ross, PM 2017, 'Ocean acidification narrows the acute thermal and salinity tolerance of the Sydney rock oyster Saccostrea glomerata', Marine Pollution Bulletin, vol. 122, no. 1-2, pp. 263-271.
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Coastal and estuarine environments are characterised by acute changes in temperature and salinity. Organisms living within these environments are adapted to withstand such changes, yet near-future ocean acidification (OA) may challenge their physiological capacity to respond. We tested the impact of CO2-induced OA on the acute thermal and salinity tolerance, energy metabolism and acid-base regulation capacity of the oyster Saccostrea glomerata. Adult S. glomerata were acclimated to three CO2 levels (ambient 380μatm, moderate 856μatm, high 1500μatm) for 5weeks (24°C, salinity 34.6) before being exposed to a series of acute temperature (15-33°C) and salinity (34.2-20) treatments. Oysters acclimated to elevated CO2 showed a significant metabolic depression and extracellular acidosis with acute exposure to elevated temperature and reduced salinity, especially at the highest CO2 of 1500μatm. Our results suggest that the acute thermal and salinity tolerance of S. glomerata and thus its distribution will reduce as OA continues to worsen.

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

Pirotta, V, Smith, A, Ostrowski, M, Russell, D, Jonsen, ID, Grech, A & Harcourt, R 2017, 'An Economical Custom-Built Drone for Assessing Whale Health', Frontiers in Marine Science, vol. 4, no. DEC, pp. 1-12.
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Drones or Unmanned Aerial Vehicles (UAVs) have huge potential to improve the safety and efficiency of sample collection from wild animals under logistically challenging circumstances. Here we present a method for surveying population health that uses UAVs to sample respiratory vapor, 'whale blow,' exhaled by free-swimming humpback whales (Megaptera novaeangliae), and coupled this with amplification and sequencing of respiratory tract microbiota. We developed a low-cost multirotor UAV incorporating a sterile petri dish with a remotely operated 'blow' to sample whale blow with minimal disturbance to the whales. This design addressed several sampling challenges: accessibility; safety; cost, and critically, minimized the collection of atmospheric and seawater microbiota and other potential sources of sample contamination. We collected 59 samples of blow from northward migrating humpback whales off Sydney, Australia and used high throughput sequencing of bacterial ribosomal gene markers to identify putative respiratory tract microbiota. Model-based comparisons with seawater and drone-captured air demonstrated that our system minimized external sources of contamination and successfully captured sufficient material to identify whale blow-specific microbial taxa. Whale-specific taxa included species and genera previously associated with the respiratory tracts or oral cavities of mammals (e.g., Pseudomonas, Clostridia, Cardiobacterium), as well as species previously isolated from dolphin or killer whale blowholes (Corynebacteria, others). Many examples of exogenous marine species were identified, including Tenacibaculum and Psychrobacter spp. that have been associated with the skin microbiota of marine mammals and fish and may include pathogens. This information provides a baseline of respiratory tract microbiota profiles of contemporary whale health. Customized UAVs are a promising new tool for marine megafauna research and may have broad application in cost-ef...

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

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

Scanes, E, Parker, LM, O'Connor, WA, Stapp, LS & Ross, PM 2017, 'Intertidal oysters reach their physiological limit in a future high-CO2 world', Journal of Experimental Biology, vol. 220, no. 5, pp. 765-774.
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ABSTRACT Sessile marine molluscs living in the intertidal zone experience periods of internal acidosis when exposed to air (emersion) during low tide. Relative to other marine organisms, molluscs have been identified as vulnerable to future ocean acidification; however, paradoxically it has also been shown that molluscs exposed to high CO2 environments are more resilient compared with those molluscs naive to CO2 exposure. Two competing hypotheses were tested using a novel experimental design incorporating tidal simulations to predict the future intertidal limit of oysters in a high-CO2 world; either high-shore oysters will be more tolerant of elevated PCO2 because of their regular acidosis, or elevated PCO2 will cause high-shore oysters to reach their limit. Sydney rock oysters, Saccostrea glomerata, were collected from the high-intertidal and subtidal areas of the shore and exposed in an orthogonal design to either an intertidal or a subtidal treatment at ambient or elevated PCO2, and physiological variables were measured. The combined treatment of tidal emersion and elevated PCO2 interacted synergistically to reduce the haemolymph pH (pHe) of oysters, and increase the PCO2 in the haemolymph (Pe,CO2) and standard metabolic rate. Oysters in the intertidal treatment also had lower condition and growth. Oysters showed a high degree of plasticity, and little evidence was found that intertidal oysters were more resilient than subtidal oysters. It is concluded that in a high-CO2 world the upper vertical limit of oyster distribution on the shore may be reduced. These results suggest that previous studies on intertidal organisms that lacked tidal simulations may have underestimated the effects of elevated PCO2.

Segečová, A, Červený, J & Roitsch, T 2017, 'Stress Response Monitoring of Photoautotrophic Higher Plant Suspension Cultures by Fluorescence Imaging for High-Throughput Toxic Compound Screening', Journal of Environmental Protection, vol. 08, no. 06, pp. 678-692.
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Seymour, JR, Amin, SA, Raina, J-B & Stocker, R 2017, 'Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships', Nature Microbiology, vol. 2, no. 7, pp. 1-12.
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© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. By controlling nutrient cycling and biomass production at the base of the food web, interactions between phytoplankton and bacteria represent a fundamental ecological relationship in aquatic environments. Although typically studied over large spatiotemporal scales, emerging evidence indicates that this relationship is often governed by microscale interactions played out within the region immediately surrounding individual phytoplankton cells. This microenvironment, known as the phycosphere, is the planktonic analogue of the rhizosphere in plants. The exchange of metabolites and infochemicals at this interface governs phytoplankton-bacteria relationships, which span mutualism, commensalism, antagonism, parasitism and competition. The importance of the phycosphere has been postulated for four decades, yet only recently have new technological and conceptual frameworks made it possible to start teasing apart the complex nature of this unique microbial habitat. It has subsequently become apparent that the chemical exchanges and ecological interactions between phytoplankton and bacteria are far more sophisticated than previously thought and often require close proximity of the two partners, which is facilitated by bacterial colonization of the phycosphere. It is also becoming increasingly clear that while interactions taking place within the phycosphere occur at the scale of individual microorganisms, they exert an ecosystem-scale influence on fundamental processes including nutrient provision and regeneration, primary production, toxin biosynthesis and biogeochemical cycling. Here we review the fundamental physical, chemical and ecological features of the phycosphere, with the goal of delivering a fresh perspective on the nature and importance of phytoplankton-bacteria interactions in aquatic ecosystems.

Startsev, MA, Ostrowski, M, Goldys, EM & Inglis, DW 2017, 'A mobility shift assay for DNA detection using nanochannel gradient electrophoresis', ELECTROPHORESIS, vol. 38, no. 2, pp. 335-341.
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Conventional detection of pathogenic or other biological contamination relies on amplification of DNA using sequence‐specific primers. Recent work in nanofluidics has shown very high concentration enhancement of biomolecules with some degree of simultaneous separation. This work demonstrates the combination of these two approaches by selectively concentrating a mobility‐shifted hybridization product, potentially enabling rapid detection of rare DNA fragments such as highly specific 16S ribosomal DNA. We have performed conductivity gradient electrofocusing within nanofluidic channels and have shown concentration of hybridized peptide nucleic acids and DNA oligomers. We also show selectivity to single base‐pair mismatch on 18‐mer oligos. This approach may enable sensitive optical detection of small amounts of DNA.

Suggett, DJ, Warner, ME & Leggat, W 2017, 'Symbiotic Dinoflagellate Functional Diversity Mediates Coral Survival under Ecological Crisis', Trends in Ecology & Evolution, vol. 32, no. 10, pp. 735-745.
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© 2017 Elsevier Ltd Coral reefs have entered an era of ‘ecological crisis’ as climate change drives catastrophic reef loss worldwide. Coral growth and stress susceptibility are regulated by their endosymbiotic dinoflagellates (genus Symbiodinium). The phylogenetic diversity of Symbiodinium frequently corresponds to patterns of coral health and survival, but knowledge of functional diversity is ultimately necessary to reconcile broader ecological success over space and time. We explore here functional traits underpinning the complex biology of Symbiodinium that spans free-living algae to coral endosymbionts. In doing so we propose a mechanistic framework integrating the primary traits of resource acquisition and utilisation as a means to explain Symbiodinium functional diversity and to resolve the role of Symbiodinium in driving the stability of coral reefs under an uncertain future. Coral ecosystem health is strongly influenced by Symbiodinium diversity. The ecological success of Symbiodinium cannot be resolved from phylogenetic diversity alone. Traits describing resource acquisition and incorporation capture the functional diversity of Symbiodinium. Symbiodinium species shifts reflect the changing metabolic requirements of the host. Functional diversity will determine the resilience of coral reefs to environmental change.

Sukačová, K & Červený, J 2017, 'Can algal biotechnology bring effective solution for closing the phosphorus cycle? Use of algae for nutrient removal: Review of past trends and future perspectives in the context of nutrient recovery', EUROPEAN JOURNAL OF ENVIRONMENTAL SCIENCES, vol. 7, no. 1, pp. 63-72.
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© 2017 The Author. Eutrophication of water by nutrient pollution is a global environmental issue. Biological methods for removing nutrients are environmentally friendly and sustainable. Therefore, this article summarizes main trends in the use of algae for removing nutrients from wastewater using both suspended and attached algal-based systems. A wide variety of algal species and experimental approaches has been tested to date. Researchers report that algae are able to effectively remove a variety of pollutants and nutrients. This review also discusses the potential of algal-based technology for nutrient, especially phosphorus, recovery. Despite the fact that effective nutrient removal has been demonstrated, there are still many challenges to be overcome in the development of succesfull technologies.

Szabó, M, Larkum, AWD, Suggett, DJ, Vass, I, Sass, L, Osmond, B, Zavafer, A, Ralph, PJ & Chow, WS 2017, 'Non-intrusive Assessment of Photosystem II and Photosystem I in Whole Coral Tissues', Frontiers in Marine Science, vol. 4, no. AUG, pp. 1-12.
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© 2017 Szabó, Larkum, Suggett, Vass, Sass, Osmond, Zavafer, Ralph and Chow. Reef building corals (phylum Cnidaria) harbor endosymbiotic dinoflagellate algae (genus Symbiodinium) that generate photosynthetic products to fuel their host's metabolism. Non-invasive techniques such as chlorophyll (Chl) fluorescence analyses of Photosystem II (PSII) have been widely used to estimate the photosynthetic performance of Symbiodinium in hospite. However, since the spatial origin of PSII chlorophyll fluorescence in coral tissues is uncertain, such signals give limited information on depth-integrated photosynthetic performance of the whole tissue. In contrast, detection of absorbance changes in the near infrared (NIR) region integrates signals from deeper tissue layers due to weak absorption and multiple scattering of NIR light. While extensively utilized in higher plants, NIR bio-optical techniques are seldom applied to corals. We have developed a non-intrusive measurement method to examine photochemistry of intact corals, based on redox kinetics of the primary electron donor in Photosystem I (P700) and chlorophyll fluorescence kinetics (Fast-Repetition Rate fluorometry, FRRf). Since the redox state of P700 depends on the operation of both PSI and PSII, important information can be obtained on the PSII-PSI intersystem electron transfer kinetics. Under moderate, sub-lethal heat stress treatments (33◦ C for~20 min), the coral Pavona decussata exhibited down-regulation of PSII electron transfer kinetics, indicated by slower rates of electron transport from QA to plastoquinone (PQ) pool, and smaller relative size of oxidized PQ with concomitant decrease of a specifically-defined P700 kinetics area, which represents the active pool of PSII. The maximum quantum efficiency of PSII (Fv /Fm ) and functional absorption cross-section of PSII (σPSII ) remained unchanged. Based on the coordinated response of P700 parameters and PSII-PSI electron transport properties, we propose...

Tout, J, Astudillo‐García, C, Taylor, MW, Tyson, GW, Stocker, R, Ralph, PJ, Seymour, JR & Webster, NS 2017, 'Redefining the sponge‐symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host‐derived compounds', Environmental Microbiology Reports, vol. 9, no. 6, pp. 750-755.
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SummaryMarine sponges host stable and species‐specific microbial symbionts that are thought to be acquired and maintained by the host through a combination of vertical transmission and filtration from the surrounding seawater. To assess whether the microbial symbionts also actively contribute to the establishment of these symbioses, we performed in situ experiments on Orpheus Island, Great Barrier Reef, to quantify the chemotactic responses of natural populations of seawater microorganisms towards cellular extracts of the reef sponge Rhopaloeides odorabile. Flow cytometry analysis revealed significant levels of microbial chemotaxis towards R. odorabile extracts and 16S rRNA gene amplicon sequencing showed enrichment of ‘sponge‐specific’ microbial phylotypes, including a cluster within the Gemmatimonadetes and another within the Actinobacteria. These findings infer a potential mechanism for how sponges can acquire bacterial symbionts from the surrounding environment and suggest an active role of the symbionts in finding their host.

Tran, N-AT, Seymour, JR, Siboni, N, Evenhuis, CR & Tamburic, B 2017, 'Photosynthetic carbon uptake induces autoflocculation of the marine microalga Nannochloropsis oculata', Algal Research, vol. 26, pp. 302-311.
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© 2017 Elsevier B.V. Microalgal biomass has been used to produce biofuels, aquaculture feed, high-value chemicals such as pigments and antioxidants, and even human food. This study addresses one of the key bottlenecks to the commercialisation of microalgal bioproducts: the high energy and environmental cost of harvesting microalgal cells out of suspension. An innovative and sustainable autoflocculation procedure was developed to pre-concentrate microalgal biomass for easier harvesting. Microalgal cell agglomeration by autoflocculation at high pH was induced for the first time, without the addition of a chemical flocculant, in the commercially-relevant microalga Nannochloropsis oculata. Photosynthetic inorganic carbon uptake, in the absence of carbon dioxide supply by mass transfer, was used to raise the culture pH. Autoflocculation started at pH 9.5 and reached a maximum flocculation efficiency of 90% at pH 10.4. Microalgal surface charge-neutralisation by calcium cations, and sweep flocculation by calcium carbonate and calcium phosphate precipitates were identified as the dominant flocculation mechanisms. This was also the first study to measure changes in bacterial community composition under autoflocculation. There was a clear shift from free-living bacteria in suspension to attached bacteria during autoflocculation, with Flavobacteriales becoming the dominant order of bacteria. This highlights the influential role of attached bacteria and bacteria-produced extracellular polymeric substances in microalgal flocculation. This study shows that regulating carbon dioxide supply is a promising green alternative to traditional microalgal flocculation processes as it alleviates the requirement for costly and harmful chemical flocculants and brings us closer to sustainable microalgal bioproducts.

Trevathan-Tackett, SM, Macreadie, PI, Sanderman, J, Baldock, J, Howes, JM & Ralph, PJ 2017, 'A Global Assessment of the Chemical Recalcitrance of Seagrass Tissues: Implications for Long-Term Carbon Sequestration', Frontiers in Plant Science, vol. 8.
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© 2017 Trevathan-Tackett, Macreadie, Sanderman, Baldock, Howes and Ralph. Seagrass ecosystems have recently been identified for their role in climate change mitigation due to their globally-significant carbon sinks; yet, the capacity of seagrasses to sequester carbon has been shown to vary greatly among seagrass ecosystems. The recalcitrant nature of seagrass tissues, or the resistance to degradation back into carbon dioxide, is one aspect thought to influence sediment carbon stocks. In this study, a global survey investigated how the macromolecular chemistry of seagrass leaves, sheaths/stems, rhizomes and roots varied across 23 species from 16 countries. The goal was to understand how this seagrass chemistry might influence the capacity of seagrasses to contribute to sediment carbon stocks. Three non-destructive analytical chemical analyses were used to investigate seagrass chemistry: thermogravimetric analysis (TGA) and solid state13 C-NMR and infrared spectroscopy. A strong latitudinal influence on carbon quality was found, whereby temperate seagrasses contained 5% relatively more labile carbon, and tropical seagrasses contained 3% relatively more refractory carbon. Sheath/stem tissues significantly varied across taxa, with larger morphologies typically containing more refractory carbon than smaller morphologies. Rhizomes were characterized by a higher proportion of labile carbon (16%of total organic matter compared to 8–10%in other tissues); however, high rhizome biomass production and slower remineralization in anoxic sediments will likely enhance these below-ground tissues’ contributions to long-termcarbon stocks. Our study provides a standardized and global dataset on seagrass carbon quality across tissue types, taxa and geography that can be incorporated in carbon sequestration and storage models as well as ecosystem valuation and management strategies.

Trevathan-Tackett, SM, Seymour, JR, Nielsen, DA, Macreadie, PI, Jeffries, TC, Sanderman, J, Baldock, J, Howes, JM, Steven, ADL & Ralph, PJ 2017, 'Sediment anoxia limits microbial-driven seagrass carbon remineralization under warming conditions', FEMS Microbiology Ecology, vol. 93, no. 6.
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© FEMS 2017. All rights reserved. Seagrass ecosystems are significant carbon sinks, and their resident microbial communities ultimately determine the quantity and quality of carbon sequestered. However, environmental perturbations have been predicted to affect microbial-driven seagrass decomposition and subsequent carbon sequestration. Utilizing techniques including 16S-rDNA sequencing, solid-state NMR and microsensor profiling, we tested the hypothesis that elevated seawater temperatures and eutrophication enhance the microbial decomposition of seagrass leaf detritus and rhizome/root tissues. Nutrient additions had a negligible effect on seagrass decomposition, indicating an absence of nutrient limitation. Elevated temperatures caused a 19% higher biomass loss for aerobically decaying leaf detritus, coinciding with changes in bacterial community structure and enhanced lignocellulose degradation. Although, community shifts and lignocellulose degradation were also observed for rhizome/root decomposition, anaerobic decay was unaffected by temperature. These observations suggest that oxygen availability constrains the stimulatory effects of temperature increases on bacterial carbon remineralization, possibly through differential temperature effects on bacterial functional groups, including putative aerobic heterotrophs (e.g. Erythrobacteraceae, Hyphomicrobiaceae) and sulfate reducers (e.g. Desulfobacteraceae). Consequently, under elevated seawater temperatures, carbon accumulation rates may diminish due to higher remineralization rates at the sediment surface. Nonetheless, the anoxic conditions ubiquitous to seagrass sediments can provide a degree of carbon protection under warming seawater temperatures.

van den Engh, GJ, Doggett, JK, Thompson, AW, Doblin, MA, Gimpel, CNG & Karl, DM 2017, 'Dynamics of Prochlorococcus and Synechococcus at Station ALOHA Revealed through Flow Cytometry and High-Resolution Vertical Sampling', Frontiers in Marine Science, vol. 4, no. NOV.
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© 2017 van den Engh, Doggett, Thompson, Doblin, Gimpel and Karl. The fluorescence and scattering properties of Prochlorococcus and Synechococcus at Station ALOHA as measured by flow cytometry (termed the FCM phenotype) vary with depth and over a variety of time scales. The variation in FCM phenotypes may reflect population selection or physiological acclimation to local conditions. Observations before, during, and after a storm with deep water mixing show a short-term homogenization of the FCM phenotypes with depth, followed by a return to the stable pattern over the time span of a few days. These dynamics indicate that, within the upper mixed-layer, the FCM phenotype distribution represents acclimation to ambient light. The populations in the pycnocline (around 100 m and below), remain stable and are invariant with light conditions. In samples where both cyanobacteria coexist, fluorescence properties of Prochlorococcus and Synechococcus are tightly correlated providing further evidence that FCM phenotype variability is caused by a common environmental factor or factors. Measurements of the dynamics of FCM phenotypes provide insights into phytoplankton physiology and adaptation. Alternatively, FCM phenotype census of a water mass may provide information about its origin and illumination history.

Wangpraseurt, D, Holm, JB, Larkum, AWD, Pernice, M, Ralph, PJ, Suggett, DJ & Kühl, M 2017, 'In vivo Microscale Measurements of Light and Photosynthesis during Coral Bleaching: Evidence for the Optical Feedback Loop?', Frontiers in Microbiology, vol. 8, no. JAN, pp. 1-12.
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© 2017 Wangpraseurt, Holm, Larkum, Pernice, Ralph, Suggett and Kühl. Climate change-related coral bleaching, i.e., the visible loss of zooxanthellae from the coral host, is increasing in frequency and extent and presents a major threat to coral reefs globally. Coral bleaching has been proposed to involve accelerating light stress of their microalgal endosymbionts via a positive feedback loop of photodamage, symbiont expulsion and excess in vivo light exposure. To test this hypothesis, we used light and O2 microsensors to characterize in vivo light exposure and photosynthesis of Symbiodinium during a thermal stress experiment. We created tissue areas with different densities of Symbiodinium cells in order to understand the optical properties and light microenvironment of corals during bleaching. Our results showed that in bleached Pocillopora damicornis corals, Symbiodinium light exposure was up to fivefold enhanced relative to healthy corals, and the relationship between symbiont loss and light enhancement was well-described by a power-law function. Cell-specific rates of Symbiodinium gross photosynthesis and light respiration were enhanced in bleached P. damicornis compared to healthy corals, while areal rates of net photosynthesis decreased. Symbiodinium light exposure in Favites sp. revealed the presence of low light microniches in bleached coral tissues, suggesting that light scattering in thick coral tissues can enable photoprotection of cryptic symbionts. Our study provides evidence for the acceleration of in vivo light exposure during coral bleaching but this optical feedback mechanism differs between coral hosts. Enhanced photosynthesis in relation to accelerating light exposure shows that coral microscale optics exerts a key role on coral photophysiology and the subsequent degree of radiative stress during coral bleaching.

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

Wilkinson, AD, Collier, CJ, Flores, F, Langlois, L, Ralph, PJ & Negri, AP 2017, 'Combined effects of temperature and the herbicide diuron on Photosystem II activity of the tropical seagrass Halophila ovalis', Scientific Reports, vol. 7, no. 1, pp. 1-11.
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AbstractTropical seagrasses are at their highest risk of exposure to photosystem II (PSII) herbicides when elevated rainfall and runoff from farms transports these toxicants into coastal habitats during summer, coinciding with periods of elevated temperature. PSII herbicides, such as diuron, can increase the sensitivity of corals to thermal stress, but little is known of the potential for herbicides to impact the thermal optima of tropical seagrass. Here we employed a well-plate approach to experimentally assess the effects of diuron on the photosynthetic performance of Halophila ovalis leaves across a 25 °C temperature range (36 combinations of these stressors across 15–40 °C). The thermal optimum for photosynthetic efficiency (▵'Equation missing') in H. ovalis was 31 °C while lower and higher temperatures reduced ▵'Equation missing' as did all elevated concentrations of diuron. There were significant interactions between the effects of temperature and diuron, with a majority of the combined stresses causing sub-additive (antagonistic) effects. However, both stressors caused negative responses and the sum of the responses was greater than that caused by temperature or diuron alone. These results indicate that improving water quality (reducing herbicide in runoff) is likely to maximise seagrass health during extreme temperature events that will become more common as the climate changes.

Wilkinson, S, Stoller, P, Ralph, P, Hamdorf, B, Catana, LN & Kuzava, GS 2017, 'Exploring the Feasibility of Algae Building Technology in NSW', Procedia Engineering, vol. 180, pp. 1121-1130.
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© 2017 The Authors. Published by Elsevier Ltd. For some time, Biochemists have been exploring the potential to produce biofuels as an alternative to fossil fuel energy. Biofuels can be derived from crops such as corn, soybean and sugarcane however these crops can contribute to water scarcity and deforestation. Furthermore, large areas of land are used that could otherwise be used for food production. Another possibility is to use microalgae, which does not have the disadvantages associated with crop-based biofuels. Depending on conditions, microalgae can produce bio compounds that are converted into biofuels. The built environment is responsible for around 40 to 50% of total greenhouse gas emissions through fossil fuel consumption. Not only is it necessary to design and to retrofit our built environment to be more energy efficient, but it is also necessary to consider alternative fuel sources. To date, this has mostly focused on solar, wind and geothermal sources, however one residential building in Hamburg Germany has adopted algae building technology in the form of façade panels which act as a source of energy for heating the apartments and for hot water. The climate in northern Germany is very different to Australia, and the question arises; what is the feasibility to adopt algae building technology in New South Wales? There are issues around the physical and technical aspects of the technology, the social and environmental aspects, the regulatory and planning aspects, as well as the economic considerations. This paper reports on a study with key stakeholders in New South Wales to explore barriers and drivers associated with the adoption of algae building technology.

Yan, J, Kuzhiumparambil, U, Bandodkar, S, Solowij, N & Fu, S 2017, 'Development and validation of a simple, rapid and sensitive LC-MS/MS method for the measurement of urinary neurotransmitters and their metabolites', Analytical and Bioanalytical Chemistry, vol. 409, no. 30, pp. 7191-7199.
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Zavřel, T, Očenášová, P & Červený, J 2017, 'Phenotypic characterization of Synechocystis sp. PCC 6803 substrains reveals differences in sensitivity to abiotic stress', PLOS ONE, vol. 12, no. 12, pp. e0189130-e0189130.
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© 2017 Zavřel et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Synechocystis sp. PCC 6803 is a widely used model cyanobacterium, whose substrains can vary on both genotype and phenotype levels. Previously described phenotypic variations include ability of mixotrophic growth, ability of movement on agar plates and variations in pigments composition or cell size. In this study, we report for the first time significant variation among Synechocystis substrains in complex cellular traits such as growth rate, photosynthesis efficiency, cellular dry weight and cellular composition (including protein or carbohydrates content). We also confirmed previously reported differences in cell size. Synechocystis cultures were cultivated in controlled environment of flat panel photobioreactors under red, blue and white light of intensities up to 790 μmol(photons) m-2 s-1, temperatures 23C–60C, input CO2 concentrations ranging from 400 to 15 000 ppm and in BG11 cultivation medium with and without addition of NaCl. Three Synechocystis substrains were used for the comparative experiments: GT-L, GT-B (Brno, CZ) and PCC-B (Brno, CZ). Growth rates of Synechocystis GT-B were inhibited under high intensities of red light (585–670 nm), and growth rates of both substrains GT-B and PCC-B were inhibited under photons of wavelengths 485–585 nm and 670–700 nm. Synechocystis GT-B was more sensitive to low temperatures than the other two tested substrains, and Synechocystis GT-L was sensitive to the presence of NaCl in the cultivation media. The results suggest that stress sensitivity of commonly used Synechocystis substrains can strongly vary, similarly as glucose tolerance or motility as reported previously. Our study further supports the previous statement that emphasizes importance of proper ...

Zhu, Y, Ishizaka, J, Tripathy, SC, Wang, S, Sukigara, C, Goes, J, Matsuno, T & Suggett, DJ 2017, 'Relationship between light, community composition and the electron requirement for carbon fixation in natural phytoplankton', Marine Ecology Progress Series, vol. 580, pp. 83-100.
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© Inter-Research 2017. Fast repetition rate fluorometry (FRRF) provides a means to examine primary productivity at high resolution across broad scales, but must be coupled with independent knowledge of the electron requirement for carbon uptake (KC) to convert FRRF-measured electron transfer rate (ETR) to an inorganic carbon (C) uptake rate. Previous studies have demonstrated that variability of KC can be explained by key environmental factors (e.g. light, nutrients, temperature). However, how such reconciliation of KC reflects changes of phytoplankton physiological status versus that of community composition has not been well resolved. Therefore, using a dataset of coupled FRRF and C uptake measurements, we examined how the environmental dependency of KC potentially varied with parallel changes in phytoplankton community structure. Data were combined from 14 campaigns conducted during the summer season throughout 2007 to 2014 in the East China Sea (ECS) and Tsushima Strait (TS). KC varied considerably, but this variability was best explained by a linear relationship with light availability (R2 = 0.66). Co-variability between KC and light availability was slightly improved by considering data as 2 clusters of physico-chemical conditions (R2 = 0.74), but was best improved as 2 taxonomic clusters: samples dominated by micro-phytoplankton (>20 μm) versus small phytoplankton (nano + pico, <20 μm; R2 = 0.70-0.81). Interaction of phytoplankton community structure with light availability therefore explains the majority of variance of KC. The algorithms generated through our analysis therefore provide a means to examine C uptake with high resolution from future FRRF observations from these waters.

Gachon, CMM, Badis, Y, Klochkova, TA, Strittmatter, M, Garvetto, A, Murua, P, Ostrowski, M, Tringe, S, Prochnik, S, Sanderson, C & Kim, GH 1970, 'HIDDEN DIVERSITY IN THE OOMYCETE GENUS OLPIDIOPSIS IS A GLOBAL THREAT TO RED ALGAL CULTIVATION', PHYCOLOGIA, INT PHYCOLOGICAL SOC, pp. 54-55.

Bouman, HA, Platt, T, Doblin, M, Figueiras, FG, Gudmudsson, K, Gudfinnsson, HG, Huang, B, Hickman, A, Hiscock, M, Jackson, T, Lutz, VA, Mélin, F, Rey, F, Pepin, P, Segura, V, Tilstone, GH, van Dongen-Vogels, V & Sathyendranath, S 2017, 'Photosynthesis-irradiance parameters of marine phytoplankton: synthesis of a global data set', Copernicus GmbH.
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Abstract. The photosynthetic performance of marine phytoplankton varies in response to a variety of factors, environmental and taxonomic. One of the aims of the MArine primary Production: model Parameters from Space (MAPPS) project of the European Space Agency is to assemble a global database of photosynthesis-irradiance (P-E) parameters from a range of oceanographic regimes as an aid to examining the basin-scale variability in the photophysiological response of marine phytoplankton and to use this information to improve the assignment of P-E parameters in the estimation of global marine primary production using satellite data. The MAPPS P-E Database, which consists of over 5000 P-E experiments, provides information on the spatio-temporal variability in the two P-E parameters (the assimilation number, PmB, and the initial slope, αB, where the superscripts B indicate normalisation to concentration of chlorophyll) that are fundamental inputs for models (satellite-based and otherwise) of marine primary production that use chlorophyll as the state variable. Quality-control measures consisted of removing samples with abnormally-high parameter values and flags were added to denote whether the spectral quality of the incubator lamp was used to calculate a broad-band value of αB. The MAPPS database provides a photophysiological dataset that is unprecedented in number of observations and in spatial coverage. The database would be useful to a variety of research communities, including marine ecologists, biogeochemical modellers, remote-sensing scientists and algal physiologists. The compiled data are available at https://doi.org/10.1594/PANGAEA.874087 (Bouman et al., 2017).

Cardona, T, Sánchez-Baracaldo, P, Rutherford, AW & Larkum, AWD 2017, 'Early Archean origin of Photosystem II', Cold Spring Harbor Laboratory.
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AbstractPhotosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of Eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale we hypothesize that this early Archean photosystem was capable of water oxidation and had already evolved some level of protection against the formation of reactive oxygen species, which would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

Faizi, M, Zavřel, T, Loureiro, C, Cerveny, J & Steuer, R 2017, 'A minimal model of protein allocation during phototrophic growth', Cold Spring Harbor Laboratory.
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AbstractPhotoautotrophic growth depends upon an optimal allocation of finite cellular resources to diverse intracellular processes. Commitment of a certain mass fraction of the proteome to a specific cellular function, typically reduces the proteome available for other cellular functions. Here, we develop a minimal semi-quantitative kinetic model of cyanobacterial phototrophic growth to describe such trade-offs of cellular protein allocation. The model is based on coarse-grained descriptions of key cellular processes, in particular carbon uptake, metabolism, photosynthesis, and protein translation. The model is parametrized using literature data and experimentally obtained growth curves. Of particular interest are the resulting cyanobacterial growth laws as fundamental characteristics of cellular growth. We show that the model gives rise to similar growth laws as observed for heterotrophic organisms, with several important differences due to the distinction between light energy and carbon uptake. We discuss recent experimental data supporting the model results and show that minimal growth models have implications for our understanding of the limits of phototrophic growth and bridge a gap between molecular physiology and ecology.

Kelleway, JJ, Saintilan, N, Macreadie, PI, Baldock, JA & Ralph, PJ 2017, 'Sediment and carbon accumulation vary among vegetation assemblages in a coastal saltmarsh', Copernicus GmbH, Copernicus GmbH.
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Abstract. Coastal saltmarshes are dynamic, intertidal ecosystems which are increasingly being recognised for their contributions to ecosystem services, including carbon (C) accumulation and storage. The survival of saltmarshes and their capacity to store C under rising sea levels, however, is partially reliant upon surface sedimentation rates and influenced by a combination of physical and biological factors. In this study, we use several complementary methods to assess short-term (days) deposition and medium-term (months) accretion dynamics within three saltmarsh vegetation types common throughout southeast (SE) Australia. We found that surface accretion varies among vegetation assemblages, with medium-term (19 month) bulk accretion rates in the upper marsh rush (Juncus) assemblage (1.74 ± 0.13 mm y−1) consistently in excess of estimated local sea level rise (1.15 mm y−1). Accretion was lower and less consistent in both the succulent (Sarcocornia) (0.78 ± 0.18 mm y−1) and grass (Sporobolus) (0.88 ± 0.22 mm y−1) assemblages located lower in the tidal frame. Short-term (6 d) experiments showed deposition within Juncus plots to be dominated by autochthonous organic inputs with C deposition rates ranging from 0.41 ± 0.15 g C cm−2 y−1 (neap tidal period) to 0.87 ± 0.16 g C cm−2 y−1 (spring tidal period), while minerogenic inputs and lower C deposition dominated Sarcocornia (0.03 ± 0.01 to 0.23 ± 0.03 g C cm−2 y−1) and Sporobolus (0.06 ± 0.01 to 0.15 ± 0.03 g C cm−2 y−1) assemblages. Elemental (C : N), isotopic (δ13C), mid infrared (MIR) and 13C NMR analyses revealed little difference in either the source or character of materials being deposited among neap versus spring tidal periods. Instead, these analyses point to substantial redistribution of materials within the Sarcocornia and Sporobolus assemblages, compared to high retention and preservation of organic inputs in the Juncus assemblage. By combining medium-term accretion quantification with short-term d...

Kumar, M & Ralph, P 2017, 'Systems Biology of Marine Ecosystems', Springer International Publishing, pp. 1-351.
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© Springer International Publishing AG 2017. This book describes the latest advances in systems biology in four plant-based marine ecosystems: seaweeds, seagrasses, microalgae, and corals. Marine organisms that inhabit the oceanic environment experience a diverse range of environmental fluctuations, anthropogenic stress, and threats from invasive species and pathogens. System biology integrates physiology, genomics, transcriptomics, proteomics, and metabolomics into numerical models and is emerging as an important approach to elucidate the functional adaptations of marine organisms to adverse environmental conditions. This book focuses on how ecophysiology, omics platforms, their integration (a systems biology perspective), and next generation sequencing tools are being used to address the stress response of marine seaweeds, seagrasses, corals, marine microbe diversity, and micro-and macroalgae/corals-bacterial interactions to global climate change and anthropogenic activities. The contents of the book are of special interest to graduate and postgraduate marine biology students and marine biology researchers, particularly those interested in marine ecology, stress physiology of marine macrophytes/corals/phytoplankton, and environmental microbiology. This book would also be of interest to marine engineers engaged in the management and conservation of our valuable marine resources.