Publications

Larkum, AWD, Kendrick, GA & Ralph, PJ 2018, Preface.
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Larkum, AWD, Kendrick, GA & Ralph, PJ 2018, Seagrasses of Australia: Structure, ecology and conservation.
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© Springer International Publishing AG, part of Springer Nature 2018. All rights reserved. This book takes the place of "Biology of Seagrasses: A Treatise on the Biology of Seagrasses with Special Reference to the Australian Region", co-edited by A.W.D. Larkum, A.J. MaCComb and S.A. Shepherd and published by Elsevier in 1989. The first book has been influential, but it is now 25 years since it was published and seagrass studies have progressed and developed considerably since then. The design of the current book follows in the steps of the first book. There are chapters on taxonomy, floral biology, biogeography and regional studies. The regional studies emphasize the importance of Australia having over half of the world's 62 species, including some ten species published for Australia since the previous book. There are a number of chapters on ecology and biogeography; fish biology and fisheries and dugong biology are prominent chapters. Physiological aspects again play an important part, including new knowledge on the role of hydrogen sulphide in sediments and on photosynthetic processes. Climate change, pollution and environmental degradation this time gain an even more important part of the book. Decline of seagrasses around Australia are also discussed in detail in several chapters. Since the first book was published two new areas have received special attention: blue carbon and genomic studies. Seagrasses are now known to be a very important player in the formation of blue carbon, i.e. carbon that has a long turnover time in soils and sediments. Alongside salt marshes and mangroves, seagrasses are now recognized as playing a very important role in the formation of blue carbon. And because Australia has such an abundance and variety of seagrasses, their role in blue carbon production and turnover is of great importance. The first whole genomes of seagrasses are now available and Australia has played an important role here. It appears that seagrasses have severa...

Brodersen, KE, Kühl, M, Nielsen, DA, Pedersen, O & Larkum, AWD 2018, 'Rhizome, root/sediment interactions, aerenchyma and internal pressure changes in seagrasses' in Seagrasses of Australia: Structure, Ecology and Conservation, Springer, Germany, pp. 393-418.
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© Springer International Publishing AG, part of Springer Nature 2018. Life in seawater presents several challenges for seagrasses owing to low O 2 and CO 2 solubility and slow gas diffusion rates. Seagrasses have evolved numerous adaptations to these environmental conditions including porous tissue providing low-resistance internal gas channels (aerenchyma) and carbon concentration mechanisms involving the enzyme carbonic anhydrase. Moreover, seagrasses grow in reduced, anoxic sediments, and aerobic metabolism in roots and rhizomes therefore has to be sustained via rapid O 2 transport through the aerenchyma. Tissue aeration is driven by internal concentration gradients between leaves and belowground tissues, where the leaves are the source of O 2 and the rhizomes and roots function as O 2 sinks. Inadequate internal aeration e.g., due to low O 2 availability in the surrounding water during night time, can lead to sulphide intrusion into roots and rhizomes, which has been linked to enhanced seagrass mortality. Under favourable conditions, however, seagrasses leak O 2 and dissolved organic carbon into the rhizosphere, where it maintains oxic microzones protecting the plant against reduced phytotoxic compounds and generates dynamic chemical microgradients that modulate the rhizosphere microenvironment. Local radial O 2 loss from belowground tissues of seagrasses leads to sulphide oxidation in the rhizosphere, which generates protons and results in local acidification. Such low-pH microniches can lead to dissolution of carbonates and protolytic phosphorus solubilisation in carbonate-rich sediments. The seagrass rhizosphere is also characterised by numerous high-pH microniches indicative of local stimulation of proton consuming microbial processes such as sulphate reduction via root/rhizome exudates and/or release of alkaline substances. High sediment pH shifts the sulphide speciation away from H 2 S towards non-tissue-penetrating HS - ions, which can alleviate the be...

Koren, K & Kühl, M 2018, 'CHAPTER 7: Optical O2 Sensing in Aquatic Systems and Organisms' in RSC Detection Science, pp. 145-174.
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© The Royal Society of Chemistry 2018. Optical O2 measurements with fiber-optic, planar or particle-based opt(r)odes have become widespread in aquatic science since the first O2 microopt(r)odes were introduced in 1995. A wide variety of measuring systems are now available both for lab-based and in situ field measurements at spatial scales ranging from m to m's, and temporal scales ranging from <1 s to several months. Furthermore, the market has seen an explosion in commercially available optical O2 sensor and measuring systems, which complement or have replaced electrochemical O2 sensors in several areas of application. In this chapter, we give a broad overview of measuring schemes and instruments used for optical O2 sensing, and illustrate their application in various aquatic environments. We also address demands and challenges related to optical O2 sensing in aquatic systems.

Larkum, A 2018, 'Evolution and Biogeography of Seagrasses' in Seagrasses of Australia: Structure, Ecology and Conservation, Springer, Switzerland, pp. 3-30.
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Larkum, AWD, Pernice, M, Schliep, M, Davey, P, Szabo, M, Raven, JA, Lichtenberg, M, Brodersen, KE & Ralph, PJ 2018, 'Photosynthesis and metabolism of seagrasses' in Seagrasses of Australia: Structure, Ecology and Conservation, Springer, Switzerland, pp. 315-342.
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© Springer International Publishing AG, part of Springer Nature 2018. Seagrasses have a unique leaf morphology where the major site for chloroplasts is in the epidermal cells, stomata are absent and aerenchyma is present inside the epidermis. This means that the major site for photosynthesis is in the epidermis. Furthermore the lack of stomata means that the route for carbon uptake is via inorganic carbon (C i ) uptake across the vestigial cuticle and through the outer plasma membranes. Since the leaf may at times be in an unstirred situation diffusion through an unstirred layer outside the leaf may be a large obstacle to carbon uptake. The existence of a carbon concentrating mechanism is discussed, but its existence to date is not proven. Active bicarbonate uptake across the plasmalemma does not seem to operate; an external carbonic anhydrase and an extrusion of protons seem to play a role in enhancing CO 2 uptake. There is some evidence that a C4 mechanism plays a role in carbon fixation but more evidence from "omics" is required. Photorespiration certainly occurs in seagrasses and an active xanthophyll cycle is present to cope with damaging high light, but both these biochemical mechanisms need further work. Finally, epiphytes pose a problem which impedes the uptake of C i and modifies the light environment inside the leaves.

Ralph, P 2018, 'Estimating Seagrass Blue Carbon and Policy Implications: The Australian Perspective' in Seagrasses of Australia: Structure, Ecology and Conservation, Springer, Switzerland, pp. 743-758.
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Seymour, JR, Laverock, B, Nielsen, DA, Trevathan-Tackett, SM & Macreadie, PI 2018, 'The microbiology of seagrasses' in Seagrasses of Australia: Structure, Ecology and Conservation, pp. 343-392.
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© Springer International Publishing AG, part of Springer Nature 2018. Like both terrestrial plants and other benthic marine organisms, seagrasses host abundant and diverse communities of microorganisms. These microbes fundamentally influence seagrass physiology and health, while also regulating the biogeochemical dynamics of entire seagrass meadows. Discrete populations of bacteria, fungi, microalgae, archaea and viruses inhabit seagrass leaves, roots and rhizomes and the surrounding sediments. The plethora of ecological interactions taking place between seagrasses and this microbiome span the continuum of symbiotic relationships from mutualism to parasitism. Indeed, the metabolic activities of some seagrass associated microbes, such as diazotrophic and sulphur oxidizing bacteria, govern the local chemical environment in ways that facilitate seagrass survival. On the other hand, pathogens, such as the protozoan parasite Labyrinthula cause disease outbreaks that can lead to mass seagrass die offs. While the role of the seagrass microbiome in defining the success of seagrass habitats is becoming increasingly apparent, there is still much to be learnt. For instance, the development of an understanding of how seagrass associated microbes may buffer or augment the negative impacts of growing environmental pressures will be valuable for informing decisions regarding the management and conservation of threatened seagrass habitats. In this chapter we will synthesise the current state of knowledge on the microbiology of seagrasses, with a goal of conveying the often overlooked importance of the seagrass microbiome in governing seagrass health and the biogeochemical stability of seagrass ecosystems.

Abbriano, R, Vardar, N, Yee, D & Hildebrand, M 2018, 'Manipulation of a glycolytic regulator alters growth and carbon partitioning in the marine diatom Thalassiosira pseudonana', ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, vol. 32, pp. 250-258.
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Achlatis, M, Pernice, M, Green, K, Guagliardo, P, Kilburn, MR, Hoegh-Guldberg, O & Dove, S 2018, 'Single-cell measurement of ammonium and bicarbonate uptake within a photosymbiotic bioeroding sponge.', The ISME journal, vol. 12, no. 5, pp. 1308-1318.
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Some of the most aggressive coral-excavating sponges host intracellular dinoflagellates from the genus Symbiodinium, which are hypothesized to provide the sponges with autotrophic energy that powers bioerosion. Investigations of the contribution of Symbiodinium to host metabolism and particularly inorganic nutrient recycling are complicated, however, by the presence of alternative prokaryotic candidates for this role. Here, novel methods are used to study nutrient assimilation and transfer within and between the outer-layer cells of the Indopacific bioeroding sponge Cliona orientalis. Combining stable isotope labelling, transmission electron microscopy (TEM) and nanoscale secondary ion mass spectrometry (NanoSIMS), we visualize and measure metabolic activity at the individual cell level, tracking the fate of 15N-ammonium and 13C-bicarbonate within the intact holobiont. We found strong uptake of both inorganic sources (especially 13C-bicarbonate) by Symbiodinium cells. Labelled organic nutrients were translocated from Symbiodinium to the Symbiodinium-hosting sponge cells within 6 h, and occasionally to other sponge cells within 3 days. By contrast, prokaryotic symbionts were not observed to participate in inorganic nutrient assimilation in the outer layers of the sponge. Our findings strongly support the metabolic interaction between the sponge and dinoflagellates, shedding light on the ecological advantages and adaptive capacity of photosymbiotic bioeroding sponges in oligotrophic marine habitats.

Ajani, PA, Kahlke, T, Siboni, N, Carney, R, Murray, S & Seymour, J 2018, 'The microbiome of the cosmopolitan diatom Leptocylindrus reveals significant spatial and temporal variability', Frontiers in Microbiology, vol. 9.
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Ajani, PA, Larsson, M, Woodcock, S, Rubio, A, Farrell, H, Brett, S & Murray, S 2018, 'Bloom drivers of the potentially harmful dinoflagellate Prorocentrum minimum (Pavillard) Schiller in a south eastern temperate Australian estuary', Estuarine, Coastal and Shelf Science, vol. 215.
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Ajani, PA, McGinty, N, Finkel, ZV & Irwin, AJ 2018, 'Phytoplankton Realized Niches Track Changing Oceanic Conditions at a Long-Term Coastal Station off Sydney Australia', Frontiers in Marine Science, vol. 5, pp. 1-12.
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Ajani, PA, Verma, A, Lassudrie, M, Doblin, MA & Murray, SA 2018, 'A new diatom species P. hallegraeffii sp. nov. belonging to the toxic genus Pseudo-nitzschia (Bacillariophyceae) from the East Australian Current.', PloS one, vol. 13, no. 4, pp. e0195622-e0195622.
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A new species belonging to the toxin producing diatom genus Pseudo-nitzschia, P. hallegraeffii sp. nov., is delineated and described from the East Australian Current (EAC). Clonal cultures were established by single cell isolation from phytoplankton net hauls collected as part of a research expedition in the EAC region in 2016 on the RV Investigator. Cultures were assessed for their morphological and genetic characteristics, their sexual compatibility with other Pseudo-nitzschia species, and their ability to produce domoic acid. Light and transmission electron microscopy revealed cells which differed from their closest relatives by their cell width, rows of poroids, girdle band structure and density of band straie. Phylogenetic analyses based on sequencing of nuclear-encoded ribosomal deoxyribonucleic acid (rDNA) regions showed this novel genotype clustered within the P. delicatissima complex, but formed a discrete clade from its closest relatives P. dolorosa, P. simulans, P. micropora and P. delicatissima. Complementary base changes (CBCs) were observed in the secondary structure of the 3' nuclear ribosomal transcribed spacer sequence region (ITS2) between P. hallegraeffii sp. nov. and its closest related taxa, P. simulans and P. dolorosa. Under laboratory conditions, and in the absence of any zooplankton cues, strains of P. hallegraeffii sp. nov. did not produce domoic acid (DA) and were not sexually compatible with any other Pseudo-nitzschia clones tested. A total of 18 Pseudo-nitzschia species, including three confirmed toxigenic species (P. cuspidata, P. multistriata and P. australis) have now been unequivocally confirmed from eastern Australia.

Ashworth, J 2018, 'Transcriptomic biomarkers for prediction/classification of sample conditions in marine microeukaryotes (diatoms)'.
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Marine microeukaryotes express large and complex transcriptomes that often respond dynamically to environmental and physiological conditions. In parallel to developments in human disease research, the opportunity exists to employ transcriptomic features as "biomarkers" to understand and predict cellular and environmental states. Here, the prediction and classification of basic physiological and environmental states including light, growth phase and inorganic carbon status was explored for the model diatom T. pseudonana using publicly available data including 56 microarray and 316 mRNA-seq samples. Simple "machine learning" methods combined with integrative bootstrapped clustering were able to detect, recapitulate and expand biologically and environmentally relevant signals evident across hundreds of samples collected and processed independently by multiple laboratories. Agnostic, integrative and empirical "data-driven" approaches are likely applicable to modern questions in new environmental and experimental contexts.

Baker, KG, Radford, DT, Evenhuis, C, Kuzhiumparam, U, Ralph, PJ & Doblin, MA 2018, 'Thermal niche evolution of functional traits in a tropical marine phototroph.', Journal of phycology, vol. 54, no. 6, pp. 799-810.
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Land-based plants and ocean-dwelling microbial phototrophs known as phytoplankton, are together responsible for almost all global primary production. Habitat warming associated with anthropogenic climate change has detrimentally impacted marine primary production, with the effects observed on regional and global scales. In contrast to slower-growing higher plants, there is considerable potential for phytoplankton to evolve rapidly with changing environmental conditions. The energetic constraints associated with adaptation in phytoplankton are not yet understood, but are central to forecasting how global biogeochemical cycles respond to contemporary ocean change. Here, we demonstrate a number of potential trade-offs associated with high-temperature adaptation in a tropical microbial eukaryote, Amphidinium massartii (dinoflagellate). Most notably, the population became high-temperature specialized (higher fitness within a narrower thermal envelope and higher thermal optimum), and had a greater nutrient requirement for carbon, nitrogen and phosphorus. Evidently, the energetic constraints associated with living at elevated temperature alter competiveness along other environmental gradients. While high-temperature adaptation led to an irreversible change in biochemical composition (i.e., an increase in fatty acid saturation), the mechanisms underpinning thermal evolution in phytoplankton remain unclear, and will be crucial to understanding whether the trade-offs observed here are species-specific or are representative of the evolutionary constraints in all phytoplankton.

Behrendt, L, Raina, J-B, Lutz, A, Kot, W, Albertsen, M, Halkjær-Nielsen, P, Sørensen, SJ, Larkum, AW & Kühl, M 2018, 'In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina.', The ISME Journal, vol. 12, pp. 556-567.
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The tropical ascidian Lissoclinum patella hosts two enigmatic cyanobacteria: (1) the photoendosymbiont Prochloron spp., a producer of valuable bioactive compounds and (2) the chlorophyll-d containing Acaryochloris spp., residing in the near-infrared enriched underside of the animal. Despite numerous efforts, Prochloron remains uncultivable, restricting the investigation of its biochemical potential to cultivation-independent techniques. Likewise, in both cyanobacteria, universally important parameters on light-niche adaptation and in situ photosynthetic regulation are unknown. Here we used genome sequencing, transcriptomics and metabolomics to investigate the symbiotic linkage between host and photoendosymbiont and simultaneously probed the transcriptional response of Acaryochloris in situ. During high light, both cyanobacteria downregulate CO2 fixing pathways, likely a result of O2 photorespiration on the functioning of RuBisCO, and employ a variety of stress-quenching mechanisms, even under less stressful far-red light (Acaryochloris). Metabolomics reveals a distinct biochemical modulation between Prochloron and L. patella, including noon/midnight-dependent signatures of amino acids, nitrogenous waste products and primary photosynthates. Surprisingly, Prochloron constitutively expressed genes coding for patellamides, that is, cyclic peptides of great pharmaceutical value, with yet unknown ecological significance. Together these findings shed further light on far-red-driven photosynthesis in natural consortia, the interplay of Prochloron and its ascidian partner in a model chordate photosymbiosis and the uncultivability of Prochloron.The ISME Journal advance online publication, 31 October 2017; doi:10.1038/ismej.2017.192.

Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2018, 'Acid-Catalyzed Conversion of Carbohydrates into Value-Added Small Molecules in Aqueous Media and Ionic Liquids.', ChemSusChem, vol. 11.
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Biomass is the only realistic major alternative source (to crude oil) of hydrocarbon substrates for the commercial synthesis of bulk and fine chemicals. Within biomass, terrestrial sources are the most accessible, and therein lignocellulosic materials are most abundant. Although lignin shows promise for the delivery of certain types of organic molecules, cellulose is a biopolymer with significant potential for conversion into high-volume and high-value chemicals. This review covers the acid-catalyzed conversion of lower value (poly)carbohydrates into valorized organic building-block chemicals (platform molecules). It focuses on those conversions performed in aqueous media or ionic liquids to provide the reader with a perspective on what can be considered a best case scenario, that is, that the overall process is as sustainable as possible.

Bouman, HA, Platt, T, Doblin, M, Figueiras, FG, Gudmundsson, 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 2018, 'Photosynthesis-irradiance parameters of marine phytoplankton: Synthesis of a global data set', Earth System Science Data, vol. 10, no. 1, pp. 251-266.
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© Author(s) 2018. 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 data set that is unprecedented in number of observations and in spatial coverage. The database will 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).

Bramucci, AR, Labeeuw, L, Orata, FD, Ryan, EM, Malmstrom, RR & Case, RJ 2018, 'The bacterial symbiont Phaeobacter inhibens Shapes the life history of its algal host emiliania huxleyi', Frontiers in Marine Science, vol. 5.
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© 2018 Bramucci, Labeeuw, Orata, Ryan, Malmstrom and Case. Marine microbes form host-associated biofilm communities that are shaped by complex interactions between bacteria and their host. The roseobacter Phaeobacter inhibens exploits both symbiotic and pathogenic niches while interacting with its microalgal host Emiliania huxleyi. During co-cultivation over extended periods with E. huxleyi, we show that P. inhibens selectively kills two host cell types, the diploid calcifying strain and the haploid flagellated strain. Meanwhile, various non-calcifying diploid strains are resistant to this pathogen or the pathogen is avirulent to this cell type. This differential pathogenesis has the potential of dramatically altering the composition of E. huxleyi blooms, which are typically dominated by the roseobacter-susceptible calcifying strain. This cell type makes calcite plates, which are an important sink in the marine carbon cycle and forms part of the marine paleobotanic record. P. inhibens kills the haploid cells, which have been proposed as critical to the survival of the algae, as they readily escape both eukaryotic predation and viral infection. Consequently, bacteria such as P. inhibens could influence E. huxleyi's life history by selective pathogenesis, thereby altering the composition of cell types within E. huxleyi populations and its bloom-bust lifestyle.

Brodersen, KE, Siboni, N, Nielsen, DA, Pernice, M, Ralph, PJ, Seymour, J & Kühl, M 2018, 'Seagrass rhizosphere microenvironment alters plant-associated microbial community composition.', Environmental microbiology, vol. 20, no. 8, pp. 2854-2864.
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The seagrass rhizosphere harbors dynamic microenvironments, where plant-driven gradients of O2 and dissolved organic carbon form microhabitats that select for distinct microbial communities. To examine how seagrass-mediated alterations of rhizosphere geochemistry affect microbial communities at the microscale level, we applied 16S rRNA amplicon sequencing of artificial sediments surrounding the meristematic tissues of the seagrass Zostera muelleri together with microsensor measurements of the chemical conditions at the basal leaf meristem (BLM). Radial O2 loss (ROL) from the BLM led to ∼ 300 µm thick oxic microzones, wherein pronounced decreases in H2 S and pH occurred. Significantly higher relative abundances of sulphate-reducing bacteria were observed around the meristematic tissues compared to the bulk sediment, especially around the root apical meristems (RAM; ∼ 57% of sequences). Within oxic microniches, elevated abundances of sulphide-oxidizing bacteria were observed compared to the bulk sediment and around the RAM. However, sulphide oxidisers within the oxic microzone did not enhance sediment detoxification, as rates of H2 S re-oxidation here were similar to those observed in a pre-sterilized root/rhizome environment. Our results provide novel insights into how chemical and microbiological processes in the seagrass rhizosphere modulate plant-microbe interactions potentially affecting seagrass health.

Brown, MV, van de Kamp, J, Ostrowski, M, Seymour, JR, Ingleton, T, Messer, LF, Jeffries, T, Siboni, N, Laverock, B, Bibiloni-Isaksson, J, Nelson, TM, Coman, F, Davies, CH, Frampton, D, Rayner, M, Goossen, K, Robert, S, Holmes, B, Abell, GCJ, Craw, P, Kahlke, T, Sow, SLS, McAllister, K, Windsor, J, Skuza, M, Crossing, R, Patten, N, Malthouse, P, van Ruth, PD, Paulsen, I, Fuhrman, JA, Richardson, A, Koval, J, Bissett, A, Fitzgerald, A, Moltmann, T & Bodrossy, L 2018, 'Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative.', Scientific data, vol. 5, pp. 180130-180130.
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Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.

Camp, EF, Schoepf, V & Suggett, DJ 2018, 'How can "Super Corals" facilitate global coral reef survival under rapid environmental and climatic change?', Global change biology, vol. 24, no. 7, pp. 2755-2757.
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Coral reefs are in a state of rapid global decline via environmental and climate change, and efforts have intensified to identify or engineer coral populations with increased resilience. Concurrent with these efforts has been increasing use of the popularized term "Super Coral" in both popular media and scientific literature without a unifying definition. However, how this subjective term is currently applied has the potential to mislead inference over factors contributing to coral survivorship, and the future trajectory of coral reef form and functioning. Here, we discuss that the information required to support a single definition does not exist, and in fact may never be appropriate, i.e. "How Super is Super"? Instead, we advocate caution of this term, and suggest a workflow that enables contextualization and clarification of superiority to ensure that inferred or asserted survivorship is appropriate into future reef projections. This is crucial to robustly unlock how "Super Corals" can be integrated into the suite of management options required to facilitate coral survival under rapid environmental and climate change.

Camp, EF, Schoepf, V, Mumby, PJ & Suggett, DJ 2018, 'The Future of Coral Reefs Subject to Rapid Climate Change: Lessons From Natural Extreme Environments', FRONTIERS IN MARINE SCIENCE, vol. 5.
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Camp, EF, Schoepf, V, Mumby, PJ, Hardtke, LA, Rodolfo-Metalpa, R, Smith, DJ & Suggett, DJ 2018, 'The Future of Coral Reefs Subject to Rapid Climate Change: Lessons from Natural Extreme Environments', FRONTIERS IN MARINE SCIENCE, vol. 5.
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Chartrand, KM, Szabó, M, Sinutok, S, Rasheed, MA & Ralph, PJ 2018, 'Living at the margins - The response of deep-water seagrasses to light and temperature renders them susceptible to acute impacts.', Marine environmental research, vol. 136, pp. 126-138.
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Seagrasses inhabit environments where light varies at different timescales, nonetheless are acutely sensitive to reductions in light beyond some conditional bounds. Two tropical deep-water seagrasses, Halophila decipiens and Halophila spinulosa, from the Great Barrier Reef were tested for their response to defined light and temperature regimes to identify their growth requirements and potential thresholds of mortality. Species were exposed to two light intensities, saturating (75 μmol photons m-2 s-1) and limiting (25 μmol photons m-2 s-1) light and two temperature treatments (26 °C and 30 °C) over a four-week period. Wavelength-specific parameters of PSII photochemistry were evaluated for seagrass leaves, as well as shoot density, gas exchange, and pigment content. Both species were sustained under saturating light levels (3.2 mol photons m-2 d-1) while limiting light led to decreased shoot density for H. decipiens and H. spinulosa after two and four weeks, respectively. Wavelength-specific photochemistry was also affected under light-limiting treatments for both species while the functional absorption cross section was highly conserved. Photoacclimation and physiological adjustments by either species was not adequate to compensate for reduced irradiance suggesting these plants reside at the margins of their functional limits. As such, relatively short periods of light attenuating events, like dredging or flood plumes, may be detrimental to deep-water seagrass populations.

Clark, JS, Poore, AGB & Doblin, MA 2018, 'Shaping up for stress: Physiological flexibility is key to survivorship in a habitat-forming macroalga.', Journal of plant physiology, vol. 231, pp. 346-355.
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Organisms from all domains of life can have highly variable morphologies, with this plasticity suggested to increase fitness and survivability under stressful conditions. Predicting how organisms will adapt to environmental change requires an understanding of how variable morphologies perform under environmental stress. Morphological plasticity has been documented within marine macroalgae inhabiting environmental gradients, however the functional consequences of this variation has been rarely tested. In this study, form-function was assessed in the habitat-forming, intertidal macroalga Hormosira banksii. Morphological variation was quantified on two spatial scales (tidal gradient versus latitudinal gradient) and the performance tested (relative water content and photosynthetic efficiency) of morphological variants during heat and desiccation stress. At regional scales, individuals at the warm distributional edge were overall smaller in size, and had smaller vesicles (higher surface area to volume ratio; SA:VOL) than those from central populations. At local scales, individuals high on the shore were generally shorter and had larger vesicles than those low on the shore. Vesicle morphology (SA:VOL) was found to predict relative water content and photosynthetic performance during desiccation and rehydration. Differences in SA:VOL of vesicles between heights on the shore may reflect water requirements needed to maintain tissue hydration for photosynthesis during low tide. Warm-edge populations showed increased thermal sensitivity as indicated by decreased photosynthetic yield of PSII and delays in recovery after desiccation. Sensitivities to higher temperatures amongst warm-edge populations are potentially due to smaller fluctuations in regional temperatures as well as their morphology. This study provides a mechanistic understanding of the morphological variation among H. banksii populations. It suggests that H. banksii has a high degree of morphological plasticity r...

Copeland, E, Leonard, K, Carney, R, Kong, J, Forer, M, Naidoo, Y, Oliver, BGG, Seymour, JR, Woodcock, S, Burke, CM & Stow, NW 2018, 'Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites', Frontiers in Cellular and Infection Microbiology, vol. 8, pp. 1-14.
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Curson, ARJ, Williams, BT, Pinchbeck, BJ, Sims, LP, Martínez, AB, Rivera, PPL, Kumaresan, D, Mercadé, E, Spurgin, LG, Carrión, O, Moxon, S, Cattolico, RA, Kuzhiumparambil, U, Guagliardo, P, Clode, PL, Raina, J-B & Todd, JD 2018, 'DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton.', Nature microbiology, vol. 3, no. 4, pp. 430-439.
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Dimethylsulfoniopropionate (DMSP) is a globally important organosulfur molecule and the major precursor for dimethyl sulfide. These compounds are important info-chemicals, key nutrients for marine microorganisms, and are involved in global sulfur cycling, atmospheric chemistry and cloud formation1-3. DMSP production was thought to be confined to eukaryotes, but heterotrophic bacteria can also produce DMSP through the pathway used by most phytoplankton 4 , and the DsyB enzyme catalysing the key step of this pathway in bacteria was recently identified 5 . However, eukaryotic phytoplankton probably produce most of Earth's DMSP, yet no DMSP biosynthesis genes have been identified in any such organisms. Here we identify functional dsyB homologues, termed DSYB, in many phytoplankton and corals. DSYB is a methylthiohydroxybutryate methyltransferase enzyme localized in the chloroplasts and mitochondria of the haptophyte Prymnesium parvum, and stable isotope tracking experiments support these organelles as sites of DMSP synthesis. DSYB transcription levels increased with DMSP concentrations in different phytoplankton and were indicative of intracellular DMSP. Identification of the eukaryotic DSYB sequences, along with bacterial dsyB, provides the first molecular tools to predict the relative contributions of eukaryotes and prokaryotes to global DMSP production. Furthermore, evolutionary analysis suggests that eukaryotic DSYB originated in bacteria and was passed to eukaryotes early in their evolution.

Dann, LM, McKerral, JC, Smith, RJ, Tobe, SS, Paterson, JS, Seymour, JR, Oliver, RL & Mitchell, JG 2018, 'Microbial micropatches within microbial hotspots.', PLoS ONE, vol. 13, no. 5, pp. 1-22.
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The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have 'hotspots' of high abundance, and 'coldspots' of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.

Davey, PA, Pernice, M, Ashworth, J, Kuzhiumparambil, U, Szabó, M, Dolferus, R & Ralph, PJ 2018, 'A new mechanistic understanding of light-limitation in the seagrass Zostera muelleri.', Marine Environmental Research, vol. 134, pp. 55-67.
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In this study we investigated the effect of light-limitation (∼20 μmol photons m-2 s-1) on the southern hemisphere seagrass, Zostera muelleri. RNA sequencing, chlorophyll fluorometry and HPLC techniques were used to investigate how the leaf-specific transcriptome drives changes in photosynthesis and photo-pigments in Z. muelleri over 6 days. 1593 (7.51%) genes were differentially expressed on day 2 and 1481 (6.98%) genes were differentially expressed on day 6 of the experiment. Differential gene expression correlated with significant decreases in rETRMax, Ik, an increase in Yi (initial photosynthetic quantum yield of photosystem II), and significant changes in pigment composition. Regulation of carbohydrate metabolism was observed along with evidence that abscisic acid may serve a role in the low-light response of this seagrass. This study provides a novel understanding of how Z. muelleri responds to light-limitation in the marine water column and provides potential molecular markers for future conservation monitoring efforts.

Davies, CH, Ajani, P, Armbrecht, L, Atkins, N, Baird, ME, Beard, J, Bonham, P, Burford, M, Clementson, L, Coad, P, Crawford, C, Dela-Cruz, J, Doblin, MA, Edgar, S, Eriksen, R, Everett, JD, Furnas, M, Harrison, DP, Hassler, C, Henschke, N, Hoenner, X, Ingleton, T, Jameson, I, Keesing, J, Leterme, SC, McLaughlin, MJ, Miller, M, Moffatt, D, Moss, A, Nayar, S, Patten, NL, Patten, R, Pausina, SA, Proctor, R, Raes, E, Robb, M, Rothlisberg, P, Saeck, EA, Scanes, P, Suthers, IM, Swadling, KM, Talbot, S, Thompson, P, Thomson, PG, Uribe-Palomino, J, van Ruth, P, Waite, AM, Wright, S & Richardson, AJ 2018, 'A database of chlorophyll a in Australian waters', SCIENTIFIC DATA, vol. 5.
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De Clerck, O, Kao, S-M, Bogaert, KA, Blomme, J, Foflonker, F, Kwantes, M, Vancaester, E, Vanderstraeten, L, Aydogdu, E, Boesger, J, Califano, G, Charrier, B, Clewes, R, Del Cortona, A, D'Hondt, S, Fernandez-Pozo, N, Gachon, CM, Hanikenne, M, Lattermann, L, Leliaert, F, Liu, X, Maggs, CA, Popper, ZA, Raven, JA, Van Bel, M, Wilhelmsson, PKI, Bhattacharya, D, Coates, JC, Rensing, SA, Van Der Straeten, D, Vardi, A, Sterck, L, Vandepoele, K, Van de Peer, Y, Wichard, T & Bothwell, JH 2018, 'Insights into the Evolution of Multicellularity from the Sea Lettuce Genome.', Current biology : CB, vol. 28, no. 18, pp. 2921-2933.
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We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva's rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance "green tides." Ulvophytes are key to understanding the evolution of multicellularity in the green lineage, and Ulva morphogenesis is dependent on bacterial signals, making it an important species with which to study cross-kingdom communication. Our sequenced genome informs these aspects of ulvophyte cell biology, physiology, and ecology. Gene family expansions associated with multicellularity are distinct from those of freshwater algae. Candidate genes, including some that arose following horizontal gene transfer from chromalveolates, are present for the transport and metabolism of DMSP. The Ulva genome offers, therefore, new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage.

Faizi, M, Zavrel, T, Loureiro, C, Cerveny, J & Steuer, R 2018, 'A model of optimal protein allocation during phototrophic growth', BIOSYSTEMS, vol. 166, pp. 26-36.
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Farrell, H, Ajani, PA, Murray, S, Baker, P, Webster, G, Brett, S & Zammit, A 2018, 'Diarrhetic Shellfish Toxin Monitoring in Commercial Wild Harvest Bivalve Shellfish in New South Wales, Australia', Toxins, vol. 10, no. 11.
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Frommlet, JC, Wangpraseurt, D, Sousa, ML, Guimaraes, B, da Silva, MM, Kuhl, M & Serodio, J 2018, 'Symbiodinium-Induced Formation of Microbialites: Mechanistic Insights From in Vitro Experiments and the Prospect of Its Occurrence in Nature', FRONTIERS IN MICROBIOLOGY, vol. 9.
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Fujise, L, Nitschke, MR, Frommlet, JC, Serôdio, J, Woodcock, S, Ralph, PJ & Suggett, DJ 2018, 'Cell Cycle Dynamics of Cultured Coral Endosymbiotic Microalgae (Symbiodinium) Across Different Types (Species) Under Alternate Light and Temperature Conditions', Journal of Eukaryotic Microbiology, vol. 65, pp. 505-517.
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Geoghegan, JL, Pirotta, V, Harvey, E, Smith, A, Buchmann, JP, Ostrowski, M, Eden, J-S, Harcourt, R & Holmes, EC 2018, 'Virological Sampling of Inaccessible Wildlife with Drones.', Viruses, vol. 10, no. 6.
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There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We characterized the virome of the exhaled breath (or blow) of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome diversity, a meta-transcriptomic analysis was performed on 19 pooled whale blow samples collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3 km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. To our knowledge, this is the first time that UAVs have been used to sample viruses. Despite the relatively small number of animals surveyed in this initial study, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, diversity, and evolution.

Giardina, M, Cheong, S, Marjo, CE, Clode, PL, Guagliardo, P, Pickford, R, Pernice, M, Seymour, JR & Raina, J-B 2018, 'Quantifying Inorganic Nitrogen Assimilation by Synechococcus Using Bulk and Single-Cell Mass Spectrometry: A Comparative Study.', Frontiers in microbiology, vol. 9.
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Microorganisms drive most of the major biogeochemical cycles in the ocean, but the rates at which individual species assimilate and transform key elements is generally poorly quantified. One of these important elements is nitrogen, with its availability limiting primary production across a large proportion of the ocean. Nitrogen uptake by marine microbes is typically quantified using bulk-scale approaches, such as Elemental Analyzer-Isotope Ratio Mass Spectrometry (EA-IRMS), which averages uptake over entire communities, masking microbial heterogeneity. However, more recent techniques, such as secondary ion mass spectrometry (SIMS), allow for elucidation of assimilation rates at the scale at which they occur: the single-cell level. Here, we combine and compare the application of bulk (EA-IRMS) and single-cell approaches (NanoSIMS and Time-of-Flight-SIMS) for quantifying the assimilation of inorganic nitrogen by the ubiquitous marine primary producer Synechococcus. We aimed to contrast the advantages and disadvantages of these techniques and showcase their complementarity. Our results show that the average assimilation of 15N by Synechococcus differed based on the technique used: values derived from EA-IRMS were consistently higher than those derived from SIMS, likely due to a combination of previously reported systematic depletion as well as differences in sample preparation. However, single-cell approaches offered additional layers of information, whereby NanoSIMS allowed for the quantification of the metabolic heterogeneity among individual cells and ToF-SIMS enabled identification of nitrogen assimilation into peptides. We suggest that this coupling of stable isotope-based approaches has great potential to elucidate the metabolic capacity and heterogeneity of microbial cells in natural environments.

Giordano, M, Olivieri, C, Ratti, S, Norici, A, Raven, JA & Knoll, AH 2018, 'A tale of two eras: Phytoplankton composition influenced by oceanic paleochemistry.', Geobiology, vol. 16, no. 5, pp. 498-506.
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We report the results of simple experiments which support the hypothesis that changes in ocean chemistry beginning in the Mesozoic Era resulted in an increase in the nutritional quality per mole of C and per cell of planktonic algal biomass compared to earlier phytoplankton. We cultured a cyanobacterium, a diatom, a dinoflagellate, and a green alga in media mimicking aspects of the chemistry of Palaeozoic and Mesozoic-Cenozoic oceans. Substantial differences emerged in the quality of algal biomass between the Palaeozoic and Mesozoic-Cenozoic growth regimes; these differences were strongly affected by interspecific interactions (i.e., the co-existence of different species alters responses to the chemistry of the medium). The change was in the direction of a Mesozoic-Cenozoic biomass enriched in protein per mole C, although cells contained less carbon overall. This would lead to a lower C:N ratio. On the assumption that Mesozoic-Cenozoic grazers' assimilation of total C was similar to that of their earlier counterparts, their diet would be stoichiometrically closer to their C:N requirement. This, along with an increase in mean cell size among continental shelf phytoplankton, could have helped to facilitate observed evolutionary changes in the Mesozoic marine fauna. In turn, increased grazing pressure would have operated as a selective force for the radiation of phytoplankton clades better equipped with antigrazing capabilities (sensu lato), as found widely in phytoplankton with biomineralization. Our results emphasize potential links between changing seawater chemistry, increased predation pressure and the rise to ecological dominance of chlorophyll a+c algae in Mesozoic oceans. The experiments also suggest a potential role for ocean chemistry in changes of marine trophic structure from the Palaeozoic to the later Mesozoic Era.

Goessling, JW, Frankenbach, S, Ribeiro, L, Serôdio, J & Kühl, M 2018, 'Modulation of the light field related to valve optical properties of raphid diatoms: Implications for niche differentiation in the microphytobenthos', Marine Ecology Progress Series, vol. 588, pp. 29-42.
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© Inter-Research 2018. Differences in the spectral light absorption of photopigments allow for niche differentiation and coexistence of cyanobacteria and diatoms. Evolution in the microphytobenthos could have further been shaped by the photonic crystal-like structures in the frustule of diatoms interacting with sunlight. We studied the optical properties in water of the valves of 3 pennate diatom species collected from an intertidal estuarine mudflat. We observed forward scattering of blue light in the valve, while the angle of incident white light at which this phenomenon was visible differed between the 3 tested raphid species. A slurry of oxidized frustules enhanced scalar irradiance in the blue spectral range by up to 120% compared to downwelling irradiance. Blue light induced higher relative electron transport rates at photosystem II and non-photochemical quenching compared to red actinic light. We hypothesize that structures in the pennate diatom frustule modulate microalgal light absorption for efficient photosynthesis and thereby contribute to niche differentiation of diatoms in the microphytobenthos.

Goessling, JW, Su, Y, Cartaxana, P, Maibohm, C, Rickelt, LF, Trampe, ECL, Walby, SL, Wangpraseurt, D, Wu, X, Ellegaard, M & Kühl, M 2018, 'Structure-based optics of centric diatom frustules: modulation of the in vivo light field for efficient diatom photosynthesis.', New Phytologist, vol. 219, no. 1, pp. 122-134.
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The optical properties of diatom silicate frustules inspire photonics and nanotechnology research. Whether light interaction with the nano-structure of the frustule also affects diatom photosynthesis has remained unclear due to lack of information on frustule optical properties under more natural conditions. Here we demonstrate that the optical properties of the frustule valves in water affect light harvesting and photosynthesis in live cells of centric diatoms (Coscinodiscus granii). Microscale cellular mapping of photosynthesis around localized spot illumination demonstrated optical coupling of chloroplasts to the valve wall. Photonic structures of the three-layered C. granii valve facilitated light redistribution and efficient photosynthesis in cell regions distant from the directly illuminated area. The different porous structure of the two sides of the valve exhibited photon trapping and forward scattering of blue light enhancing photosynthetic active radiation inside the cell. Photonic structures of diatom frustules thus alter the cellular light field with implications on diatom photobiology.

Haydon, TD, Seymour, JR & Suggett, DJ 2018, 'Soft corals are significant DMSP producers in tropical and temperate reefs', Marine Biology, vol. 165, no. 7.
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© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. Corals synthesise large quantities of the sulphur metabolite dimethylsulphoniopropionate (DMSP), which contributes to key roles in coral reef ecology including the capacity of corals to withstand various stressors. While closely related to scleractinian corals and often occupying similar ecological niche space, it is currently poorly defined to what extent soft corals produce DMSP. We, therefore, examined DMSP content within four key species of soft coral in February and July–August of 2017, including two temperate species from Sydney Harbour (Erythropodium hicksoni, Capnella gaboensis) and two tropical species from the Great Barrier Reef (Sinularia sp., Sarcophyton sp.). We compared DMSP content of these soft coral species to that of commonly occurring temperate (Plesiastrea versipora) and tropical (Acropora aspera) scleractinian coral species. DMSP content was normalised to coral protein content, with soft coral DMSP content highly variable across species and locations [56–539 nmol (mg protein)−1], and lower than for the tropical [1242–4710 nmol (mg protein)−1], but not temperate [465–1984 nmol (mg protein)−1] scleractinian species. Further comparison with previously published values demonstrated that soft coral DMSP content falls within the “low–mid range” of scleractinian corals. Notably, DMSP content was also higher in summer samples than winter samples for the scleractinian corals, but did not differ between seasons for soft corals. Such contrasting dynamics of DMSP production by soft corals compared to scleractinian corals indicates that the regulation of DMSP content differs between these two important benthic cnidarian groups, potentially as a consequence of dissimilar ecophysiological roles for this compound.

Herschend, J, Koren, K, Roder, HL, Brejnrod, A, Kuhl, M & Burmolle, M 2018, 'In Vitro Community Synergy between Bacterial Soil Isolates Can Be Facilitated by pH Stabilization of the Environment', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 84, no. 21.
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Høj, L, Levy, N, Baillie, BK, Clode, PL, Strohmaier, RC, Siboni, N, Webster, NS, Uthicke, S & Bourne, DG 2018, 'Crown-of-thorns sea star, Acanthaster cf. solaris, have tissue-characteristic microbiomes with potential roles in health and reproduction.', Applied and environmental microbiology, vol. 84, no. 13.
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Outbreaks of coral-eating crown-of-thorns sea stars (CoTS; Acanthaster spp. complex) cause substantial coral loss, hence there is considerable interest in developing prevention and control strategies. We characterised the microbiome of captive CoTS and assessed whether dysbiosis was evident in sea stars during a disease event. Most tissue types had a distinct microbiome. The exception was female gonads, which were highly variable amongst individuals. Male gonads were dominated (>97% of reads) by a single Mollicutes-related OTU. Detailed phylogenetic and microscopy analysis demonstrated the presence of a novel Spiroplasma-related bacterium in the spermatogenic layer. Body wall samples had high relative abundance (43-64% of reads) of spirochetes, likely corresponding to subcuticular symbionts reported from many echinoderms. Tube feet were characterised by Hyphomonadaceae (24-55% of reads). Pyloric caeca microbiomes had high alpha diversity, comprising many taxa commonly found in gastro-intestinal systems. The order Oceanospirillales (genera Endozoicomonas and Kistimonas) was detected in all tissues. A microbiome shift occurred in diseased individuals, although differences between tissue types were retained. The relative abundance of spirochetes was significantly reduced in diseased individuals. Kistimonas was present in all diseased individuals and significantly associated with diseased tube feet, but its role in disease causation is unknown. While Arcobacter was significantly associated with diseased tissues and Vibrionaceae increased in diversity, no single OTUs were detected in all diseased individuals suggesting opportunistic proliferation of these taxa in this case. This study shows that CoTS have tissue-characteristic bacterial communities and identifies taxa that could play a role in reproduction and host health.IMPORTANCECoral-eating crown of thorns sea stars (CoTS; Acanthaster spp. complex) are native to the Indo-Pacific, but during periodic population out...

Hughes, DJ, Campbell, DA, Doblin, MA, Kromkamp, JC, Lawrenz, E, Moore, CM, Oxborough, K, Prášil, O, Ralph, PJ, Alvarez, MF & Suggett, DJ 2018, 'Roadmaps and Detours: Active Chlorophyll- a Assessments of Primary Productivity Across Marine and Freshwater Systems.', Environmental science & technology, vol. 52, pp. 12039-12054.
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Assessing phytoplankton productivity over space and time remains a core goal for oceanographers and limnologists. Fast Repetition Rate fluorometry (FRRf) provides a potential means to realize this goal with unprecedented resolution and scale yet has not become the "go-to" method despite high expectations. A major obstacle is difficulty converting electron transfer rates to equivalent rates of C-fixation most relevant for studies of biogeochemical C-fluxes. Such difficulty stems from methodological inconsistencies and our limited understanding of how the electron requirement for C-fixation (Φe,C) is influenced by the environment and by differences in the composition and physiology of phytoplankton assemblages. We outline a "roadmap" for limiting methodological bias and to develop a more mechanistic understanding of the ecophysiology underlying Φe,C. We 1) re-evaluate core physiological processes governing how microalgae invest photosynthetic electron transport-derived energy and reductant into stored carbon versus alternative sinks. Then, we 2) outline steps to facilitate broader uptake and exploitation of FRRf, which could transform our knowledge of aquatic primary productivity. We argue it is time to 3) revise our historic methodological focus on carbon as the currency of choice, to 4) better appreciate that electron transport fundamentally drives ecosystem biogeochemistry, modulates cell-to-cell interactions, and ultimately modifies community biomass and structure.

Hughes, DJ, Varkey, D, Doblin, MA, Ingleton, T, Mcinnes, A, Ralph, PJ, van Dongen-Vogels, V & Suggett, DJ 2018, 'Impact of nitrogen availability upon the electron requirement for carbon fixation in Australian coastal phytoplankton communities', Limnology and Oceanography, vol. 63, no. 5, pp. 1891-1910.
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© 2018 Association for the Sciences of Limnology and Oceanography Nitrogen (N) availability affects phytoplankton photosynthetic performance and regulates marine primary production (MPP) across the global coast and oceans. Bio-optical tools including Fast Repetition Rate fluorometry (FRRf) are particularly well suited to examine MPP variability in coastal regions subjected to dynamic spatio-temporal fluctuations in nutrient availability. FRRf determines photosynthesis as an electron transport rate through Photosystem II (ETRPSII), requiring knowledge of an additional parameter, the electron requirement for carbon fixation (KC), to retrieve rates of CO2-fixation. KC strongly depends upon environmental conditions regulating photosynthesis, yet the importance of N-availability to this parameter has not been examined. Here, we use nutrient bioassays to isolate how N (relative to other macronutrients P, Si) regulates KC of phytoplankton communities from the Australian coast during summer, when N-availability is often highly variable. KC consistently responded to N-amendment, exhibiting up to a threefold reduction and hence an apparent increase in the efficiency with which electrons were used to drive C-fixation. However, the process driving this consistent reduction was dependent upon initial conditions. When diatoms dominated assemblages and N was undetectable (e.g., post bloom), KC decreased predominantly via a physiological adjustment of the existing community to N-amendment. Conversely, for mixed assemblages, N-addition achieved a similar reduction in KC through a change in community structure toward diatom domination. We generate new understanding and parameterization of KC that is particularly critical to advance how FRRf can be applied to examine C-uptake throughout the global ocean where nitrogen availability is highly variable and thus frequently limits primary productivity.

Kahlke, T, Jumppanen, P, Westram, R, Abell, GCG & Bodrossy, L 2018, 'ProbeSpec: batch specificity testing and visualization of oligonucleotide probe sets implemented in ARB'.
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High-throughput molecular methods such as quantitative polymerase chain reaction (qPCR) and environmental microarrays are cost-effective methods for semi-quantitative assessment of bacterial community structure and the identification of specific target organisms. Both techniques rely on short nucleotide sequences, so-called oligonucleotide probes, which require high specificity to the organisms in question to avoid cross-hybridization with non-target taxa. However, designing oligonucleotide probes for novel taxa or marker genes that show sufficient phylogenetic sensitivity and specificity is often time- and labor-intensive, as each probe has to be in-silico tested for its specificity and sensitivity. Here we present ProbeSpec, to our knowledge the first batch sensitivity and specificity estimation and visualization tool for oligonucleotide probes integrated into the widely used ARB software. Using ProbeSpec’s interactive “mismatch threshold” and “clade marked threshold” we were able to reduce the development time of highly specific probes for a recently published environmental oligonucleotide microarray from several months to one week.

Kim, M, Brodersen, KE, Szabó, M, Larkum, AWD, Raven, JA, Ralph, PJ & Pernice, M 2018, 'Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass Zostera muelleri.', Photosynthesis Research, vol. 136, no. 2, pp. 147-160.
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Seagrasses are a diverse group of angiosperms that evolved to live in shallow coastal waters, an environment regularly subjected to changes in oxygen, carbon dioxide and irradiance. Zostera muelleri is the dominant species in south-eastern Australia, and is critical for healthy coastal ecosystems. Despite its ecological importance, little is known about the pathways of carbon fixation in Z. muelleri and their regulation in response to environmental changes. In this study, the response of Z. muelleri exposed to control and very low oxygen conditions was investigated by using (i) oxygen microsensors combined with a custom-made flow chamber to measure changes in photosynthesis and respiration, and (ii) reverse transcription quantitative real-time PCR to measure changes in expression levels of key genes involved in C4 metabolism. We found that very low levels of oxygen (i) altered the photophysiology of Z. muelleri, a characteristic of C3 mechanism of carbon assimilation, and (ii) decreased the expression levels of phosphoenolpyruvate carboxylase and carbonic anhydrase. These molecular-physiological results suggest that regulation of the photophysiology of Z. muelleri might involve a close integration between the C3 and C4, or other CO2 concentrating mechanisms metabolic pathways. Overall, this study highlights that the photophysiological response of Z. muelleri to changing oxygen in water is capable of rapid acclimation and the dynamic modulation of pathways should be considered when assessing seagrass primary production.

Laiolo, L, Matear, R, Baird, ME, Soja-Wozniak, M & Doblin, M 2018, 'Information content of in situ and remotely sensed chlorophyll-a: Learning from size-structured phytoplankton model', Journal of Marine Systems, vol. 183, pp. 1-12.
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© 2018 Chlorophyll-a measurements in the form of in situ observations and satellite ocean colour products are commonly used in data assimilation to calibrate marine biogeochemical models. Here, a two size-class phytoplankton biogeochemical model, with a 0D configuration, was used to simulate the surface chlorophyll-a dynamics (simulated surface Chl-a) for cyclonic and anticyclonic eddies off East Australia. An optical model was then used to calculate the inherent optical properties from the simulation and convert them into remote-sensing reflectance (Rrs). Subsequently, Rrs was used to produce a satellite-like estimate of the simulated surface Chl-a concentrations through the MODIS OC3M algorithm (simulated OC3M Chl-a). Identical parameter optimisation experiments were performed through the assimilation of the two separate datasets (simulated surface Chl-a and simulated OC3M Chl-a), with the purpose of investigating the contrasting information content of simulated surface Chl-a and remotely-sensed data sources. The results we present are based on the analysis of the distribution of a cost function, varying four parameters of the biogeochemical model. In our idealized experiments the simulated OC3M Chl-a product is a poor proxy for the total simulated surface Chl-a concentration. Furthermore, our result show the OC3M algorithm can underestimate the simulated chlorophyll-a concentration in offshore eddies off East Australia (Case I waters), because of the weak relationship between large-sized phytoplankton and remote-sensing reflectance. Although Case I waters are usually characteristic of oligotrophic environments, with a photosynthetic community typically represented by relatively small-sized phytoplankton, mesoscale features such as eddies can generate seasonally favourable conditions for a photosynthetic community with a greater proportion of large phytoplankton cells. Furthermore, our results show that in mesoscale features such as eddies, in situ chlorophyll-...

Larkum, AWD, Ritchie, RJ & Raven, JA 2018, 'Living off the Sun: chlorophylls, bacteriochlorophylls and rhodopsins', PHOTOSYNTHETICA, vol. 56, no. 1, pp. 11-43.
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Larsson, M, Laczka, O, Suthers, I, Ajani, PA & Doblin, M 2018, 'Hitchhiking in the East Australian Current: rafting as a dispersal mechanism for harmful epibenthic dinoflagellates', Marine Ecology Progress Series.
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Larsson, ME, Laczka, OF, Harwood, DT, Lewis, RJ, Himaya, SWA, Murray, SA & Doblin, MA 2018, 'Toxicology of Gambierdiscus spp. (Dinophyceae) from Tropical and Temperate Australian Waters.', Marine drugs, vol. 16, no. 1.
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Ciguatera Fish Poisoning (CFP) is a human illness caused by the consumption of marine fish contaminated with ciguatoxins (CTX) and possibly maitotoxins (MTX), produced by species from the benthic dinoflagellate genus Gambierdiscus. Here, we describe the identity and toxicology of Gambierdiscus spp. isolated from the tropical and temperate waters of eastern Australia. Based on newly cultured strains, we found that four Gambierdiscus species were present at the tropical location, including G. carpenteri, G. lapillus and two others which were not genetically identical to other currently described species within the genus, and may represent new species. Only G. carpenteri was identified from the temperate location. Using LC-MS/MS analysis we did not find any characterized microalgal CTXs (P-CTX-3B, P-CTX-3C, P-CTX-4A and P-CTX-4B) or MTX-1; however, putative maitotoxin-3 (MTX-3) was detected in all species except for the temperate population of G. carpenteri. Using the Ca2+ influx SH-SY5Y cell Fluorescent Imaging Plate Reader (FLIPR) bioassay we found CTX-like activity in extracts of the unidentified Gambierdiscus strains and trace level activity in strains of G. lapillus. While no detectable CTX-like activity was observed in tropical or temperate strains of G. carpenteri, all species showed strong maitotoxin-like activity. This study, which represents the most comprehensive analyses of the toxicology of Gambierdiscus strains isolated from Australia to date, suggests that CFP in this region may be caused by currently undescribed ciguatoxins and maitotoxins.

Lavoie, M, Duval, JFL, Raven, JA, Maps, F, Béjaoui, B, Kieber, DJ & Vincent, WF 2018, 'Carbonate Disequilibrium in the External Boundary Layer of Freshwater Chrysophytes: Implications for Contaminant Uptake.', Environmental Science and Technology, vol. 52, no. 16, pp. 9403-9411.
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The interplay between biological and chemical reactions in the freshwater phytoplankton phycosphere and the resulting modulations of contaminant speciation and uptake is poorly characterized. Here we modeled the effect of algal C and N uptake on carbonate cycling and speciation of selected contaminants in the phycosphere (external boundary layer) of chrysophytes, a key phytoplankton group in oligotrophic systems. We calculated an enrichment in H+ concentration relative to that in the bulk solution (pH 7.0) of approximately 40% or a depletion of approximately 30% for NH4+ or NO3--grown cells, respectively, at the algal membrane surface of a 5-μm radius cell. Such changes are mainly due to direct H+ uptake or release at the plasmalemma if NO3- or NH4+ is the N source, respectively. Due to these pH changes in the external boundary layer, competition between H+ and metals for uptake is enhanced, for NH4+-grown cells which contributes to a decrease in potential metal uptake. Our model suggests that the uptake of protonated weakly acidic organic acids (HA) is greater in NH4+-grown cells compared to that in NO3--grown cells. The account of chemical reactions in the algal external boundary layer could improve ecological risk assessments for a wide range of contaminants.

Lawson, CA, Raina, J-B, Kahlke, T, Seymour, JR & Suggett, DJ 2018, 'Defining the core microbiome of the symbiotic dinoflagellate, Symbiodinium.', Environmental microbiology reports, vol. 10, no. 1, pp. 7-11.
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Dinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterized the bacterial communities living in association with a wide phylogenetic diversity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome. Similar to other systems, bacteria were nearly two orders of magnitude more numerically abundant than Symbiodinium cells and we identified three operational taxonomic units (OTUs) which were present in all cultures. These represented the α-proteobacterium Labrenzia and the γ-proteobacteria Marinobacter and Chromatiaceae. Based on the abundance and functional potential of bacteria harboured in these cultures, their contribution to Symbiodinium physiology can no longer be ignored.

Litaker, RW, Fraga, S, Montresor, M, Brosnahan, M, Anderson, D, Hoppenrath, M, Murray, S, Wolny, J, John, U, Sampedro, N, Larsen, J & Calado, A 2018, 'A practical guide to the new nomenclature for species within the "Alexandrium tamarense" species complex', Harmful algae news / Unesco; IOC; Intergovernmental Oceanographic Commission, vol. 61, pp. 13-15.

Matthews, JL, Oakley, CA, Lutz, A, Hillyer, KE, Roessner, U, Grossman, AR, Weis, VM & Davy, SK 2018, 'Partner switching and metabolic flux in a model cnidarian-dinoflagellate symbiosis.', Proceedings. Biological sciences, vol. 285, no. 1892.
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Metabolite exchange is fundamental to the viability of the cnidarian-Symbiodiniaceae symbiosis and survival of coral reefs. Coral holobiont tolerance to environmental change might be achieved through changes in Symbiodiniaceae species composition, but differences in the metabolites supplied by different Symbiodiniaceae species could influence holobiont fitness. Using 13C stable-isotope labelling coupled to gas chromatography-mass spectrometry, we characterized newly fixed carbon fate in the model cnidarian Exaiptasia pallida (Aiptasia) when experimentally colonized with either native Breviolum minutum or non-native Durusdinium trenchii Relative to anemones containing B. minutum, D. trenchii-colonized hosts exhibited a 4.5-fold reduction in 13C-labelled glucose and reduced abundance and diversity of 13C-labelled carbohydrates and lipogenesis precursors, indicating symbiont species-specific modifications to carbohydrate availability and lipid storage. Mapping carbon fate also revealed significant alterations to host molecular signalling pathways. In particular, D. trenchii-colonized hosts exhibited a 40-fold reduction in 13C-labelled scyllo-inositol, a potential interpartner signalling molecule in symbiosis specificity. 13C-labelling also highlighted differential antioxidant- and ammonium-producing pathway activities, suggesting physiological responses to different symbiont species. Such differences in symbiont metabolite contribution and host utilization may limit the proliferation of stress-driven symbioses; this contributes valuable information towards future scenarios that select in favour of less-competent symbionts in response to environmental change.

McCauley, JI, Winberg, PC, Meyer, BJ & Skropeta, D 2018, 'Effects of nutrients and processing on the nutritionally important metabolites of Ulva sp. (Chlorophyta)', Algal Research, vol. 35, pp. 586-594.
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© 2018 Elsevier B.V. In consideration that, fatty acids bound within phospholipids may exhibit greater levels of bioavailability than neutral lipids, we investigated the effect of nutrient starvation on the phospholipid content and composition of cultivated Ulva biomass. Furthermore, we explored the simultaneous effects on the pigment and phenolic profiles and then correlation analysis to anti-oxidant and anti-inflammatory activity. High nutrient cultivation (nitrogen replete) provided a biomass with desirable n-6/n-3 (0.3) and 18:2n-6/18:3n-3 (0.5) ratios and beneficial 18:4n-3, 20:5n-3, 22:5n-3 fatty acids. These fatty acids dominated the abundant neutral lipid fraction, which comprised 62% of the lipid extract. The remaining phospholipids (38%) were characterised by high 16:0 (49.6%), 18:1n-7 (14.6%) and 18:3n-3 (13.6%) fatty acids. Nutrient-depleted samples had a 3-fold higher total fatty acid (TFA) content (12.05 mg·g−1 d.w, p < 0.0001) compared to nutrient replete samples (3.35 mg·g−1 d.w.). This occurred mostly within the neutral fraction, which represented 88% of the total lipids and the fatty acids 16:0 (4.02 ± 0.15 mg·g−1), 18:1n-7 (1.79 ± 0.06 mg·g−1), 18:2n-6 (2.30 ± 0.08 mg·g−1) and 18:3n-3 (1.09 ± 0.03 mg·g−1 d.w). Nutrient replete biomass yielded 1.5 mg·g−1 total chlorophyll, 0.1 mg·g−1 carotenoids and 1.6 mg·g−1 phenolics, whilst low nutrient growth conditions reduced the presence of pigments by 98%, phenolics by 34% and anti-oxidant activity by 87%. Significantly higher yields of pigment and phenolics were obtained using 95% ethanol for the extraction process, whilst acetone extracts were characterised by a higher proportion of carotenoids. All extracts from cultivated Ulva samples inhibited nitric oxide (NO) (≥81%) with acetone extracts demonstrating higher inhibition (94–97%) than 95% ethanol extracts (81–90%) with no significant effects observed between the two treatments. Thus, Ulva cultivated under high nutrients offers a sustainable source ...

Mosshammer, M, Schrameyer, V, Jensen, PO, Koren, K & Kuhl, M 2018, 'Extracellular hydrogen peroxide measurements using a flow injection system in combination with microdialysis probes - Potential and challenges', FREE RADICAL BIOLOGY AND MEDICINE, vol. 128, pp. 111-123.
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Newton, K, Jeffries, TC, Smith, RJ, Seymour, JR, Seuront, L & Mitchell, JG 2018, 'Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs', Journal of Oceanology and Limnology, vol. 36, no. 6, pp. 2033-2049.
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© 2018, Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag GmbH Germany, part of Springer Nature. The Coorong estuary lies at the terminus of Australia’s largest river system, the Murray-Darling; both are strongly influenced by human activities; including farming and extensive flow modification. Metagenomic approaches were used to determine the planktonic bacterial community composition and potential metabolic function at two extremes in the Coorong, the river mouth which exhibits marine-like salinity, and the hypersaline upper-reaches of the estuary. Significant shifts in taxa and metabolic function were seen between the two sites. The river mouth exhibited an increase in abundance of Rhodobacteriaceae and Alteromonadaceae; families readily able to adapt to change in nutrient conditions; and the potentially pathogenic families Brucellaceae, Enterobacteriaceae and Vibrionaceae. Metabolisms over-represented include motility and chemotaxis, RNA metabolism and membrane transport, all of which are involved in actively searching for and obtaining nutrients. Also over-represented were metabolisms involved in population succession and stress response. An over-representation of taxa and metabolisms indicative of environmental change is reflective of anthropogenically affected riverine input. In the hypersaline upper reaches of the estuary, the halophilic family Ectothiorhodospiraceae was over-represented, as were the families Flavobacteriaceae, Cytophagaceae and Nocardioidaceae, members of which are able to survive over a wide salinity range. Metabolisms over-represented here were reflective of increased bacterial growth, characteristic of hypersaline environments, and included DNA metabolism, nucleotide and nucleoside synthesis and cell cycle. Coorong metagenomes clustered taxonomically and metabolically with other planktonic metagenomes, but remained an outlier of this group with only 71% and 84% similarity, respectively. This indicates tha...

Nielsen, S, Joseph, S, Ye, J, Chia, C, Munroe, P, van Zwieten, L & Thomas, T 2018, 'Crop-season and residual effects of sequentially applied mineral enhanced biochar and N fertiliser on crop yield, soil chemistry and microbial communities', AGRICULTURE ECOSYSTEMS & ENVIRONMENT, vol. 255, pp. 52-61.
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Nitschke, MR, Gardner, SG, Goyen, S, Fujise, L, Camp, EF, Ralph, PJ & Suggett, DJ 2018, 'Utility of photochemical traits as diagnostics of thermal tolerance amongst great barrier reef corals', Frontiers in Marine Science, vol. 5, no. FEB.
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© 2018 Nitschke, Gardner, Goyen, Fujise, Camp, Ralph and Suggett. Light availability is considered a key factor regulating the thermal sensitivity of reef building corals, where excessive excitation of photosystem II (PSII) further exacerbates pressure on photochemical pathways already compromised by heat stress. Coral symbionts acclimate to changes in light availability (photoacclimation) by continually fine-tuning the photochemical operating efficiency of PSII. However, how this process adjusts throughout the warmest months in naturally heat-tolerant or sensitive species is unknown, and whether this influences the capacity to tolerate transient heat stress is untested. We therefore examined the PSII photophysiology of 10 coral species (with known thermal tolerances) from shallow reef environments at Heron Island (Great Barrier Reef, Australia), in spring (October-November, 2015) vs. summer (February-March, 2016). Corals were maintained in flow-through aquaria and rapid light curve (RLC) protocols using pulse amplitude modulated (PAM) fluorometry captured changes in the PSII photoacclimation strategy, characterized as the minimum saturating irradiance (Ek), and the extent of photochemical ([1-C], operating efficiency) vs. non-photochemical ([1-Q]) energy dissipation. Values of Ekacross species were > 2-fold higher in all coral species in spring, consistent with a climate of higher overall light exposure (i.e., higher PAR from lower cloud cover, rainfall and wind speed) compared with summer. Summer decreases in Ekwere combined with a shift toward preferential photochemical quenching in all species. All coral species were subsequently subjected to thermal stress assays. An equivalent temperature-ramping profile of 1°C increase per day and then maintenance at 32°C was applied in each season. Despite the significant seasonal photoacclimation, the species hierarchy of thermal tolerance [maximum quantum yields of PSII (Fv/Fm), monitored at dawn and dusk] did not shift...

Osman, EO, Smith, DJ, Ziegler, M, Kürten, B, Conrad, C, El-Haddad, KM, Voolstra, CR & Suggett, DJ 2018, 'Thermal refugia against coral bleaching throughout the northern Red Sea.', Global Change Biology, vol. 24, no. 2, pp. e474-e484.
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Tropical reefs have been impacted by thermal anomalies caused by global warming that induced coral bleaching and mortality events globally. However, there have only been very few recordings of bleaching within the Red Sea despite covering a latitudinal range of 15° and consequently it has been considered a region that is less sensitive to thermal anomalies. We therefore examined historical patterns of sea surface temperature (SST) and associated anomalies (1982-2012) and compared warming trends with a unique compilation of corresponding coral bleaching records from throughout the region. These data indicated that the northern Red Sea has not experienced mass bleaching despite intensive Degree Heating Weeks (DHW) of >15°C-weeks. Severe bleaching was restricted to the central and southern Red Sea where DHWs have been more frequent, but far less intense (DHWs <4°C-weeks). A similar pattern was observed during the 2015-2016 El Niño event during which time corals in the northern Red Sea did not bleach despite high thermal stress (i.e. DHWs >8°C-weeks), and bleaching was restricted to the central and southern Red Sea despite the lower thermal stress (DHWs < 8°C-weeks). Heat stress assays carried out in the northern (Hurghada) and central (Thuwal) Red Sea on four key reef-building species confirmed different regional thermal susceptibility, and that central Red Sea corals are more sensitive to thermal anomalies as compared to those from the north. Together, our data demonstrate that corals in the northern Red Sea have a much higher heat tolerance than their prevailing temperature regime would suggest. In contrast, corals from the central Red Sea are close to their thermal limits, which closely match the maximum annual water temperatures. The northern Red Sea harbours reef-building corals that live well below their bleaching thresholds and thus we propose that the region represents a thermal refuge of global importance.

Rädecker, N, Raina, J-B, Pernice, M, Perna, G, Guagliardo, P, Kilburn, MR, Aranda, M & Voolstra, CR 2018, 'Corrigendum: Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses.', Frontiers in physiology, vol. 9.
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[This corrects the article on p. 214 in vol. 9, PMID: 29615919.].

Raedecker, N, Raina, J-B, Pernice, M, Perna, G, Guagliardo, P, Kilburn, MR, Aranda, M & Voolstra, CR 2018, 'Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses', FRONTIERS IN PHYSIOLOGY, vol. 9.
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Raes, EJ, Bodrossy, L, van de Kamp, J, Bissett, A, Ostrowski, M, Brown, MV, Sow, SLS, Sloyan, B & Waite, AM 2018, 'Oceanographic boundaries constrain microbial diversity gradients in the South Pacific Ocean.', Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, pp. E8266-E8275.
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Marine microbes along with microeukaryotes are key regulators of oceanic biogeochemical pathways. Here we present a high-resolution (every 0.5° of latitude) dataset describing microbial pro- and eukaryotic richness in the surface and just below the thermocline along a 7,000-km transect from 66°S at the Antarctic ice edge to the equator in the South Pacific Ocean. The transect, conducted in austral winter, covered key oceanographic features including crossing of the polar front (PF), the subtropical front (STF), and the equatorial upwelling region. Our data indicate that temperature does not determine patterns of marine microbial richness, complementing the global model data from Ladau et al. [Ladau J, et al. (2013) ISME J 7:1669-1677]. Rather, NH4+, nanophytoplankton, and primary productivity were the main drivers for archaeal and bacterial richness. Eukaryote richness was highest in the least-productive ocean region, the tropical oligotrophic province. We also observed a unique diversity pattern in the South Pacific Ocean: a regional increase in archaeal and bacterial diversity between 10°S and the equator. Rapoport's rule describes the tendency for the latitudinal ranges of species to increase with latitude. Our data showed that the mean latitudinal ranges of archaea and bacteria decreased with latitude. We show that permanent oceanographic features, such as the STF and the equatorial upwelling, can have a significant influence on both alpha-diversity and beta-diversity of pro- and eukaryotes.

Raina, J-B 2018, 'The Life Aquatic at the Microscale.', mSystems, vol. 3, no. 2.
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There are more than one million microbial cells in every drop of seawater, and their collective metabolisms not only recycle nutrients that can then be used by larger organisms but also catalyze key chemical transformations that maintain Earth's habitability. Understanding how these microbes interact with each other and with multicellular hosts is critical to reliably quantify any functional aspect of their metabolisms and to predict their outcomes on larger scales. Following a large body of literature pioneered by Farooq Azam and colleagues more than 30 years ago, I emphasize the importance of studying microbial interactions at the appropriate scale if we want to fully decipher the roles that they play in oceanic ecosystems.

Raina, J-B, Eme, L, Pollock, FJ, Spang, A, Archibald, JM & Williams, TA 2018, 'Symbiosis in the microbial world: from ecology to genome evolution.', Biology open, vol. 7, no. 2.
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The concept of symbiosis - defined in 1879 by de Bary as 'the living together of unlike organisms' - has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists' workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired.

Raven, J 2018, 'Blue carbon: past, present and future, with emphasis on macroalgae', BIOLOGY LETTERS, vol. 14, no. 10.
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Raven, JA 2018, 'Evolution and palaeophysiology of the vascular system and other means of long-distance transport', PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 373, no. 1739.
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Raven, JA 2018, 'How long have photosynthetic organisms been aggregating soils?', The New phytologist, vol. 219, no. 4, pp. 1139-1141.
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Raven, JA 2018, 'The potential effect of low cell osmolarity on cell function through decreased concentration of enzyme substrates.', Journal of experimental botany, vol. 69, no. 20, pp. 4667-4673.
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Some freshwater algae have lower (<130 osmol m-3) intracellular osmolarities than most others (>180 osmol m-3). Low osmolarities are related to the presence of flagella and the low energy cost of active water efflux following downhill water influx unconstrained by cell walls covering the plasmalemma, and the low resource cost of cell wall synthesis with the same mechanical degree of safety. One consequence of low intracellular osmolarity is limitation on the concentration of metabolites, that is, substrates and products of enzyme activity. Models of the flux through metabolic pathways, and hence the specific growth rate, using steady-state concentrations of enzymes and metabolites have involved organisms with intracellular metabolite osmolarities >280 osmol m-3, where the metabolite concentrations are much greater than the total osmolarity of some freshwater algae. Since the protein concentration (mol m-3) in the cells and the specific growth rates of freshwater cells with low and with higher intracellular osmolarity are highly similar, the models of trade-offs between enzyme and metabolite concentrations for cells with high intracellular osmolarity need modification for cells with low intracellular osmolarity. The soluble free-radical scavenger ascorbate can constitute as little as 0.2% of the low intracellular metabolite concentration (mol m-3) of low-intracellular-osmolarity cells.

Raven, JA & Giordano, M 2018, 'Acquisition and metabolism of carbon in the Ochrophyta other than diatoms (vol 372, 20160400, 2017)', PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 373, no. 1739.
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Richier, S, Achterberg, EP, Humphreys, MP, Poulton, AJ, Suggett, DJ, Tyrrell, T & Moore, CM 2018, 'Geographical CO2 sensitivity of phytoplankton correlates with ocean buffer capacity.', Global Change Biology, vol. 24, no. 9, pp. 4438-4452.
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Accumulation of anthropogenic CO2 is significantly altering ocean chemistry. A range of biological impacts resulting from this oceanic CO2 accumulation are emerging, however, the mechanisms responsible for observed differential susceptibility between organisms and across environmental settings remain obscure. A primary consequence of increased oceanic CO2 uptake is a decrease in the carbonate system buffer capacity, which characterizes the system's chemical resilience to changes in CO2 , generating the potential for enhanced variability in pCO2 and the concentration of carbonate [CO32-], bicarbonate [HCO3-], and protons [H+ ] in the future ocean. We conducted a meta-analysis of 17 shipboard manipulation experiments performed across three distinct geographical regions that encompassed a wide range of environmental conditions from European temperate seas to Arctic and Southern oceans. These data demonstrated a correlation between the magnitude of natural phytoplankton community biological responses to short-term CO2 changes and variability in the local buffer capacity across ocean basin scales. Specifically, short-term suppression of small phytoplankton (<10 μm) net growth rates were consistently observed under enhanced pCO2 within experiments performed in regions with higher ambient buffer capacity. The results further highlight the relevance of phytoplankton cell size for the impacts of enhanced pCO2 in both the modern and future ocean. Specifically, cell size-related acclimation and adaptation to regional environmental variability, as characterized by buffer capacity, likely influences interactions between primary producers and carbonate chemistry over a range of spatio-temporal scales.

Ritchie, RJ, Larkum, AWD & Ribas, I 2018, 'Could photosynthesis function on Proxima Centauri b?', International Journal of Astrobiology, vol. 17, no. 2, pp. 147-176.
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© Copyright Cambridge University Press 2017. Could oxygenic and/or anoxygenic photosynthesis exist on planet Proxima Centauri b? Proxima Centauri (spectral type - M5.5 V, 3050 K) is a red dwarf, whereas the Sun is type G2 V (5780 K). The light regimes on Earth and Proxima Centauri b are compared with estimates of the planet's suitability for Chlorophyll a (Chl a) and Chl d-based oxygenic photosynthesis and for bacteriochlorophyll (BChl)-based anoxygenic photosynthesis. Proxima Centauri b has low irradiance in the oxygenic photosynthesis range (400-749 nm: 64-132 μmol quanta m -2 s -1 ). Much larger amounts of light would be available for BChl-based anoxygenic photosynthesis (350-1100 nm: 724-1538 μmol quanta m -2 s -1 ). We estimated primary production under these light regimes. We used the oxygenic algae Synechocystis PCC6803, Prochlorothrix hollandica, Acaryochloris marina, Chlorella vulgaris, Rhodomonas sp. and Phaeodactylum tricornutum and the anoxygenic photosynthetic bacteria Rhodopseudomonas palustris (BChl a), Afifella marina (BChl a), Thermochromatium tepidum (BChl a), Chlorobaculum tepidum (BChl a + c) and Blastochloris viridis (BChl b) as representative photosynthetic organisms. Proxima Centauri b has only ≈3% of the PAR (400-700 nm) of Earth irradiance, but we found that potential gross photosynthesis (P g ) on Proxima Centauri b could be surprisingly high (oxygenic photosynthesis: earth ≈0.8 gC m -2 h -1 ; Proxima Centauri b ≈0.14 gC m -2 h -1 ). The proportion of PAR irradiance useable by oxygenic photosynthetic organisms (the sum of Blue + Red irradiance) is similar for the Earth and Proxima Centauri b. The oxygenic photic zone would be only ≈10 m deep in water compared with ≈200 m on Earth. The P g of an anoxic Earth (gC m -2 h -1 ) is ≈0.34-0.59 (land) and could be as high as ≈0.29-0.44 on Proxima Centauri b. 1 m of water does not affect oxygenic or anoxygenic photosynthesis on Earth, but on Proxima Centauri b oxygenic P g is reduced by ≈50%. Eff...

Ruvindy, R, Bolch, CJ, MacKenzie, L, Smith, KF & Murray, SA 2018, 'qPCR Assays for the Detection and Quantification of Multiple Paralytic Shellfish Toxin-Producing Species of Alexandrium.', Frontiers in microbiology, vol. 9.
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Paralytic shellfish toxin producing dinoflagellates have negatively impacted the shellfish aquaculture industry worldwide, including in Australia and New Zealand. Morphologically identical cryptic species of dinoflagellates that may differ in toxicity, in particular, species of the former Alexandrium tamarense species complex, co-occur in Australia, as they do in multiple regions in Asia and Europe. To understand the dynamics and the ecological drivers of the growth of each species in the field, accurate quantification at the species level is crucial. We have developed the first quantitative polymerase chain reaction (qPCR) primers for A. australiense, and new primers targeting A. ostenfeldii, A. catenella, and A. pacificum. We showed that our new primers for A. pacificum are more specific than previously published primer pairs. These assays can be used to quantify planktonic cells and cysts in the water column and in sediment samples with limits of detection of 2 cells/L for the A. catenella and A. australiense assays, 2 cells/L and 1 cyst/mg sediment for the A. pacificum assay, and 1 cells/L for the A. ostenfeldii assay, and efficiencies of >90%. We utilized these assays to discriminate and quantify co-occurring A. catenella, A. pacificum, and A. australiense in samples from the east coast of Tasmania, Australia.

Sablok, G, Hayward, RJ, Davey, PA, Santos, RP, Schliep, M, Larkum, A, Pernice, M, Dolferus, R & Ralph, PJ 2018, 'SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants', SCIENTIFIC REPORTS, vol. 8.
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Schrameyer, V, York, PH, Chartrand, K, Ralph, PJ, Kühl, M, Brodersen, KE & Rasheed, MA 2018, 'Contrasting impacts of light reduction on sediment biogeochemistry in deep- and shallow-water tropical seagrass assemblages (Green Island, Great Barrier Reef).', Marine environmental research, vol. 136, pp. 38-47.
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Seagrass meadows increasingly face reduced light availability as a consequence of coastal development, eutrophication, and climate-driven increases in rainfall leading to turbidity plumes. We examined the impact of reduced light on above-ground seagrass biomass and sediment biogeochemistry in tropical shallow- (∼2 m) and deep-water (∼17 m) seagrass meadows (Green Island, Australia). Artificial shading (transmitting ∼10-25% of incident solar irradiance) was applied to the shallow- and deep-water sites for up to two weeks. While above-ground biomass was unchanged, higher diffusive O2 uptake (DOU) rates, lower O2 penetration depths, and higher volume-specific O2 consumption (R) rates were found in seagrass-vegetated sediments as compared to adjacent bare sand (control) areas at the shallow-water sites. In contrast, deep-water sediment characteristics did not differ between bare sand and vegetated sites. At the vegetated shallow-water site, shading resulted in significantly lower hydrogen sulphide (H2S) levels in the sediment. No shading effects were found on sediment biogeochemistry at the deep-water site. Overall, our results show that the sediment biogeochemistry of shallow-water (Halodule uninervis, Syringodium isoetifolium, Cymodocea rotundata and C. serrulata) and deep-water (Halophila decipiens) seagrass meadows with different species differ in response to reduced light. The light-driven dynamics of the sediment biogeochemistry at the shallow-water site could suggest the presence of a microbial consortium, which might be stimulated by photosynthetically produced exudates from the seagrass, which becomes limited due to lower seagrass photosynthesis under shaded conditions.

Segecova, A, Cerveny, J & Roitsch, T 2018, 'Advancement of the cultivation and upscaling of photoautotrophic suspension cultures using Chenopodium rubrum as a case study', PLANT CELL TISSUE AND ORGAN CULTURE, vol. 135, no. 1, pp. 37-51.
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Seymour, JR & Raina, J-B 2018, 'Swimming in the sea: chemotaxis by marine bacteria', Microbiology Australia, vol. 39, no. 1, pp. 12-16.
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Sonderholm, M, Koren, K, Wangpraseurt, D, Jensen, PO, Kolpen, M, Kragh, KN, Bjarnsholt, T & Kuehl, M 2018, 'Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate bead model', NPJ BIOFILMS AND MICROBIOMES, vol. 4.
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Sutherland, DL, Heubeck, S, Park, J, Turnbull, MH & Craggs, RJ 2018, 'Seasonal performance of a full-scale wastewater treatment enhanced pond system', WATER RESEARCH, vol. 136, pp. 150-159.
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Tamburic, B, Evenhuis, CR, Crosswell, JR & Ralph, PJ 2018, 'An empirical process model to predict microalgal carbon fixation rates in photobioreactors', Algal Research, vol. 31, pp. 334-346.
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© 2018 Elsevier B.V. An empirical process model was developed to infer the instantaneous net photosynthesis and carbon fixation rates from continuous pH and dissolved oxygen measurements during microalgal cultivation in photobioreactors. The model is based on the physical and chemical processes that govern the relationship between inorganic carbon supplied to a microalgal culture and the organic carbon fixed into microalgal biomass, with a particular focus on carbonate chemistry and mass transfer. Bayesian statistics were used to estimate the uncertainty in state variables, such as pH, net photosynthesis rate, and bicarbonate ion concentration, based on the constraints imposed by prior knowledge about these variables. The model was verified by batch-culturing the chlorophyte microalga Chlorella vulgaris in a photobioreactor under both bicarbonate-replete and bicarbonate-limiting conditions in order to test its predictive ability under different operational settings. The replicate photobioreactors were set up to simulate a scaled-down vertical cross-section of a typical raceway pond. This model could be used to test the activity and efficiency of carbon concentrating mechanisms in different microalgal species. It also provides a detailed understanding of how the rate of photosynthesis depends on dissolved inorganic carbon concentration, which could lead to better management of carbon supply in large-scale microalgal cultivation facilities.

Tian, C, Doblin, MA, Dafforn, KA, Johnston, EL, Pei, H & Hu, W 2018, 'Dinoflagellate cyst abundance is positively correlated to sediment organic carbon in Sydney Harbour and Botany Bay, NSW, Australia.', Environmental science and pollution research international, vol. 25, no. 6, pp. 5808-5821.
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There is growing public concern about the global expansion of harmful algal bloom species (HABs), with dinoflagellate microalgae comprising the major portion of the harmful taxa. These motile, unicellular organisms have a lifecycle involving sexual reproduction and resting cyst formation whereby cysts can germinate from sediments and 'seed' planktonic populations. Thus, investigation of dinoflagellate cyst (dinocyst) distribution in sediments can provide significant insights into HAB dynamics and contribute to indices of habitat quality. Species composition and abundance of dinocysts in relation to sediment characteristics were studied at 18 stations in two densely populated temperate Australian estuaries, Sydney Harbour (Parramatta River/Port Jackson; PS) and Botany Bay (including Georges River; GB). Eighteen dinocyst taxa were identified, dominated by Protoceratium reticulatum and Gonyaulax sp.1 in the PS estuary, together with Archaeperidinium minutum and Gonyaulax sp.1 in the GB estuary. Cysts of Alexandrium catenella, which is one of the causative species of paralytic shellfish poisoning (PSP), were also detected in both estuaries. Out of the measured sediment characteristics (TOC, Cd, Cr, Cu, Fe, Pb, Mn, Ni, Zn and polycyclic aromatic hydrocarbons), TOC was the parameter explaining most of the variation in dinocyst assemblages and was positively correlated to most of the heavy metals. Given the significant relationship between sediment TOC and dinocyst abundance and heavy metal concentrations, this study suggests that sediment TOC could be broadly used in risk management for potential development of algal blooms and sediment contamination in these estuaries.

Tian, C, Hao, D, Pei, H, Doblin, MA, Ren, Y, Wei, J & Feng, Y 2018, 'Phytoplankton Functional Groups Variation and Influencing Factors in a Shallow Temperate Lake', WATER ENVIRONMENT RESEARCH, vol. 90, no. 6, pp. 510-519.
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Trampe, E, Koren, K, Akkineni, AR, Senwitz, C, Krujatz, F, Lode, A, Gelinsky, M & Kühl, M 2018, 'Functionalized Bioink with Optical Sensor Nanoparticles for O2 Imaging in 3D-Bioprinted Constructs', Advanced Functional Materials, vol. 28, no. 45.
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© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Research on 3D bioprinting of living cells has strong focus on printable biocompatible materials and monitoring of cell growth in printed constructs, while cell metabolism is mostly measured in media surrounding the constructs or by destructive sample analyses. Bioprinting is combined with online imaging of O2 by functionalizing a hydrogel bioink via addition of luminescent optical sensor nanoparticles. Rheological properties of the bioink enable 3D printing of hydrogel layers with uniform response to O2 concentration. Co-immobilization of sensor nanoparticles with green microalgae and/or mesenchymal stem cells does not affect cell viability over several days. Interference from microalgal autofluorescence on the O2 imaging is negligible, and no leakage or photobleaching of nanoparticles is observed over 2–3 days. Oxygen dynamics due to respiration and photosynthesis of cells can be imaged online and the metabolic activity of different cell types can be discriminated in intact 3D structures. Bioinks containing chemical sensor particles enable noninvasive mapping of cell metabolism and spatiotemporal dynamics of their chemical microenvironment in 3D-printed structures. This major advance now facilitates rapid evaluation of cell activity in printed constructs as a function of structural complexity, metabolic interactions in mixed species bioprints, and in response to external incubation conditions.

Trevathan‐Tackett, SM, Caitlin Wessel, Just Cebrián, Peter J. Ralph, Pere Masqué & Peter I. Macreadie 2018, 'Effects of small‐scale, shading‐induced seagrass loss on blue carbon storage: Implications for management of degraded seagrass ecosystems', The Journal of Applied Ecology, vol. 55, no. 3, pp. 1351-1359.
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Seagrass meadows are important global blue carbon sinks. Despite a 30% loss of seagrasses globally during the last century, there is limited empirical research investigating the effects of disturbance and loss of seagrass on blue carbon stocks. In this study, we hypothesised that seagrass loss would reduce blue carbon stocks. Using shading cloth, we simulated small‐scale die‐offs of two subtropical seagrass species, Halodule wrightii and Thalassia testudinum, in a dynamic northern Gulf of Mexico lagoon. The change in quantity and quality of sediment organic matter (OM) and organic carbon was compared among die‐off, control and bare plots before the die‐off treatment, shortly after the die‐off treatment and 11 months after the die‐off treatment. ²¹⁰Pb age dating was performed on bare and Thalassia plots at 11 months to evaluate the impact of sediment erosion in the absence of vegetation. The small‐scale die‐off led to a 50%–65% OM loss in the sediment in the top 8 cm of Halodule plots. Thalassia plots lost significant portions of OM (50%) and organic carbon (Cₒᵣg; 21%–47%) in only the top 1 cm of sediment. The ²¹⁰Pb profiles indicated Thalassia die‐off reduced the Cₒᵣg sequestration rate by 10%, in addition to a loss of c. 1 year's worth of Cₒᵣg stocks (c. 22 g/m²). Furthermore, analyses on OM/Cₒᵣg quality indicated a loss of labile OM/Cₒᵣg and enhanced remineralisation by microbes. Synthesis and applications. This study provides empirical evidence that small‐scale shading‐induced seagrass die‐offs can reduce seagrass carbon sequestration capacity and trigger losses of blue carbon stocks. While the losses recorded here are modest, these losses in blue carbon storage capacity are notable due to the proximity of shading structures (e.g. boat docks) to seagrass habitats. Thus, policies to avoid or protect seagrass habitats from common small‐scale, shading disturbances are important for optimising both carbon sequestration capacity and coastline development and manage...

Trevathan-Tackett, SM, Thomson, ACG, Ralph, PJ & Macreadie, PI 2018, 'Fresh carbon inputs to seagrass sediments induce variable microbial priming responses.', Science of the Total Environment, vol. 621, pp. 663-669.
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Microbes are the 'gatekeepers' of the marine carbon cycle, yet the mechanisms for how microbial metabolism drives carbon sequestration in coastal ecosystems are still being defined. The proximity of coastal habitats to runoff and disturbance creates ideal conditions for microbial priming, i.e., the enhanced remineralisation of stored carbon in response to fresh substrate availability and oxygen introduction. Microbial priming, therefore, poses a risk for enhanced CO2 release in these carbon sequestration hotspots. Here we quantified the existence of priming in seagrass sediments and showed that the addition of fresh carbon stimulated a 1.7- to 2.7-fold increase in CO2 release from recent and accumulated carbon deposits. We propose that priming taking place at the sediment surface is a natural occurrence and can be minimised by the recalcitrant components of the fresh inputs (i.e., lignocellulose) and by reduced metabolism in low oxygen and high burial rate conditions. Conversely, priming of deep sediments after the reintroduction to the water column through physical disturbances (e.g., dredging, boat scars) would cause rapid remineralisation of previously preserved carbon. Microbial priming is identified as a process that weakens sediment carbon storage capacity and is a pathway to CO2 release in disturbed or degraded seagrass ecosystems; however, increased management and restoration practices can reduce these anthropogenic disturbances and enhance carbon sequestration capacity.

Tschitschko, B, Erdmann, S, DeMaere, MZ, Roux, S, Panwar, P, Allen, MA, Williams, TJ, Brazendale, S, Hancock, AM, Eloe-Fadrosh, EA & Cavicchioli, R 2018, 'Genomic variation and biogeography of Antarctic haloarchaea.', Microbiome, vol. 6, no. 1, pp. 113-113.
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BACKGROUND:The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised. RESULTS:The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica. CONCLUSION:The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography o...

Unnikrishnan, A, Vo, ANQ, Pickford, R, Raftery, MJ, Nunez, AC, Verma, A, Hesson, LB & Pimanda, JE 2018, 'AZA-MS: a novel multiparameter mass spectrometry method to determine the intracellular dynamics of azacitidine therapy in vivo.', Leukemia, vol. 32, no. 4, pp. 900-910.
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The cytidine analogue, 5-azacytidine (AZA; 5-AZA-cR), is the primary treatment for myelodysplastic syndrome and chronic myelomonocytic leukaemia. However, only ~50% of treated patients will respond to AZA and the drivers of AZA resistance in vivo are poorly understood. To better understand the intracellular dynamics of AZA upon therapy and decipher the molecular basis for AZA resistance, we have developed a novel, multiparameter, quantitative mass spectrometry method (AZA-MS). Using AZA-MS, we have accurately quantified the abundance of the ribonucleoside (5-AZA-cR) and deoxyribonucleoside (5-AZA-CdR) forms of AZA in RNA, DNA and the cytoplasm within the same sample using nanogram quantities of input material. We report that although AZA induces DNA demethylation in a dose-dependent manner, it has no corresponding effect on RNA methylation. By applying AZA-MS to primary bone marrow samples from patients undergoing AZA therapy, we have identified that responders accumulate more 5-AZA-CdR in their DNA compared with nonresponders. AZA resistance was not a result of impaired AZA metabolism or intracellular accumulation. Furthermore, AZA-MS has helped to uncover different modes of AZA resistance. Whereas some nonresponders fail to incorporate sufficient 5-AZA-CdR into DNA, others incorporate 5-AZA-CdR and effect DNA demethylation like AZA responders, but show no clinical benefit.

Valderrama Ballesteros, L, Matthews, JL & Hoeksema, BW 2018, 'Pollution and coral damage caused by derelict fishing gear on coral reefs around Koh Tao, Gulf of Thailand', Marine Pollution Bulletin, vol. 135, pp. 1107-1116.
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van de Water, JAJM, Chaib De Mares, M, Dixon, GB, Raina, J-B, Willis, BL, Bourne, DG & van Oppen, MJH 2018, 'Antimicrobial and stress responses to increased temperature and bacterial pathogen challenge in the holobiont of a reef-building coral.', Molecular ecology, vol. 27, no. 4, pp. 1065-1080.
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Global increases in coral disease prevalence have been linked to ocean warming through changes in coral-associated bacterial communities, pathogen virulence and immune system function. However, the interactive effects of temperature and pathogens on the coral holobiont are poorly understood. Here, we assessed three compartments of the holobiont (host, Symbiodinium and bacterial community) of the coral Montipora aequituberculata challenged with the pathogen Vibrio coralliilyticus and the commensal bacterium Oceanospirillales sp. under ambient (27°C) and elevated (29.5 and 32°C) seawater temperatures. Few visual signs of bleaching and disease development were apparent in any of the treatments, but responses were detected in the holobiont compartments. V. coralliilyticus acted synergistically and negatively impacted the photochemical efficiency of Symbiodinium at 32°C, while Oceanospirillales had no significant effect on photosynthetic efficiency. The coral, however, exhibited a minor response to the bacterial challenges, with the response towards V. coralliilyticus being significantly more pronounced, and involving the prophenoloxidase-activating system and multiple immune system-related genes. Elevated seawater temperatures did not induce shifts in the coral-associated bacterial community, but caused significant gene expression modulation in both Symbiodinium and the coral host. While Symbiodinium exhibited an antiviral response and upregulated stress response genes, M. aequituberculata showed regulation of genes involved in stress and innate immune response processes, including immune and cytokine receptor signalling, the complement system, immune cell activation and phagocytosis, as well as molecular chaperones. These observations show that M. aequituberculata is capable of maintaining a stable bacterial community under elevated seawater temperatures and thereby contributes to preventing disease development.

Varkey, D, Mazard, S, Jeffries, T, Hughes, D, Seymour, J, Paulsen, IT & Ostrowski, M 2018, 'Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary', PLoS ONE, vol. 13, no. 12, pp. e0209857-e0209857.
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Sydney Harbour is subjected to persistent stress associated with anthropogenic activity and global climate change, but is particularly subjected to pulse stress events associated with stormwater input during episodic periods of high rainfall. Photosynthetic microbes underpin metazoan diversity within estuarine systems and are therefore important bioindicators of ecosystem health; yet how stormwater input affects their occurrence and distribution in Sydney Harbour remains poorly understood. We utilised molecular tools (16S/18S rRNA and petB genes) to examine how the phytoplankton community structure (both prokaryotes and eukaryotes) within Sydney Harbour varies between high and low rainfall periods. The relative proportion of phytoplankton sequences was more abundant during the high rainfall period, comprising mainly of diatoms, an important functional group supporting increased productivity within estuarine systems, together with cyanobacteria. Increased spatial variability in the phytoplankton community composition was observed, potentially driven by the steepened physico-chemical gradients associated with stormwater inflow. Conversely, during a low rainfall period, the proportion of planktonic photosynthetic microbes was significantly lower and the persistent phytoplankton were predominantly represented by chlorophyte and dinoflagellate sequences, with lower overall diversity. Differences in phytoplankton composition between the high and low rainfall periods were correlated with temperature, salinity, total nitrogen and silicate. These results suggest that increased frequency of high-rainfall events may change the composition, productivity and health of the estuary. Our study begins to populate the knowledge gap in the phytoplankton community structure and substantial changes associated with transient environmental perturbations, an essential step towards unravelling the dynamics of primary production in a highly urbanised estuarine ecosystem in response to cli...

Vavitsas, K, Fabris, M & Vickers, CE 2018, 'Terpenoid Metabolic Engineering in Photosynthetic Microorganisms.', Genes, vol. 9, no. 11.
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Terpenoids are a group of natural products that have a variety of roles, both essential and non-essential, in metabolism and in biotic and abiotic interactions, as well as commercial applications such as pharmaceuticals, food additives, and chemical feedstocks. Economic viability for commercial applications is commonly not achievable by using natural source organisms or chemical synthesis. Engineered bio-production in suitable heterologous hosts is often required to achieve commercial viability. However, our poor understanding of regulatory mechanisms and other biochemical processes makes obtaining efficient conversion yields from feedstocks challenging. Moreover, production from carbon dioxide via photosynthesis would significantly increase the environmental and potentially the economic credentials of these processes by disintermediating biomass feedstocks. In this paper, we briefly review terpenoid metabolism, outline some recent advances in terpenoid metabolic engineering, and discuss why photosynthetic unicellular organisms-such as algae and cyanobacteria-might be preferred production platforms for the expression of some of the more challenging terpenoid pathways.

Vuppaladadiyam, AK, Yao, JG, Florin, N, George, A, Wang, X, Labeeuw, L, Jiang, Y, Davis, RW, Abbas, A, Ralph, P, Fennell, PS & Zhao, M 2018, 'Impact of Flue Gas Compounds on Microalgae and Mechanisms for Carbon Assimilation and Utilization.', ChemSusChem, vol. 11, no. 2, pp. 334-355.
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To shift the world to a more sustainable future, it is necessary to phase out the use of fossil fuels and focus on the development of low-carbon alternatives. However, this transition has been slow, so there is still a large dependence on fossil-derived power, and therefore, carbon dioxide is released continuously. Owing to the potential for assimilating and utilizing carbon dioxide to generate carbon-neutral products, such as biodiesel, the application of microalgae technology to capture CO2 from flue gases has gained significant attention over the past decade. Microalgae offer a more sustainable source of biomass, which can be converted into energy, over conventional fuel crops because they grow more quickly and do not adversely affect the food supply. This review focuses on the technical feasibility of combined carbon fixation and microalgae cultivation for carbon reuse. A range of different carbon metabolisms and the impact of flue gas compounds on microalgae are appraised. Fixation of flue gas carbon dioxide is dependent on the selected microalgae strain and on flue gas compounds/concentrations. Additionally, current pilot-scale demonstrations of microalgae technology for carbon dioxide capture are assessed and its future prospects are discussed. Practical implementation of this technology at an industrial scale still requires significant research, which necessitates multidisciplinary research and development to demonstrate its viability for carbon dioxide capture from flue gases at the commercial level.

Watanabe, S, Kuzhiumparambil, U & Fu, S 2018, 'In vitro metabolism of synthetic cannabinoid AM1220 by human liver microsomes and Cunninghamella elegans using liquid chromatography coupled with high resolution mass spectrometry', FORENSIC TOXICOLOGY, vol. 36, no. 2, pp. 435-446.
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Watanabe, S, Kuzhiumparambil, U & Fu, S 2018, 'Structural Elucidation of Metabolites of Synthetic Cannabinoid UR-144 by Cunninghamella elegans Using Nuclear Magnetic Resonance (NMR) Spectroscopy.', The AAPS journal, vol. 20, no. 2.
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The number of new psychoactive substances keeps on rising despite the controlling efforts by law enforcement. Although metabolism of the newly emerging drugs is continuously studied to keep up with the new additions, the exact structures of the metabolites are often not identified due to the insufficient sample quantities for techniques such as nuclear magnetic resonance (NMR) spectroscopy. The aim of the study was to characterise several metabolites of the synthetic cannabinoid (1-pentyl-1H-indol-3-yl) (2,2,3,3-tetramethylcyclopropyl) methanone (UR-144) by NMR spectroscopy after the incubation with the fungus Cunninghamella elegans. UR-144 was incubated with C. elegans for 72 h, and the resulting metabolites were chromatographically separated. Six fractions were collected and analysed by NMR spectroscopy. UR-144 was also incubated with human liver microsomes (HLM), and the liquid chromatography-high resolution mass spectrometry analysis was performed on the HLM metabolites with the characterised fungal metabolites as reference standards. Ten metabolites were characterised by NMR analysis including dihydroxy metabolites, carboxy and hydroxy metabolites, a hydroxy and ketone metabolite, and a carboxy and ketone metabolite. Of these metabolites, dihydroxy metabolite, carboxy and hydroxy metabolites, and a hydroxy and ketone metabolite were identified in HLM incubation. The results indicate that the fungus is capable of producing human-relevant metabolites including the exact isomers. The capacity of the fungus C. elegans to allow for NMR structural characterisation by enabling production of large amounts of metabolites makes it an ideal model to complement metabolism studies.

White, RA, Wong, HL, Ruvindy, R, Neilan, BA & Burns, BP 2018, 'Viral communities of Shark Bay modern stromatolites', Frontiers in Microbiology, vol. 9, no. JUN.
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© 2018 White, Wong, Ruvindy, Neilan and Burns. Single stranded DNA viruses have been previously shown to populate the oceans on a global scale, and are endemic in microbialites of both marine and freshwater systems. We undertook for the first time direct viral metagenomic shotgun sequencing to explore the diversity of viruses in the modern stromatolites of Shark Bay Australia. The data indicate that Shark Bay marine stromatolites have similar diversity of ssDNA viruses to that of Highbourne Cay, Bahamas. ssDNA viruses in cluster uniquely in Shark Bay and Highbourne Cay, potentially due to enrichment by phi29-mediated amplification bias. Further, pyrosequencing data was assembled from the Shark Bay systems into two putative viral genomes that are related to Genomoviridae family of ssDNA viruses. In addition, the cellular fraction was shown to be enriched for antiviral defense genes including CRISPR-Cas, BREX (bacteriophage exclusion), and DISARM (defense island system associated with restriction-modification), a potentially novel finding for these systems. This is the first evidence for viruses in the Shark Bay stromatolites, and these viruses may play key roles in modulating microbial diversity as well as potentially impacting ecosystem function through infection and the recycling of key nutrients.

Ye, J, Perez, PG, Zhang, R, Nielsen, S, Huang, D & Thomas, T 2018, 'Effects of different C/N ratios on bacterial compositions and processes in an organically managed soil', BIOLOGY AND FERTILITY OF SOILS, vol. 54, no. 1, pp. 137-147.
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Zavrel, T, Chmelik, D, Sinetova, MA & Cerveny, J 2018, 'Spectrophotometric Determination of Phycobiliprotein Content in Cyanobacterium Synechocystis', JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, no. 139.
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Zavřel, T, Faizi, M, Loureiro, C, Poschmann, G, Stühler, K, Sinetova, M, Zorina, A, Steuer, R & Červený, J 2018, 'Quantitative insights into the cyanobacterial cell economy'.
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Abstract Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological adaptations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial adaptations to different growth rates have implications to understand and optimize photosynthetic productivity.

Zavřel, T, Szabó, M, Tamburic, B, Evenhuis, C, Kuzhiumparambil, U, Literáková, P, Larkum, AWD, Raven, JA, Červený, J & Ralph, PJ 2018, 'Effect of carbon limitation on photosynthetic electron transport in Nannochloropsis oculata.', Journal of photochemistry and photobiology. B, Biology, vol. 181, pp. 31-43.
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This study describes the impacts of inorganic carbon limitation on the photosynthetic efficiency and operation of photosynthetic electron transport pathways in the biofuel-candidate microalga Nannochloropsis oculata. Using a combination of highly-controlled cultivation setup (photobioreactor), variable chlorophyll a fluorescence and transient spectroscopy methods (electrochromic shift (ECS) and P700 redox kinetics), we showed that net photosynthesis and effective quantum yield of Photosystem II (PSII) decreased in N. oculata under carbon limitation. This was accompanied by a transient increase in total proton motive force and energy-dependent non-photochemical quenching as well as slightly elevated respiration. On the other hand, under carbon limitation the rapid increase in proton motive force (PMF, estimated from the total ECS signal) was also accompanied by reduced conductivity of ATP synthase to protons (estimated from the rate of ECS decay in dark after actinic illumination). This indicates that the slow operation of ATP synthase results in the transient build-up of PMF, which leads to the activation of fast energy dissipation mechanisms such as energy-dependent non-photochemical quenching. N. oculata also increased content of lipids under carbon limitation, which compensated for reduced NAPDH consumption during decreased CO2 fixation. The integrated knowledge of the underlying energetic regulation of photosynthetic processes attained with a combination of biophysical methods may be used to identify photo-physiological signatures of the onset of carbon limitation in microalgal cultivation systems, as well as to potentially identify microalgal strains that can better acclimate to carbon limitation.

Zhang, X, Wang, N, Xie, Z, Ma, X & Huete, A 2018, 'Water loss due to increasing planted vegetation over the Badain Jaran Desert, China', Remote Sensing, vol. 10, no. 1.
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© 2018 by the authors. Water resources play a vital role in ecosystem stability, human survival, and social development in drylands. Human activities, such as afforestation and irrigation, have had a large impact on the water cycle and vegetation in drylands over recent years. The Badain Jaran Desert (BJD) is one of the driest regions in China with increasing human activities, yet the connection between human management and the ecohydrology of this area remains largely unclear. In this study, we firstly investigated the ecohydrological dynamics and their relationship across different spatial scales over the BJD, using multi-source observational data from 2001 to 2014, including: total water storage anomaly (TWSA) from Gravity Recovery and Climate Experiment (GRACE), normalized difference vegetation index (NDVI) from Moderate Resolution Imaging Spectroradiometer (MODIS), lake extent from Landsat, and precipitation from in situ meteorological stations. We further studied the response of the local hydrological conditions to large scale vegetation and climatic dynamics, also conducting a change analysis of water levels over four selected lakes within the BJD region from 2011. To normalize the effect of inter-annual variations of precipitation on vegetation, we also employed a relationship between annual average NDVI and annual precipitation, or modified rain-use efficiency, termed the RUEmo. A focus of this study is to understand the impact of the increasing planted vegetation on local ecohydrological systems over the BJD region. Results showed that vegetation increases were largely found to be confined to the areas intensely influenced by human activities, such as croplands and urban areas. With precipitation patterns remaining stable during the study period, there was a significant increasing trend in vegetation greenness per unit of rainfall, or RUEmo over the BJD, while at the same time, total water storage as measured by satellites has been continually decreasin...

Ajani, P, Larsson, M, Rubio, A, Bush, S, Brett, S, Woodcock, S, Farrell, H & Murray, S 2018, 'Modelling harmful algal blooms in the Hawkesbury River, Australia (Oral Presentation)', Australian Shellfish Quality Assurance Advisory Committee Science Day, UTS.

Ajani, PA, Larsson, M, Rubio, A, Bush, S, Brett, S, Woodcock, S, Farrell, H & Murray, S 2018, 'Modelling harmful algal blooms in the Hawkesbury River, Australia (Oral Presentation)', Estuarine and Coastal Science Association Conference, Perth, WA.

Barua, A, Ajani, P & Murray, S 2018, 'Diversity of Alexandrium species in Hawkesbury River (Poster Presentation)', Estuarine and Coastal Science Association Conference, Perth. WA.

Benes, N, Brim, L, Pastva, S, Safranek, D, Trojak, M, Cerveny, J & Salagovic, J 2018, 'Fully automated attractor analysis of cyanobacteria models', 2018 22nd International Conference on System Theory, Control and Computing, ICSTCC 2018 - Proceedings, International Conference on System Theory, Control and Computing, IEEE, Romania, pp. 354-359.
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© 2018 IEEE. Complex dynamics arising in biological systems can be characterised by various kinds of attractors. To that end, the task of determining attractors becomes important in modern systems analysis. Biological systems are typically formalised as highly parametrised continuous-time ODE models. Such models can be abstracted in the form of parametrised graphs. In such abstractions, attractors are observed in the form of terminal strongly connected components (tSCCs). In this paper, we demonstrate a novel method for detecting tSCCs in parametrised graphs on several models of cyanobacteria taken from the domain-specific online platform e-cyanobacterium.org.

Bhullar, K, Thevarajah, J, Rebmann, A, Cheevers, S, Wuhrer, R, Castignolles, P & Gaborieau, M 2018, 'Characterisation of industrial adhesives with (solid-state) NMR spectroscopy', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 255th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nexus of Food, Energy, and Water, AMER CHEMICAL SOC, New Orleans, LA.

Cerveny, J, Schreiber, I & Safranek, D 2018, 'Systems biology approaches for advancing biotechnology of microalgae', BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY, WILEY, pp. 8-8.

Chia, Q, Brown, P, Labeeuw, L, Bajada, C, Ghannam, S, Pham, H, Wright, A & Ralph, P 2018, 'Comparing alternative algal cultivation systems for biodiesel production by utilizing an integrated model of sustainability', 17th Australasian - Centre for Social and Environmental Accounting Research Conference, Melbourne.

Coade, P, Rubio, A, Ajani, PA & Murray, S 2018, 'Local government requirements for managing estuarine algal blooms (Oral Presentation).', Estuarine and Coastal Science Association Conference (ESCA57), Perth, WA.

de Lima Ribeiro, A, Ajani, PA, Derkenne, C, Artlett, C & Pask, H 2018, 'Fluorescence impact on raman remote sensing of water temperature', International Conference for Southern Hemisphere Meteorology and Oceanography, Sydney, Australia.

Farrell, H, Webster, G, Baker, P, Zammit, A, Ajani, PA, Murray, S & Brett, S 2018, 'Developing phytoplankton and biotoxin risk assessments for both shellfish aquaculture and wild harvest shellfish in New South Wales (Oral Presentation)', Australian Shellfish Quality Assurance Advisory Committee Science Day, UTS.

Murray, S, Verma, A, Ajani, P, Zammit, A, Farrell, H, Palanisami, S & O'Connor, W 2018, 'Building profitability and sustainability in the NSW oyster industry (Oral Presentation)', Australian Shellfish Quality Assurance Advisory Committee Science Day, UTS.

Thevarajah, J, van Leeuwen, M, Heuls, M, Rouilly, A, Ward, R, Gilbert, E, Graf, R, Castignolles, P & Gaborieau, M 2018, 'Insights into the heterogeneity of polysaccharides with solid-state NMR spectroscopy', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 255th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nexus of Food, Energy, and Water, AMER CHEMICAL SOC, New Orleans, LA.

Verma, A, Kohli, G, Hoppenrath, M, Harwood, T, Kuzhiumparambil, U, Ralph, P & Murray, S 2016, 'Systematics and diversity of the genus Ostreopsis in the East Australian Current region', Marine and Fresh-Water Harmful Algae. Proceedings of the 17th International Conference on Harmful Algae., International Conference on Harmful Algae, International Society for Study of Harmful Algae, Brazil, pp. 84-88.
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Kennedy, P & Sutherland, DL 2018, Assessment of effects of proposed infrastructure development for AC36 on the nearshore marine environment in the Port of Auckland, Auckland, New Zealand.

Ruvindy, R, Ajani, PA & Murray, S 2018, Microalgal Community Composition Assessment in Warringah Lagoons 2017-2018. A report to Warringah Council, August 2018., pp. 1-29, Sydney, Australia.
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Sutherland, DL 2018, Assessment of effects of brewery wastewater discharge on the instream aquatic environment, Christchurch, New Zealand.

Sutherland, DL 2018, Cyanobacteria management in Pegasus Lake, Christchurch, New Zealand.

Sutherland, DL 2018, Environmental management plan for proposed mine closure, Christchurch, New Zealand.

Sutherland, DL 2018, Water quality parameters and the proposed Northland Regional Plan, Statement of Evidence, Christchurch, NZ.

Ralph, P, de Beyer, L & Hardtke, L 2018, 'Living Lights', Vivid Sydney.
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Living Lights is a ‘forest’ made entirely of living, breathing algae that welcomes visitors with an energetic, bubbling ‘blurp’. Growing and sustaining itself by harvesting the energy of the sun, in just three weeks Living Lights will produce more oxygen than a suburban park does in a year! Created by the University of Technology Sydney and the Deep Green Biotech Hub this installation aims to increase public awareness of algae as a highly versatile and sustainable resource for a wide range of industries. In nature, algae are responsible for half of the air we breathe; But it’s only now that the global potential of these naturally occurring organisms is being realised as they are harvested for use in next-generation medicines, cosmetics, food and drink. The installation has 18 reactors of varying heights up to 2.5 metres tall, containing three different strains of algae – two sourced from CSIRO’s Australian National Algae Culture Collection. The organisms’ naturally varying colours of bright red, gold and fluorescent green are lit up with LEDs. Visitors to Living Lights will be drawn to the illuminated beauty of this little-known organism, which has the potential to shape our sustainable future.

Ashworth, J & Ralph, P 2018, 'An explorable public transcriptomics compendium for eukaryotic microalgae'.
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Abstract Eukaryotic microalgae dominate primary photosynthetic productivity in fluctuating nutrient-rich environments, including coastal, estuarine and polar regions, where competition and complexity are presumably adaptive and dynamic traits. Numerous genomes and transcriptomes of these species have been carefully sequenced, providing an unprecedented view into the vast genetic repertoires and the diverse transcriptional programs operating inside these organisms. Here we collected, re-mapped, quantified and clustered publicly available transcriptome data for ten different eukaryotic microalgae in order to develop new insights into their molecular systems biology, as well as to provide a large new resource of integrated information to facilitate the efforts of others to further compare and contextualize the results of individual and new experiments within and between species. This is summarized herein and provided for public use by the eukaryotic microalgae research community.

Wilkinson, SJ & Ralph, P 2018, 'Algae Building Technology: Is it the Next Sustainable Technology?', Australia, pp. 31-36.