Publications

Larkum, AWD 2009, A Natural Calling, Springer Netherlands.
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Suggett, DJ & Moore, CM 2009, 'Fluorometry for Biological Sensing' in Encyclopedia of Ocean Sciences, pp. 581-588.
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Light-absorbing pigments cause many marine organisms to naturally fluoresce, a phenomenon whereby light is emitted at a longer wavelength following light absorption at a shorter wavelength. Fluorescence provides a relatively unobtrusive signature of organism abundance and physiology; consequently, a wide variety of fluorescence techniques are now routinely employed in marine biological investigations. Important technological advances throughout the last 20 years have enabled exploration of the taxonomy and physiology of marine organisms with increasing complexity. In particular, the intracellular use of fluorescent tags, molecules, and dyes that covalently bind to sensing biomolecules. However, many such techniques require samples to be removed from nature. Most widespread for assaying biology in situ exploits the fluorescence emitted from chlorophyll a, the predominant light harvesting pigment inherent to all (micro)algae, cyanobacteria, and aquatic vascular plants. Measurements of chlorophyll a fluorescence were introduced in the 1960s to improve estimates of phytoplankton abundance. By the 1990s, this field had evolved to enable the physiology and productivity of primary producers to be examined at scales from the single cell to entire ocean basins. Current remote sensing algorithms concentrate on better describing the relationship between primary productivity and natural fluorescence that is emitted from solar excitation. While several major challenges exist in achieving this goal, such approaches provide great promise for accurately characterizing the role of marine primary productivity during this period of extreme climate change. © 2009 Copyright © 2009 Elsevier Ltd. All rights reserved.

Suggett, DJ & Moore, MC 2009, 'Fluorometry for biological sensing' in Encyclopedia of Ocean Sciences, Springer, Switerland, pp. 87-93.
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© 2009 Elsevier Ltd. Light-absorbing pigments cause many marine organisms to naturally fluoresce, a phenomenon whereby light is emitted at a longer wavelength following light absorption at a shorter wavelength. Fluorescence provides a relatively unobtrusive signature of organism abundance and physiology; consequently, a wide variety of fluorescence techniques are now routinely employed in marine biological investigations. Important technological advances throughout the last 20 years have enabled exploration of the taxonomy and physiology of marine organisms with increasing complexity. In particular, the intracellular use of fluorescent tags, molecules, and dyes that covalently bind to sensing biomolecules. However, many such techniques require samples to be removed from nature. Most widespread for assaying biology in situ exploits the fluorescence emitted from chlorophyll a, the predominant light harvesting pigment inherent to all (micro)algae, cyanobacteria, and aquatic vascular plants. Measurements of chlorophyll a fluorescence were introduced in the 1960s to improve estimates of phytoplankton abundance. By the 1990s, this field had evolved to enable the physiology and productivity of primary producers to be examined at scales from the single cell to entire ocean basins. Current remote sensing algorithms concentrate on better describing the relationship between primary productivity and natural fluorescence that is emitted from solar excitation. While several major challenges exist in achieving this goal, such approaches provide great promise for accurately characterizing the role of marine primary productivity during this period of extreme climate change.

Acuna Alvarez, L, Exton, D, Timmis, K, Suggett, DJ & Mcgenity, T 2009, 'Characterization Of Marine Isoprene-degrading Communities', Environmental Microbiology, vol. 11, no. 12, pp. 3280-3291.
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P>Isoprene is a volatile and climate-altering hydrocarbon with an atmospheric concentration similar to that of methane. It is well established that marine algae produce isoprene; however, until now there was no specific information about marine isoprene sinks. Here we demonstrate isoprene consumption in samples from temperate and tropical marine and coastal environments, and furthermore show that the most rapid degradation of isoprene coincides with the highest rates of isoprene production in estuarine sediments. Isoprene-degrading enrichment cultures, analysed by denaturing gradient gel electrophoresis and 454 pyrosequencing of the 16S rRNA gene and by culturing, were generally dominated by Actinobacteria, but included other groups such as Alphaproteobacteria and Bacteroidetes, previously not known to degrade isoprene. In contrast to specialist methane-oxidizing bacteria, cultivated isoprene degraders were nutritionally versatile, and nearly all of them were able to use n-alkanes as a source of carbon and energy. We therefore tested and showed that the ubiquitous marine hydrocarbon-degrader, Alcanivorax borkumensis, could also degrade isoprene. A mixture of the isolates consumed isoprene emitted from algal cultures, confirming that isoprene can be metabolized at low, environmentally relevant concentrations, and suggesting that, in the absence of spilled petroleum hydrocarbons, algal production of isoprene could maintain viable populations of hydrocarbon-degrading microbes. This discovery of a missing marine sink for isoprene is the first step in obtaining more robust predictions of its flux, and suggests that algal-derived isoprene provides an additional source of carbon for diverse microbes in the oceans.

Arotsker, L, Siboni, N, Ben-Dov, E, Kramarsky-Winter, E, Loya, Y & Kushmaro, A 2009, 'Vibrio sp as a potentially important member of the Black Band Disease (BBD) consortium in Favia sp corals', FEMS MICROBIOLOGY ECOLOGY, vol. 70, no. 3, pp. 515-524.
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Baird, AH, Bhagooli, R, Ralph, PJ & Takahashi, S 2009, 'Coral bleaching: the role of the host', Trends In Ecology & Evolution, vol. 24, no. 1, pp. 16-20.
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Coral bleaching caused by global warming is one of the major threats to coral reefs. Very recently, research has focused on the possibility of corals switching symbionts as a means of adjusting to accelerating increases in sea surface temperature. Although symbionts are clearly of fundamental importance, many aspects of coral bleaching cannot be readily explained by differences in symbionts among coral species. Here we outline several potential mechanisms by which the host might influence the bleaching response, and conclude that predicting the fate of corals in response to climate change requires both members of the symbiosis to be considered equally.

Bartlett, CY, Manua, C, Cinner, J, Sutton, S, Jimmy, R, South, R, Nilson, J & Raina, J 2009, 'Comparison of Outcomes of Permanently Closed and Periodically Harvested Coral Reef Reserves', Conservation Biology, vol. 23, no. 6, pp. 1475-1484.
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In many areas of the developing world, the establishment of permanent marine reserves is inhibited by cultural norms or socioeconomic pressures. Community conserved areas that are periodically harvested are increasingly being implemented as fisheries management tools, but few researchers have empirically compared them with permanently closed reserves. We used a hierarchal control-impact experimental design to compare the abundance and biomass of reef fishes, invertebrates, and substrate composition in periodically harvested and permanent reserves and in openly fished (control sites) of the South Pacific island country of Vanuatu. Fished species had significantly higher biomass in periodically harvested reserves than in adjacent openly fished areas. We did not detect differences in substratum composition between permanent reserves and openly fished areas or between permanent reserves and periodically harvested reserves. Giant clams (tridacnids) and top shells (Trochus niloticus) were vulnerable to periodic harvest, and we suggest that for adequate management of these species, periodically harvested community conservation areas be used in conjunction with other management strategies. Periodic harvest within reserves is an example of adaptive and flexible management that may meet conservation goals and that is suited to the social, economic, and cultural contexts of many coastal communities in the developing world.

Bar-zeev, E, Berman-frank, I, Stambler, N, Vazquez-dominguez, E, Zohary, T, Capuzzo, E, Meeder, E, Suggett, DJ, Iluz, D, Dishon, G & Berman, T 2009, 'Transparent exopolymer particles (TEP) link phytoplankton and bacterial production in the Gulf of Aqaba', Aquatic Microbial Ecology, vol. 56, no. 2-3, pp. 217-225.
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Variations in transparent exopolymer particles (TEP), bacterial biomass production (BP) and primary productivity (PP) were followed over 52 h at a deep water station in the Gulf of Aqaba (Eilat, Israel) during the spring, in April 2008. About 20 h after the start of the study, there was a short (~15 h) but intense storm event that probably caused a nutrient pulse and, subsequently, a brief outgrowth of diatoms in the euphotic layer. Concentrations of TEP and BP ranged from 23 to 228 µg gum xanthan equivalents l1 and from 0.2 to 0.6 µg C l1 h1, respectively. Concentrations of TEP and BP were measured in unfiltered and in GF/C (1.2 µm)-prefiltered samples. Most of the TEP (59 ± 21% of total TEP, mean ± SD) were in the smaller (GF/C-filtered) size fraction (0.41.2 µm); however, after the crash of the diatom bloom, the majority of TEP were in the >1.2 µm size fraction. In the GF/C-filtered fraction, BP averaged 59 ± 12% and 93 ± 5% of total BP in the upper water column and from 300 m, respectively. Significant correlations were observed between TEP and BP, suggesting that active heterotrophic bacteria may have been associated with these particles. During the 3 d of our study, PP and BP in the euphotic zone averaged 480 and 225 mg C m2 d1, respectively, suggesting that about half or more of the primary produced carbon was metabolized by heterotrophic bacteria in the upper water column. Coincident with strong mixing caused by the storm, TEP concentrations decreased in the surface water and increased at depth. We suggest that TEP acted to link carbon flux between the primary producers and heterotrophic bacteria, and that the downward movement of TEP from the upper water layers may be an important process in transferring organic carbon to deeper waters of the Gulf of Aquaba. Sinking TEP could provide not only organic carbon substrates for associated bacteria but also form `hot spots of elevated microbial metabolism and nutrient cycling throughout the water column.

Buxton, LJ, Badger, M & Ralph, PJ 2009, 'Effects Of Moderate Heat Stress And Dissolved Inorganic Carbon Concentration On Photosynthesis And Respiration Of Symbiodinium Sp (Dinophyceae) In Culture And In Symbiosis', Journal of Phycology, vol. 45, no. 2, pp. 357-365.
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The influence of temperature and inorganic carbon (C-i) concentration on photosynthesis was examined in whole corals and samples of cultured symbiotic dinoflagellates (Symbiodinium sp.) using combined measurements from a membrane inlet mass spectrometer and chl a fluorometer. In whole corals, O-2 production at 26 degrees C was significantly limited at C-i concentrations below ambient seawater (similar to 2.2 mM). Further additions of C-i up to similar to 10 mM caused no further stimulation of oxygenic photosynthesis. Following exposure to 30 degrees C (2 d), net oxygen production decreased significantly in whole corals, as a result of reduced production of photosynthetically derived oxygen rather than increased host consumption. Whole corals maintained a rate of oxygen evolution around eight times lower than cultured Symbiodinium sp. at inorganic carbon concentrations < 2 mM, but cultures displayed greater levels of photoinhibition following heat treatment (30 degrees C, 2 d). Whole corals and cultured zooxanthellae differed considerably in their responses to C-i concentration and moderate heat stress, demonstrating that cultured Symbiodinium make an incongruous model for those in hospite. Reduced net oxygen evolution, in whole corals, under conditions of low C-i (< 2 mM) has been interpreted in terms of possible sink limitation leading to increased nonphotochemical energy dissipation. The advantages of combined measurement of net gas exchange and fluorometry offered by this method are discussed.

Cerveny, J & Nedbal, L 2009, 'Metabolic Rhythms of the Cyanobacterium Cyanothece sp ATCC 51142 Correlate with Modeled Dynamics of Circadian Clock', JOURNAL OF BIOLOGICAL RHYTHMS, vol. 24, no. 4, pp. 295-303.
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Cerveny, J, Setlik, I, Trtilek, M & Nedbal, L 2009, 'Photobioreactor for cultivation and real-time, in-situ measurement of O-2 and CO2 exchange rates, growth dynamics, and of chlorophyll fluorescence emission of photoautotrophic microorganisms', ENGINEERING IN LIFE SCIENCES, vol. 9, no. 3, pp. 247-253.
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Cinner, JE, McClanahan, TR, Graham, NAJ, Pratchett, MS, Wilson, SK & Raina, J 2009, 'Gear-based fisheries management as a potential adaptive response to climate change and coral mortality', Journal of Applied Ecology, vol. 46, pp. 724-732.
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Collier, C, Lavery, P, Ralph, PJ & Masini, R 2009, 'Shade-induced response and recovery of the seagrass Posidonia sinuosa', Journal Of Experimental Marine Biology And Ecology, vol. 370, no. 1-2, pp. 89-103.
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The effect of shading on the seagrass Posidonia sinuosa Cambridge et Kuo was investigated to identify mechanisms that prolong its survival during periods of low light and permit its subsequent recovery. We also tested whether the responses were consistent in plants growing at different depths. Shade treatments were low (LS; 70 - 100% of ambient Photosynthetic Photon Flux Density), medium (MS; 12 - 39%) and heavy (HS; 5 - 4%) at the shallow (3 - 4 m) site, whilst the deep (7 - 8 m) site had no HS treatment. HS at the shallow and MS at the deep site were below minimum light requirements (MLR) for the long-term survival of P. sinuoso.

Dondrup, M, Albaum, SP, Griebel, T, Henckel, K, Juenemann, S, Kahlke, T, Kleindt, CK, Kuester, H, Linke, B, Mertens, D, Mittard-Runte, V, Neuweger, H, Runte, KJ, Tauch, A, Tille, F, Puehler, A & Goesmann, A 2009, 'EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data', BMC BIOINFORMATICS, vol. 10.
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Duxbury, Z, Schliep, MT, Ritchie, RJ, Larkum, A & Chen, M 2009, 'Chromatic photoacclimation extends utilisable photosynthetically active radiation in the chlorophyll d-containing cyanobacterium, Acaryochloris marina', Photosynthesis Research, vol. 101, no. 1, pp. 69-75.
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Chromatic photoacclimation and photosynthesis were examined in two strains of Acaryochloris marina (MBIC11017 and CCMEE5410) and in Synechococcus PCC7942. Acaryochloris contains Chl d, which has an absorption peak at ca 710 nm in vivo. Cultures were grown in one of the three wavelengths (525 nm, 625 nm and 720 nm) of light from narrow-band photodiodes to determine the effects on pigment composition, growth rate and photosynthesis: no growth occurred in 525 nm light. Synechococcus did not grow in 720 nm light because Chl a does not absorb effectively at this long wavelength. Acaryochloris did grow in 720 nm light, although strain MBIC11017 showed a decrease in phycobilins over time. Both Synechococcus and Acaryochloris MBIC11017 showed a dramatic increase in phycobilin content when grown in 625 nm light. Acaryochloris CCMEE5410, which lacks phycobilins, would not grow satisfactorily under 625 nm light. The cells adjusted their pigment composition in response to the light spectral conditions under which they were grown. Photoacclimation and the Q (y) peak of Chl d could be understood in terms of the ecological niche of Acaryochloris, i.e. habitats enriched in near infrared radiation.

Fahnenstiel, G, Hong, Y, Millie, D, Doblin, MA, Johengen, T & Reid, D 2009, 'Marine dinoflagellate cysts in the ballast tank sediments of ships entering the Laurentian Great Lakes', Verhandlungen Internationale Verein Limnology, vol. 30, no. 7, pp. 1035-1038.

Gribben, PE, Wright, JT, O'Connor, W, Doblin, MA, Eyre, B & Steinberg, P 2009, 'Reduced performance of native infauna following recruitment to a habitat-forming invasive marine alga', Oecologia, vol. 158, no. 4, pp. 733-745.
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Despite well-documented negative impacts of invasive species on native biota, evidence for the facilitation of native organisms, particularly by habitat-forming invasive species, is increasing. However, most of these studies are conducted at the population or community level, and we know little about the individual fitness consequences of recruitment to habitat-forming invasive species and, consequently, whether recruitment to these habitats is adaptive. We determined the consequences of recruitment to the invasive green alga Caulerpa taxifolia on the native soft-sediment bivalve Anadara trapezia and nearby unvegetated sediment. Initially, we documented the growth and survivorship of A. trapezia following a natural recruitment event, to which recruitment to C. taxifolia was very high. After 12 months, few clams remained in either habitat, and those that remained showed little growth. Experimental manipulations of recruits demonstrated that all performance measures (survivorship, growth and condition) were significantly reduced in C. taxifolia sediments compared to unvegetated sediments. Exploration of potential mechanisms responsible for the reduced performance in C. taxifolia sediments showed that water flow and water column dissolved oxygen (DO) were significantly reduced under the canopy of C. taxifolia and that sediment anoxia was significantly higher and sediment sulphides greater in C. taxifolia sediments. However, phytoplankton abundance (an indicator of food supply) was significantly higher in C. taxifolia sediments than in unvegetated ones. Our results demonstrate that recruitment of native species to habitat-forming invasive species can reduce growth, condition and survivorship and that studies conducted at the community level may lead to erroneous conclusions about the impacts of invaders and should include studies on life-history traits, particularly juveniles.

Haapkyla, J, Seymour, AS, Barneah, O, Brickner, I, Hennige, S, Suggett, DJ & Smith, D 2009, 'Association of Waminoa sp. (Acoela) with corals in the Wakatobi Marine Park, South-East Sulawesi, Indonesia', Marine Biology, vol. 156, no. 5, pp. 1021-1027.
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This is the first quantitative study on the prevalence of epizoic Waminoa sp. acoel worms and their association with corals in the Wakatobi Marine National Park (WMNP), South-East Sulawesi, Indonesia. Three replicate transects were laid on the reef crest

Hennige, SJ, Suggett, DJ, Warner, ME, McDougall, KE & Smith, DJ 2009, 'Photobiology of Symbiodinium revisited: bio-physical and bio-optical signatures', Coral Reefs, vol. 28, no. 1, pp. 179-195.
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Light is often the most abundant resource within the nutrient-poor waters surrounding coral reefs. Consequently, zooxanthellae (Symbiodinium spp.) must continually photoacclimate to optimise productivity and ensure coral success. In situ coral photobiolo

Hill, R, Ulstrup, K & Ralph, PJ 2009, 'Temperature Induced Changes In Thylakoid Membrane Thermostability Of Cultured, Freshly Isolated, And Expelled Zooxanthellae From Scleractinian Corals', Bulletin of Marine Science, vol. 85, no. 3, pp. 223-244.
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Coral bleaching events are characterized by a dysfunction between the cnidarian coral host and the symbiotic dinoflagellate algae, known as zooxanthellae (genus Symbiodinium). Elevated temperature and intense light induce coral bleaching, where zooxanthellae are expelled from the host tissue. The primary cellular process in zooxanthellae which leads to coral bleaching is unresolved, and here, we investigated the sensitivity of the thylakoid membrane in a Symbiodinium culture and in genetically identified freshly isolated and expelled Symbiodinium cells. The fluorescence-temperature curve technique was used to measure the critical temperature (Tc) at which irreversible damage to the thylakoid membrane occurred. The accuracy of this technique was confirmed through the collection of scanning transmission electron micrographs which demonstrated the clear relationship between Tc and thylakoid membrane degradation. Analysis of 10 coral species with a diverse range of genetically distinct Symbiodinium communities showed a decline in Tc from summer to winter. A Symbiodinium culture and fragments of Pocillopora damicornis (Linnaeus, 1758) were exposed to a series of light and temperature treatments, where Tc increased from approximately 37 °C to 42 °C upon exposure to elevated temperature. Under bleaching conditions, the thermostability of the thylakoid membrane increased within 4 hrs by 5.1 °C, to a temperature far above bleaching thresholds, in both freshly isolated and photosynthetically competent zooxanthellae expelled from P. damicornis under these conditions. It is demonstrated that the thermostability of the thylakoid membrane increases in cultured, freshly isolated, and expelled zooxanthellae exposed to bleaching stress, suggesting it is not the primary site of impact during coral bleaching events.

Mantri, VA, Thakur, MC, Kumar, M, Reddy, CRK & Jha, B 2009, 'The carpospore culture of industrially important red alga Gracilaria dura (Gracilariales, Rhodophyta)', AQUACULTURE, vol. 297, no. 1-4, pp. 85-90.
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Mohr, R, Voss, B, Schliep, MT, Kurz, T, Maldener, I, Adams, DG, Larkum, A, Chen, M & Hess, WR 2009, 'A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus Acaryochloris', ISME Journal, vol. 4, no. 11, pp. 1456-1469.
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Chlorophyll d is a photosynthetic pigment that, based on chemical analyses, has only recently been recognized to be widespread in oceanic and lacustrine environments. However, the diversity of organisms harbouring this pigment is not known. Until now, the unicellular cyanobacterium Acaryochloris marina is the only characterized organism that uses chlorophyll d as a major photopigment. In this study we describe a new cyanobacterium possessing a high amount of chlorophyll d, which was isolated from waters around Heron Island, Great Barrier Reef (23 degrees 26' 31.2 '' S, 151 degrees 54' 50.4 '' E). The 16S ribosomal RNA is 2% divergent from the two previously described isolates of A. marina, which were isolated from waters around the Palau islands (Pacific Ocean) and the Salton Sea lake (California), suggesting that it belongs to a different clade within the genus Acaryochloris. An overview sequence analysis of its genome based on Illumina technology yielded 871 contigs with an accumulated length of 8 371 965 nt. Their analysis revealed typical features associated with Acaryochloris, such as an extended gene family for chlorophyll-binding proteins. However, compared with A. marina MBIC11017, distinct genetic, morphological and physiological differences were observed. Light saturation is reached at lower light intensities, Chl d/a ratios are less variable with light intensity and the phycobiliprotein phycocyanin is lacking, suggesting that cyanobacteria of the genus Acaryochloris occur in distinct ecotypes. These data characterize Acaryochloris as a niche-adapted cyanobacterium and show that more rigorous attempts are worthwhile to isolate, cultivate and analyse chlorophyll d-containing cyanobacteria for understanding the ecophysiology of these organisms.

Moore, C, Mills, M, Achterberg, E, Geider, R, Laroche, J, Lucas, M, Mcdonagh, E, Pan, X, Poulton, A, Rijkenberg, M, Suggett, DJ, Ussher, S & Woodward, E 2009, 'Large-scale Distribution Of Atlantic Nitrogen Fixation Controlled By Iron Availability', Nature Geoscience, vol. 2, no. 12, pp. 867-871.
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Oceanic fixed-nitrogen concentrations are controlled by the balance between nitrogen fixation and denitrification(1-4). A number of factors, including iron limitation(5-7), can restrict nitrogen fixation, introducing the potential for decoupling of nitrogen inputs and losses(2,5,8). Such decoupling could significantly affect the oceanic fixed-nitrogen inventory and consequently the biological component of ocean carbon storage and hence air-sea partitioning of carbon dioxide(2,5,8,9). However, the extent to which nutrients limit nitrogen fixation in the global ocean is uncertain. Here, we examined rates of nitrogen fixation and nutrient concentrations in the surfacewaters of the Atlantic Ocean along a north-south 10,000 km transect during October and November 2005. We show that rates of nitrogen fixation were markedly higher in the North Atlantic compared with the South Atlantic Ocean. Across the two basins, nitrogen fixation was positively correlated with dissolved iron and negatively correlated with dissolved phosphorus concentrations. We conclude that inter-basin differences in nitrogen fixation are controlled by iron supply rather than phosphorus availability. Analysis of the nutrient content of deep waters suggests that the fixed nitrogen enters North Atlantic Deep Water. Our study thus supports the suggestion that iron significantly influences nitrogen fixation(5), and that subsequent interactions with ocean circulation patterns contribute to the decoupling of nitrogen fixation and loss(2,4,8).

Pernice, M, Boucher, J, Boucher-Rodoni, R, Joannot, P & Bustamante, P 2009, 'Comparative bioaccumulation of trace elements between Nautilus pompilius and Nautilus macromphalus (Cephalopoda: Nautiloidea) from Vanuatu and New Caledonia', ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY, vol. 72, no. 2, pp. 365-371.
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Petrou, K, Doblin, M, Hassler, C & Ralph, P 2009, 'MULTIPLE STRESSORS ON ANTARCTIC MICROALGAE IMPACTS OF SEASONAL FREEZING AND MELTING OF SEA-ICE', PHYCOLOGIA, vol. 48, no. 4, pp. 106-106.

Quevrain, E, Domart-Coulon, I, Pernice, M & Bourguet-Kondracki, M-L 2009, 'Novel natural parabens produced by a Microbulbifer bacterium in its calcareous sponge host Leuconia nivea', ENVIRONMENTAL MICROBIOLOGY, vol. 11, no. 6, pp. 1527-1539.
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Raina, J, Tapiolas, DM, Willis, BL & Bourne, DG 2009, 'Coral-associated bacteria and their role in the biogeochemical cycling of sulfur', Applied and Environmental Microbiology, vol. 75, no. 11, pp. 3492-3501.
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Marine bacteria play a central role in the degradation of dimethylsulfoniopropionate (DMSP) to dimethyl sulfide (DMS) and acrylic acid, DMS being critical to cloud formation and thereby cooling effects on the climate. High concentrations of DMSP and DMS have been reported in scleractinian coral tissues although, to date, there have been no investigations into the influence of these organic sulfur compounds on coralassociated bacteria. Two coral species, Montipora aequituberculata and Acropora millepora, were sampled and their bacterial communities were characterized by both culture-dependent and molecular techniques. Four genera, Roseobacter, Spongiobacter, Vibrio, and Alteromonas, which were isolated on media with either DMSP or DMS as the sole carbon source, comprised the majority of clones retrieved from coral mucus and tissue 16S rRNA gene clone libraries. Clones affiliated with Roseobacter sp. constituted 28% of the M. aequituberculata tissue libraries, while 59% of the clones from the A. millepora libraries were affiliated with sequences related to the Spongiobacter genus. Vibrio spp. were commonly isolated from DMS and acrylic acid enrichments and were also present in 16S rRNA gene libraries from coral mucus, suggesting that under ¿normal¿ environmental conditions, they are a natural component of coral-associated communities. Genes homologous to dddD, and dddL, previously implicated in DMSP degradation, were also characterized from isolated strains, confirming that bacteria associated with corals have the potential to metabolize this sulfur compound when present in coral tissues. Our results demonstrate that DMSP, DMS, and acrylic acid potentially act as nutrient sources for coral-associated bacteria and that these sulfur compounds are likely to play a role in structuring bacterial communities in corals, with important consequences for the health of both corals and coral reef ecosystems.

Rasoulouniriana, D, Siboni, N, Ben-Dov, E, Kramarsky-Winter, E, Loya, Y & Kushmaro, A 2009, 'Pseudoscillatoria coralii gen. nov., sp nov., a cyanobacterium associated with coral black band disease (BBD)', DISEASES OF AQUATIC ORGANISMS, vol. 87, no. 1-2, pp. 91-96.
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Scanlan, DJ, Ostrowski, M, Mazard, S, Dufresne, A, Garczarek, L, Hess, WR, Post, AF, Hagemann, M, Paulsen, I & Partensky, F 2009, 'Ecological Genomics of Marine Picocyanobacteria', MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, vol. 73, no. 2, pp. 249-+.
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Seuront, L, Leterme, SC, Seymour, JR, Mitchell, JG, Ashcroft, D, Noble, W, Thomson, PG, Davidson, AT, van den Enden, R, Scott, FJ, Wright, SW, Schapira, M, Chapperon, C & Cribb, N 2009, 'Role of microbial and phytoplanktonic communities in the control of seawater viscosity off East Antarctica (30-80° E)', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 57, no. 9-10, pp. 877-886.
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Despite the long-standing belief that seawater viscosity is driven by temperature and salinity, biologically increased seawater viscosity has repeatedly been reported in relation to phytoplankton exudates in shallow, productive coastal waters. Here, seawater viscosity was investigated in relation to microbial and phytoplanktonic communities off the coast of East Antarctica along latitudinal transects located between 30°E and 80°E in sub-surface waters and at the deep chlorophyll maximum (DCM). The physical component of seawater viscosity observed along each transects ranged from 1.80 to 1.95 cP, while the actual seawater viscosity ranged from 1.85 to 3.69 cP. This resulted in biologically increased seawater viscosity reaching up to 84.9% in sub-surface waters and 77.6% at the DCM. Significant positive correlations were found between elevated seawater viscosity and (i) bacterial abundance in sub-surface waters and (ii) chlorophyll a concentration and the abundance of flow cytometrically-defined auto- and heterotrophic protists at the DCM. Among the 12 groups and 108 species of protists identified under light microscopy, dinoflagellates and more specifically Alexandrium tamarense and Prorocentrum sp. were the main contributors to the patterns observed for elevated seawater viscosity. Our observations, which generalised the link previously identified between seawater viscosity and phytoplankton composition and standing stock to the Southern Ocean, are the first demonstration of increases in seawater viscosity linked to marine bacterial communities, and suggest that the microbially-increased viscosity might quantitatively be at least as important as the one related to phytoplankton secretion.

Seymour, JR, Ahmed, T & Stocker, R 2009, 'Bacterial chemotaxis towards the extracellular products of the toxic phytoplankton Heterosigma akashiwo', Journal Of Plankton Research, vol. 31, no. 12, pp. 1557-1561.
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Marine bacteria exhibit positive chemotactic responses to the extracellular exudates of the toxic phytoplankton Heterosigma akashiwo. In the environment, this will support bacteriaalgae associations with potential implications for harmful algal bloom dynamics.

Seymour, JR, Marcos & Stocker, R 2009, 'Resource Patch Formation and Exploitation throughout the Marine Microbial Food Web', AMERICAN NATURALIST, vol. 173, no. 1, pp. E15-E29.
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Siboni, N, Martinez, S, Abelson, A, Sivan, A & Kushmaro, A 2009, 'Conditioning film and initial biofilm formation on electrochemical CaCO3 deposition on a metallic net in the marine environment', BIOFOULING, vol. 25, no. 7, pp. 675-683.
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Strom, D, Ralph, PJ & Stauber, JL 2009, 'Development of a Toxicity Identification Evaluation Protocol Using Chlorophyll-a Fluorescence in a Marine Microalga', Archives Of Environmental Contamination And Toxic..., vol. 56, no. 1, pp. 30-38.
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Growth inhibition bioassays with the microalga Nitzschia closterium have recently been applied in marine Toxicity Identification Evaluation (TIE) testing. However, the 48-h test duration can result in substantial loss of toxicants over time, which might lead to an underestimation of the sample toxicity. Although shorter-term microalgal bioassays can minimize such losses, there are few bioassays available and none are adapted for marine TIE testing. The acute (5-min) chlorophyll-a fluorescence bioassay is one alternative; however, this bioassay was developed for detecting herbicides in freshwater aquatic systems and its suitability for marine TIE testing was not known. In this study, a chlorophyll-a fluorescence bioassay using the marine microalga Isochrysis galbana was able to detect contaminants other than herbicides at environmentally relevant concentrations and tolerated the physical and chemical manipulations needed for a Phase I TIE. Phase I TIE procedures were successfully developed using this chlorophyll-a fluorescence bioassay and used to identify all classes of contaminants present in a synthetic mixture of known chemical composition. In addition, TIEs with both the acute fluorescence bioassay and the standard growth inhibition bioassay identified the same classes of toxicants in a sample of an unknown complex effluent. Even though the acute chlorophyll-a fluorescence end point was less sensitive than the chronic cell division end point, TIEs with the chlorophyll-a fluorescence bioassay provided a rapid and attractive alternative to longer-duration bioassays.

Suggett, DJ, MacIntyre, HL, Kana, TM & Geider, RJ 2009, 'Comparing electron transport with gas exchange:parameterising exchange rates between alternative photosynthetic currencies for eukaryotic phytoplankton', Aquatic Microbial Ecology, vol. 56, no. 2-3, pp. 147-162.
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Estimates of aquatic primary productivity derived from in situ active chl a fluorescence have rapidly gained popularity over the past 2 decades. This trend has been driven primarily by the need to improve upon `conventional carbon (C) uptake- or oxygen (O2) evolution-based productivity estimates that require water samples to be incubated ex situ. Unlike the conventional approaches to measuring productivity, chlorophyll fluorescence measurements inherently describe only the activity of photosystem II (PSII) in the light reactions; thus, the photosynthetic `currency of the fluorescence based approach is an electron turnover rate for PSII (ETRPSII). A photosynthetic currency of electrons has limited ecological relevance but can be converted to a currency of carbon if an `exchange rate, i.e. a value or factor of equivalence for any single time point, is applied. We used fast repetition rate fluorometry (FRRf), mass inlet membrane spectrometry (MIMS) and 14C uptake to determine ETRPSII, gross and net O2 evolution and C fixation measured simultaneously for 6 microalgal species and for different steady-state growth conditions. Quantifying the PSII reaction centre (RCII) concentration and the spectral dependency of the effective absorption cross section yielded an FRRf approach that provided a robust estimate of the ETRPSII and gross O2 evolution for all species and conditions tested; however, the ETRPSII exceeded carbon dioxide (CO2) uptake by a factor of ~5.4 to 11.6. At least 3 species exhibited substantial light-dependent O2 cycling to account for ~40 to 60% of the difference between the ETRPSII and CO2 uptake. The highly variable nature of the ETRPSII:CO2 uptake `exchange rate observed here highlights the need for future studies that rely on active fluorescence to examine aquatic productivity to focus towards a systematic description of how electrons are coupled to C fixation in nature

Suggett, DJ, Moore, CM, Hickman, AE & Geider, RJ 2009, 'Interpretation of fast repetition rate (FRR) fluorescence: signatures of phytoplankton community structure versus physiological state', Marine Ecology Progress Series, vol. 376, pp. 1-19.
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Introduction of active chlorophyll a fluorescence protocols, in particular fast repetition rate (FRR) fluorometry, to oceanography and limnology 15 yr ago has enabled rapid assessment of photosynthetic physiology in situ. The FRR protocol generates simultaneous measurements of Photosystem II (PSII) effective absorption cross sections (termed sPSII) and photochemical efficiency (termed Fv/Fm). Both Fv/Fm and sPSII measurements have been utilised to examine the effects of physiological stress on the photosynthetic apparatus of phytoplankton in an ever growing number of fluorescence-based studies. However, it is now becoming clearer that in situ values of Fv/Fm and sPSII also contain taxonomic information. Here, we present a synthesis of previously unpublished and published data, which show that Fv/Fm and sPSII vary principally with broad-scale changes in community structure. These patterns observed in situ conform to trends observed in laboratory-grown cultures of a range of phytoplankton taxa. The magnitudes of variability in Fv/Fm and sPSII driven by changes in phytoplankton community structure often exceed that induced by nutrient limitation (as determined from controlled nutrient addition experiments). An exception to this general trend occurs in high-nutrient, low-chlorophyll a (HNLC) regions, where strong phenotypic changes in Fv/Fm and sPSII have been repeatedly demonstrated on relief of iron limitation. Overall, FRR fluorescence measurements of both Fv/Fm and sPSII in natural populations represent a combination of the taxonomic `signature (values of Fv/Fm and sPSII determined by the taxa present) within the phytoplankton community that is further modified according to the (photo-) physiological status. As such, fluorescence-based investigations of mixed populations must account for potential variations in phytoplankton community structure before interpretations of physiological status are made.

Sutherland, DL 2009, 'Microbial mat communities in response to recent changes in the physiochemical environment of the meltwater ponds on the McMurdo Ice Shelf, Antarctica', POLAR BIOLOGY, vol. 32, no. 7, pp. 1023-1032.
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Sutherland, DL & Hawes, I 2009, 'Annual growth layers as proxies of past growth conditions for benthic microbial mats in a perennially ice-covered Antarctic lake', FEMS MICROBIOLOGY ECOLOGY, vol. 67, no. 2, pp. 279-292.
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Thompson, PA, Baird, ME, Ingleton, T & Doblin, MA 2009, 'Long-term changes in temperate Australian coastal waters: implications for phytoplankton', Marine Ecology Progress Series, vol. 394, pp. 1-19.
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A ~60 yr physical and chemical data set from 4 coastal stations around Australia plus remotely sensed SeaWiFS and phytoplankton taxonomic data were used to evaluate the temporal and spatial variation in phytoplankton ecology. The most consistent trend observed at all stations was a long-term increase in surface salinity of ~0.003 ± 0.0008 psu yr1. All stations showed positive trends in temperature, with the fastest surface warming (0.0202°C yr1 over 60 yr) in the western Tasman Sea. Long-term trends in warming and stratification were more evident in some months and were not well characterized by annual averages. There was no general pattern of increasing stratification (0 to 50 m); only some stations and a few months showed significant changes. Long-term trends in surface nitrate and phosphate concentrations were either not significant (3 instances) or positive (5 instances) and were up to 6.1 nM phosphate yr1. A pronounced decline in silicate was evident at the 3 east coast stations, with concentrations falling by as much as 58 nM yr1 over the last ~30 yr. The western Tasman Sea experienced a ~50% decline in the growth rate and biomass of the spring bloom from 1997 to 2007, while other sites showed significant temporal variability in chlorophyll a that was associated with the Southern Oscillation Index (SOI). Diatoms tended to dominate the microplankton, especially during periods of low stratification. In conclusion, the physical, chemical and biological properties of Australian temperate waters have changed considerably over the last 60 yr in response to variation in the SOI and the strengthening East Australian Current.

Doblin, MA, Ralph, PJ, Oubelkheir, K, Hassler, CS, Suthers, I & Thompson, P 2009, 'Using IMOS to bridge the gap between direct measurements of marine primary production and models', Adelaide, Australia.

Jeffries, TC, Newton, K, Leterme, S, Seymour, JR, Dinsdale, E, Gilbert, J, Roudnew, B, Smith, R, Seuront, L & Mitchell, J 2009, 'Taxonomic clustering of microbial metagenomes in the Coorong lagoon system', Adelaide, Australia.

Jeffries, TC, Newton, K, Leterme, S, Seymour, JR, Dinsdale, E, Roudnew, B, Smith, R, Seuront, L & Mitchell, JG 2009, 'Functional metagenomics of sediment microbial communities from a hypersaline coastal lagoon', Adelaide, Australia.

Lavery, TJ, Roudnew, B, Seymour, JR, Mitchell, JG, Seuront, L & Smetacek, V 2009, 'Whales: A net sink or source of carbon to the atmosphere?', Adelaide, Australia.

Newton, K, Jeffries, TC, Seymour, JR, Leterme, S, Mitchell, J & Seuront, L 2009, 'Impact of salinity on viral morphological diversity', Adelaide, Australia.

Petrou, K, Doblin, MA, Hassler, CS & Ralph, PJ 2009, 'Multiple stressors on the sea ice diatom Fragilariopsis cylindrus - photophysiological impacts of seasonal freezing and melting of sea ice', Japan.

Seymour, JR 2009, 'Cascading resource patch exploitation in a heterogeneous microbial seascape', Adelaide, Australia.

Sinutok, S, Hill, R & Ralph, PJ 2009, 'The effect of light intensity on photosynthetic efficiency and calcification in three reef building species of Halimeda', ASPAB 2009 Conference, Townsville, Australia.
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Calcareous green algae from the genus Halimeda are widely distributed in tropical and subtropical marine environments. Halimeda is important as a carbonate sediment producer, as a source of food for herbivores, as a phototroph, and as a provider of shelter and nursery ground for invertebrates on coral reefs. Halimeda cylindracea, H. macroloba, and H. opuntia collected from the intertidal zone at Heron Island reef in the southern Great Barrier Reef of Australia were maintained in flow-through seawater tanks under three different irradiances (50, 400 and 900 µmol photon m-2 s-1) for a 4 day period. Measures of photosynthetic efficiency were investigated using Pulse Amplitude Modulated (PAM) fluorometry and chlorophyll concentrations (a and b) were determined after 4 days on an apical lobe of the thallus. Growth and calcification were examined by staining the thallus with Alizarin Red-S solution. Pigmentation, growth, and calcification were found to be independent of irradiance, remaining constant over time between treatments, except for chlorophyll a in H. cylindracea which was higher in low light than in higher light treatments. The results indicate that each species responded differently under the high light treatment at midday, with H. cylindracea and H. macroloba showing a reduction in photochemical quenching (Y(II)), indicating downregulation in photosynthetic efficiency. This was mirrored by an increase in non-regulated energy dissipation yield of PSII (Y(NO)), suggesting that photoinhibition was occurring. In comparison to this species, H. opuntia showed no changes in Y(II) and Y(NO) while H. macroloba showed higher Y(II) and lower Y(NO) only in the morning and the evening. Non-photochemical quenching yield (Y(NPQ)) was low in all treatments and in all three species which may indicate a low potential for photoprotection mechanisms in these algae. However, further investigation is required which run over an extended period of time and between seasons.

Sutherland, D, Spigel, B, Plew, D, Norton, N & Howard-Williams, C 2009, 'Limiting nutrients of phytoplankton growth in the Upper Waitaki lakes', Development workshop for the Upper Waitaki Catchment, Canterbury, New Zealand.

de Winton, M, Jellyman, D, Sutherland, D & Walsh, J 2009, A review of the potential to re-establish macrophyte beds in Te Waihora (Lake Ellesmere), Hamilton.

Hallegraeff, GM, Beardall, J, Brett, S, Doblin, MA, Hosja, W, de Salas, M & Thompson, P www.oceanclimatechange.org.au 2009, Marine climate change in Australia: Impacts and adaptation responses: Phytoplankton, pp. 1-10, Australia.

Hudson, N, Hickey, C, Nagals, J, Sutherland, D & Wells, R 2009, Joint venture discharge consent renewal – assessment of effects on the Tarawera River: Water Quality and aquatic plants, Hamilton.

Norton, N, Spigel, B, Sutherland, DL, Trolle, D & Plew, D 2009, Lake Benmore Water Quality: a modelling method to assist with assessments of nutrient loadings., Christchurch, NZ.

Salas, M, Cheal, A, Lough, J, McKinnon, D, Meekan, M, Sweatman, H, Coleman, M, Chambers, L, Dunlop, N, Church, J, Dowdney, J, Feng, M, Griffiths, S, Hobday, A, Matear, R, Poloczanska, E, Richardson, A, Ridgway, K, Risbey, J, Thompson, P, Thresher, R, Weller, E, Saintilan, N, Wilson, S, Lenanton, R, Hosja, W, Moore, P, Wernberg, T, Marshall, D, Connolly, R, Hill, K, Congdon, B, Devney, C, Fuentes, M, Graham, N, Hamann, M, Kingsford, M, Munday, P, Pratchett, M, Sheaves, M, Beardall, J, Brett, S, Waschka, M, Dann, P, Edgar, G, Swadling, K, Connell, S, Russell, B, Ward, T, Lukoschek, V, McGregor, S, Jenkins, G, Campbell, A, Steinberg, P, Anthony, K, Lovelock, C, Skilleter, G, Figueira, WF, Booth, DJ, Doblin, MA, Davidson, J, Holbrook, N, Howard, W, Kendrick, G & Smale, D NCCARF Publication 2009, Report Card of Marine Climate Change for Australia, pp. 1-2, Australia.

Sutherland, D & Edwards, T 2009, Weed surveillance of four Canterbury High Country Lakes and the Ecological Condition of Lakes Ohau and Alexandrina using LakeSPI, Christchurch.

Sutherland, D, Kelly, G, Dumas, J, Spigel, B & Norton, N 2009, Water quality parameters in the Upper Waitaki Basin December 2008 – April 2009, Christchurch.

Sutherland, DL 2009, Effects of MTAD on Te Waiwai Lagoon, Southland - Statement of Evidence, Christchurch, NZ.

Sutherland, DL 2009, Effects of the proposed MTAD on the water quality and aquatic ecology in the Southern Lakes, Statement of Evidence, Christchurch, NZ.

Norton, N, Spigel, B, Sutherland, D & Howard-Williams, C 2009, 'Waitaki Lakes Water Quality: a method to define sustainable thresholds for nutrient loading for regional planning'.

Norton, N, Spigel, B, Sutherland, D, Trolle, D & Plew, D 2009, 'Lake Benmore water quality: a modelling method to assist with assessments for nutrient loadings'.

Spigel, B, Trolle, D, Sutherland, D, Plew, DR, Norton, N & Howard-Williams, C 2009, 'Waitaki Lakes Water Quality: a method to define sustainable thresholds for nutrient loading for regional planning'.

Sutherland, D 2009, 'Results of the pre-MTAD baseline surveys in Lakes Te Anau, Manaporui, Hauroko and the Waiau Arm'.

Sutherland, D, Spigel, B, Plew, D, Norton, N & Howard-Williams, C 2009, 'Water quality, macrophyte, periphyton and phytoplankton growth in the Upper Waitaki lakes'.