Publications

Larkum, AWD, Orth, RJ & Duarte, CM 2006, Seagrasses: Biology, ecology and conservation.
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Seagrasses are unique plants; the only group of flowering plants to recolonise the sea. They occur on every continental margin, except Antarctica, and form ecosystems which have important roles in fisheries, fish nursery grounds, prawn fisheries, habitat diversity and sediment stabilisation. Over the last two decades there has been an explosion of research and information on all aspects of seagrass biology. However the compilation of all this work into one book has not been attempted previously. In this book experts in 26 areas of seagrass biology present their work in chapters which are state-of-the-art and designed to be useful to students and researchers alike. The book not only focuses on what has been discovered but what exciting areas are left to discover. The book is divided into sections on taxonomy, anatomy, reproduction, ecology, physiology, fisheries, management, conservation and landscape ecology. It is destined to become the chosen text on seagrasses for any marine biology course. © 2006/2007 Springer. All Rights Reserved.

Larkum, A, Drew, E & Ralph, PJ 2006, 'Photosynthesis and Metabolism in Seagrasses at the Cellular Level' in Larkum, AWD, Orth, RJ & Dyarte, CM (eds), Seagrasses:Biology, Ecology and Conservation, Springer, Dordrecht, The Netherlands, pp. 323-345.

Ralph, PJ, Tomasko, D, Moore, KA, Seddon, S & Macinnis-Ng, CM 2006, 'Human impacts on seagrasses: Eutrophication, sedimentation and contamination' in Larkum, AWD, Orth, RJ & Duarte, CM (eds), Seagrasses: Biology, Ecology and Conservation, Springer, The Netherlands, pp. 567-593.

Belli, SI, Smith, NC & Ferguson, DJ 2006, 'The coccidian oocyst a tough nut to crack!', Trends In Parasitology, vol. 22, no. 9, pp. 416-423.
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Coccidian parasites are transmitted between hosts by the ingestion of food or water contaminated with oocysts, followed by the release of infectious sporozoites and invasion of the gastro-intestinal tract. In the external environment, sporozoites are pro

Ben-Dov, E, Shapiro, OH, Siboni, N & Kushmaro, A 2006, 'Advantage of using inosine at the 3 ' termini of 16S rRNA gene universal primers for the study of microbial diversity', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 72, no. 11, pp. 6902-6906.
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Charles, AL, Markich, SJ & Ralph, PJ 2006, 'Toxicity of uranium and copper individually, and in combination, to a tropical freshwater macrophyte (Lemna aequinoctialis)', Chemosphere, vol. 62, no. 8, pp. 1224-1233.
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Copper (Cu) and uranium (U) are of potential ecotoxicological concern to tropical freshwater biota in northern Australia, as a result of mining activities. Few data are available on the toxicity of U, and no data are available on the toxic interaction of

Doblin, MA & Dobbs, FC 2006, 'Setting a size-exclusion limit to remove toxic dinoflagellate cysts from ships ballast water', Marine Pollution Bulletin, vol. 52, no. 3, pp. 259-263.
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Dinoflagellate cysts are well-recognized biological constituents of ships ballast tanks. They are present in ballast water, sediments and residual water in drained tanks, and in biofilms formed on interior tank Surfaces. Therefore, cysts have the potenti

Doblin, MA, Baines, SB, Cutter, LS & Cutter, GA 2006, 'Sources and biogeochemical cycling of particulate selenium in the San Francisco Bay estuary', Estuarine Coastal And Shelf Science, vol. 67, no. 4, pp. 681-694.
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As part of a study of estuarine selenium cycling, we measured the concentration, chemical form (speciation), and distribution of particulate selenium under various river flow conditions in the North San Francisco Bay (from the Golden Gate to the Sacramen

Doblin, MA, Thompson, P, Revill, A, Butler, E, Blackburn, S & Hallegraeff, GM 2006, 'Vertical migration of the toxic dinoflagellate Gymnodinium catenatum under different concentrations of nutrients and humic substances in culture', Harmful algae, vol. 5, no. 6, pp. 665-677.
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Vertical migration behaviour by the chainforming dinoflagellate Gymnodinium catenatum Graham was investigated using vertically-stratified laboratory columns. Under surface nutrient-deplete conditions, with nutrients added only at depth, 100% of cells underwent vertical migration (VM), starting downwards migration 3 h before the end of the light period and beginning upwards migration 3 h before the start of the light period. Cells in nutrient-replete columns showed no VM, but they were more dispersed in the upper layer during the dark compared to the light period. When surface layers (S) were nitrate-deplete (-N) and enriched with humic substances (H) contained in Huon River water and bottom waters (B) were nutrient replete (R) (SH-NBR), the pattern of VM was altered-50% of cells underwent migration and 50% remained at the pycnocline. In columns with nitrate-replete and humic-enriched surface layers (SHRBR), Most cells underwent VM, while 30% remained at the surface. Cells in SH-NBR columns showed increased N quotas and intra-cellular nitrate concentrations after 4 days, indicating nitrate uptake by G. catenatum in bottom layers. The concomitant increase in particulate organic nitrogen (PON) with the decrease in external nitrate concentrations in bottom layers provide convincing evidence that VM by G. catenatum facilitates nutrient retrieval at depth. However, addition of humic substances (a potential source of organic nitrogen) to surface layers did not ameliorate G. catenatum N depletion sufficiently to preclude the need for NO3- uptake at depth. Furthermore, there was no detectable pattern of increasing carbon (C) quota during the day (photosynthate accumulation) or increasing N quota during the night (nitrate assimilation).

Doubell, MJ, Seuront, L, Seymour, JR, Patten, NL & Mitchell, JG 2006, 'High-Resolution Fluorometer for Mapping Microscale Phytoplankton Distributions', Applied and Environmental Microbiology, vol. 72, no. 6, pp. 4475-4478.
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A new high-resolution, in situ profiling fluorometer maps fluorescence distributions with a spatial resolution of 0.5 to 1.5 mm to a depth of 70 m in the open ocean. We report centimeter-scale patterns for phytoplankton distributions associated with gradients exhibiting 10- to 30-fold changes in fluorescence in contrasting marine ecosystems.

Handy, SM, Coyne, KJ, Portune, KJ, Demir, E, Doblin, MA, Hare, CE, Cary, SC & Hutchins, DA 2006, 'Erratum: Evaluating vertical migration behavior of harmful raphidophytes in the Delaware Inland Bays utilizing quantitative real-time PCR (Aquatic Microbial Ecology (2005) 40, (121-132))', Aquatic Microbial Ecology, vol. 42, no. 3, p. 311.

Hill, R & Ralph, PJ 2006, 'Photosystem II Heterogeneity of in hospite Zooxanthellae in Scleractinian Corals Exposed to Bleaching Conditions', Photochemistry and Photobiology, vol. 82, no. 6, pp. 1577-1585.
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Increased ocean temperatures are thought to be triggering mass coral bleaching events around the world. The intracellular symbiotic zooxanthellae (genus Symbiodinium) are expelled from the coral host, which is believed to be a response to photosynthetic damage within these symbionts. Several sites of impact have been proposed, and here we probe the functional heterogeneity of Photosystem II (PSII) in three coral species exposed to bleaching conditions. As length of exposure to bleaching conditions (32 degrees C and 350 mu mol photons m(-2) s(-1)) increased, the Q(A)(-) reoxidation kinetics showed a rise in the proportion of inactive PSII centers (PSIIX), where Q(B) was unable to accept electrons. PSIIX contributed up to 20% of the total PSII centers in Pocillopora damicornis, 35% in Acropora nobilis and 14% in Cyphastrea serailia. Changes in F-V/F-M and amplitude of the J step along fast induction curves were found to be highly dependent upon the proportion of PSIIx centers within the total pool of PSII reaction centers. Determination of PSII antenna size revealed that under control conditions in the three coral species up to 60% of PSII centers were lacking peripheral light-harvesting complexes (PSII beta). In P. damicornis, the proportion of PSII beta increased under bleaching conditions and this could be a photoprotective mechanism in response to excess light. The rapid increases in PSIIX and PSII beta observed in these corals under bleaching conditions indicates these physiological processes are involved in the initial photochemical damage to zooxanthellae.

Jones, H, Ostrowski, M & Scanlan, DJ 2006, 'A suppression subtractive hybridization approach reveals niche-specific genes that may be involved in predator avoidance in marine Synechococcus isolates', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 72, no. 4, pp. 2730-2737.
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Kramarsky-Winter, E, Harel, M, Siboni, N, Ben Dov, E, Brickner, I, Loya, Y & Kushmaro, A 2006, 'Identification of a protist-coral association and its possible ecological role', MARINE ECOLOGY PROGRESS SERIES, vol. 317, pp. 67-73.
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Moore, CM, Suggett, DJ, Hickman, AE, Kim, Y, Tweddle, JF, Sharples, J, Geider, RJ & Holligan, PM 2006, 'Phytoplankton photoacclimation and photoadaptation in response to environmental gradients in a shelf sea', Limnology And Oceanography, vol. 51, no. 2, pp. 936-949.
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Variability in the photosynthetic performance of natural phytoplankton communities, due to both taxonomic composition and the physiological acclimation of these taxa to environmental conditions, was assessed at contrasting sites within a temperate shelf

O'Meara, T, Green, BJ, Sercombe, J & Tovey, E 2006, 'Measurement of personal exposure to outdoor aeromycota in northern New South Wales, Australia', vol. 13, no. 2, pp. 225-234.

Oren A, Pri-El N, Shapiro O & Siboni, N 2006, 'Buoyancy studies in natural communities of square gas-vacuolate archaea in saltern crystallizer ponds', Saline Systems, vol. 2.
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Patten, NL, Seymour, JR & Mitchell, JG 2006, 'Flow cytometric analysis of virus-like particles and heterotrophic bacteria within coral-associated reef water', Journal of the Marine Biological Association of the United Kingdom, vol. 86, no. 3, pp. 563-566.
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Using flow cytometry, two distinct populations of virus-like particles (VLP) and heterotrophic bacteria were defined within the 12 cm water layer immediately overlying healthy, diseased and dead acroporid corals. Bacterial abundances were similar in overlying water for all coral types, however, VLP were 30% higher above diseased corals than healthy or dead corals. Mean virus to bacteria ratios (VBR) were up to 30% higher above diseased corals than above healthy or dead coral or in distant water. Concomitant with increasing VLP concentrations within 5 cm of coral surfaces, VBR distributions were generally highest above healthy and diseased coral and depressed above dead coral. These results suggest fundamental shifts in the VLP and bacterial community in water associated with diseased corals.

Pernice, M, Deutsch, JS, Andouche, A, Boucher-Rodoni, R & Bonnaud, L 2006, 'Unexpected variation of Hox genes' homeodomains in cephalopods', MOLECULAR PHYLOGENETICS AND EVOLUTION, vol. 40, no. 3, pp. 872-879.
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Ryan, KG, Hegseth, E, Martin, A, Davy, S, O'Toole, R, Ralph, PJ, McMinn, A & Thorn, C 2006, 'Comparison of the microalgal community within fast ice two sites along the Ross Sea coast, Antarctia', Antarctic Science, vol. 18, no. 4, pp. 583-594.
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Seery, CR, Gunthorpe, L & Ralph, PJ 2006, 'Herbicide impact on Hormosira banksii gametes measured by fluorescence and germination bioassays', Environmental Pollution, vol. 140, no. 1, pp. 43-51.
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The innovative bioassay described here involves chlorophyll a fluorescence measurements of gametes from the macroalgae, Hormosira banksii, where gametes (eggs) were exposed to Diuron, Irgarol and Bromacil. Response was assessed as percent inhibition from

Seymour, JR, Seuront, L, Doubell, MJ, Waters, RL & Mitchell, JG 2006, 'Microscale patchiness of virioplankton', Journal of the Marine Biological Association of the United Kingdom, vol. 86, no. 3, pp. 551-561.
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The microscale spatial distributions of viruses were investigated in three contrasting environments including oligotrophic open ocean, eutrophic coastal and estuarine habitats. The abundances of two discrete populations of both viruses and heterotrophic bacteria were measured at spatial resolutions of between 1 and 5 cm using purpose-designed microscale sampling equipment and flow cytometric sample analysis. Within open water samples, virus distributions were characterized by non-normal distributions and by `hotspots' in abundance where concentrations varied by up to 17-fold. In contrast to patterns generally observed at larger spatiotemporal scales, there was no correlation between bacterial and viral abundance or correspondence between bacteria and virus hotspots within these samples. Consequently, strong hotspots and gradients in the virus:bacteria ratio (VBR) were also apparent within samples. Within vertical pro¢les taken from above the sediment water interface within a temperate mangrove estuary, distributions of planktonic viruses were characterized by gradients in abundance, with highest concentrations observed within the 1-2 cm immediately above the sediment surface, and virus distributions were correlated to bacterial abundance (P50.01). The patterns observed in these contrasting habitats indicate that microscale patchiness of virus abundance may be a common feature of the marine environment. This form of heterogeneity may have important implications for virus^host dynamics and subsequently in£uence microbial trophodynamics and nutrient cycling in the ocean.

Suggett, DJ, Maberly, SC & Geider, RJ 2006, 'Gross photosynthesis and lake community metabolism during the spring phytoplankton bloom', Limnology And Oceanography, vol. 51, no. 5, pp. 2064-2076.
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Daily productivity determinations of linear photosynthetic electron transfer and of net and gross inorganic CO2 uptake were determined in situ throughout a 6-week sampling period of the spring phytoplankton bloom in Esthwaite Water in the English Lake Di

Suggett, DJ, Moore, CM, Maranon, E, Omachi, C, Varela, RA, Aiken, J & Holligan, PM 2006, 'Photosynthetic electron turnover in the tropical and subtropical Atlantic Ocean', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 53, no. 14-16, pp. 1573-1592.
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Photosynthetic electron transport directly generates the energy required for carbon fixation and thus underlies the aerobic metabolism of aquatic systems. We determined photosynthetic electron turnover rates, ETRs, from ca. 100 FRR fluorescence water-column profiles throughout the subtropical and tropical Atlantic during six Atlantic Meridional Transect cruises (AMT 6, MayJune 1998, to AMT 11, SeptemberOctober 2000). Each FRR fluorescence profile yielded a water-column ETR-light response from which the maximum electron turnover rate (ETRRCIImax), effective absorption (s PSII) and light saturation parameter (E k) specific to the concentration of photosystem II reaction centres (RCIIs) were calculated. ETRRCIImax and E k increased whilst s PSII decreased with mixed-layer depth and the daily integrated photosynthetically active photon flux when all provinces were considered together. These trends suggested that variability in maximum ETR can be partly attributed to changes in effective absorption. Independent bio-optical measurements taken during AMT 11 demonstrated that s PSII variability reflects taxonomic and physiological differences in the phytoplankton communities. ETRRCIImax and Ek, but not sPSII, remained correlated with mixed-layer depth and daily integrated photosynthetically active photon flux when data from each oceanic province were considered separately, indicating a decoupling of electron turnover and carbon fixation rates within each province. Comparison of maximum ETRs with 14C-based measurements of Pmax further suggests that light absorption and C fixation are coupled to differing extents for the various oligotrophic Atlantic provinces. We explore the importance of quantifying RCII concentration for determination of ETRs and interpretation of ETR-C fixation coupling.

Ulstrup, K, Berkelmans, R, Ralph, PJ & van Oppen, MJ 2006, 'Variation in bleaching sensitivity of two coral species across a latitudinal gradient on the Great Barrier Reef: the role of zooxanthellae', Marine Ecology Progress Series, vol. 314, pp. 135-148.
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The ability of corals to cope with environmental change, such as increased temperature, relies on the physiological mechanisms of acclimatisation and long-term genetic adaptation. We experimentally examined the bleaching sensitivity exhibited by 2 species of coral, Pocillopora damicornis and Turbinaria reniformis, at 3 locations across a latitudinal gradient of almost 6 degrees on the Great Barrier Reef (GBR), Target bleaching temperature was reached by using a ramping rate of 0.2 degrees C/h. We found that the bleaching sensitivity and recovery of both species differed between corals with clade D symbionts and those with clade C. However, in F damicornis bleaching susceptibility corresponded more strongly with latitude than with zooxanthella type and hence, temperature history, suggesting that local adaptation has occurred. The observed bleaching sensitivity was shown by a decrease in photochemical efficiency (F-v/F-m) in both species of coral. The rate of recovery in T reniformis was highest in explants containing clade D symbionts. The occurrence of clade D in the northern section of the GBR may reflect a long-term response to high sea water temperatures, while the presence of clade D in low abundance in T reniformis at Heralds Prong Reef and Percy Island may be a result of recent bleaching events.

Ulstrup, K, Ralph, PJ, Larkum, A & Kuhl, M 2006, 'Intra-colonial variability in light acclimation of zooxanthellae in coral tissues of Pocillopora damicornis Received:', Marine Biology, vol. 149, pp. 1325-1335.

Willhelm, S, Carberry, M, Eldridge, M, Poorvin, L, Saxton, M & Doblin, MA 2006, 'Marine and Freshwater Cyanophages in a Laurentian Great Lake: Evidence from Infectivity Assays and Molecular Anayses of g20 genes', Applied and Environmental Microbiology, vol. 72, no. 7, pp. 4957-4963.
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While it is well established that viruses play an important role in the sturcture of marine microbisal food webs, few studies have directly addresed their role in large lake systems. As part of an ongoing study of the microbial acology of Lake Erie, we have examined the distribution and diversity of viruses in this system. One surprising result has bee the pervasive distribution of cyanophages that infect the marine cyanobacterial isolate Synechococcus sp. strain WH7803. Viruses that typically infect this cyanobacterium wre identified throughout the western basin of Lake Erie, as well as in locations within the central and eastern basins. Analyses of the gene encoding the g20 viral capsid assembly protein (a conservative phylogenetic marker for the cyanophage) indicate that these viruses as well as amplicons from natural populations and the ballast of commercial ships are related to marine cyanophages but in some cases form a unique clade, leaving questions concerning the native hosts of these viruses. The results suggest that cyanophages may be as important in freshwater systems as they are known to be in marine systems.

Humphreys, WF, Seymour, JR & Mitchell, JG 2006, 'Stratification of microbial communities in an anchialine sinkhole', Romania.

Salih, A, Wiedenmann, J, Matz, M, Larkum, AW & Cox, G 2006, 'Photoinduced activation of GFP-like proteins in tissues of REEF corals', Progress in Biomedical Optics and Imaging - Proceedings of SPIE.
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A variety of fluorescent and chromophoric proteins homologous to the green fluorescent protein (GFP) has been recently discovered and cloned from non-bioluminescent marine animals, such as corals, and now provide a multitude of colors for use in fluorescence imaging applications. Recently, a novel fluorescence imaging methodology has emerged that utilizes the unique photoactivatory property of several GFP-like proteins, which respond to irradiation by altering their optical properties, thereby providing a new spatio-temporal capability to the GFP-based imaging applications. During our studies of GFP-like proteins from the Great Barrier Reef corals, several novel photoactivatable (PA) GFP-like proteins have been discovered. These include fluorescence photo-amplifiers and reversible photoswitchers, similar to PA jelly-fish derived PA-GFP and Dronpa, that greatly increase their emissions following ultraviolet-A (UVA) irradiation; the red-to-green (R-to-G) converters, similar to DsRed, that rapidly change to green color following single- or 2-photon irradiation; the green-to-red (G-to-R) converters, that acquire bright red fluorescence following UV-violet irradiation, similar to Kaede-like proteins; and the kindling GFP-like proteins, that are non fluorescent, but rapidly acquire bright fluorescence after green light irradiation. We report on the various optical characteristics of these coral PA proteins that may be used to expand the scope of the available fluorescence bio-imaging technologies.

Seymour, JR & Stocker, R 2006, 'The causes and implications of microscale patchiness in the ocean studied using microfluidics.', United States.

Stocker, R, Seymour, JR & Marcos, M 2006, 'Microfluidics for studying microbial ecology', United States.

Sutherland, D & Hawes, I 2006, 'Inland Antarctic aquatic ecosystems – algal communities across environmental gradients', Antarctica New Zealand conference.

Biggs, B, Sutherland, D, Unwin, M & Kilroy, C 2006, Resuming the Mararoa River diversion into the Waiau Arm, Lake Manapouri: recommendations and associated monitoring programmes, Christchurch.

Spigel, B, Sorrell, B & Sutherland, D 2006, Waiau Arm Water Quality Study: September 2004 – May 2005, Christchurch.

Biggs, B, Unwin, M & Sutherland, D 2006, 'Strategy for trialling rediversion of the Mararoga River into Lake Manapouri and associated monitoring programme'.