Publications

Raven, JA & Edwards, D 2004, 'Physiological evolution of lower embryophytes: Adaptations to the terrestrial environment' in The Evolution of Plant Physiology, pp. 17-41.
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This chapter examines the differences in physiology among embryophytes and their algal ancestors, with particular emphasis on their water relations. The embryophytes have very significant variations in water relations and the chapter considers their evolution within the embryophytes as well as the evolution of embryophyte water relations from those of their algal ancestors. The chapter also examines the relationship of the likely evolution of embryophyte water relations to cladistic analyses of embryophyte phylogeny and to the fossil record. The physiological changes that occurred in the evolution from algal ancestors to the different grades of organization of embryophytes has been determined from the physiology of extant plants in relation to their phylogeny as determined by cladistic analysis and from the order in which anatomical features appeared in the fossil record. The fossil record of embryophytes also reveals certain characteristics of organisms that are not found today. The fossil record is not helpful in providing some information such as desiccation tolerance or intolerance, except by applying an empirical correlation from extant plants that no embryophyte more than 1 meter in height is desiccation tolerant in the vegetative phase. Overall, lines of evidence indicate that the earliest embryophytes were desiccation tolerant and poikilohydric. © 2004 Elsevier Ltd. All rights reserved.

Andrews, M, Lea, PJ, Raven, JA & Lindsey, K 2004, 'Can genetic manipulation of plant nitrogen assimilation enzymes result in increased crop yield and greater N-use efficiency? An assessment', ANNALS OF APPLIED BIOLOGY, vol. 145, no. 1, pp. 25-40.
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Aridgides, LJ, Doblin, MA, Berke, T, Dobbs, FC, Matson, DO & Drake, L 2004, 'Multiplex PCR allows simultaneous detection of pathogens in ships' ballast water', Marine Pollution Bulletin, vol. 48, no. 11-12, pp. 1096-1101.
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There is enormous potential for global transfer of microorganisms, including pathogens, in ships' ballast water. We contend that a major advancement in the study of ballast-water microorganisms in particular, and of aquatic pathogens in general, will be expedited sample analysis, such as provided by the elegant technology of DNA microarrays. In order to use DNA microarrays, however, one must establish the appropriate conditions to bind target sequences in samples to multiple probes on the microarrays. We conducted proof-of-concept experiments to optimize simultaneous detection of multiple microorganisms using polymerase chain reaction (PCR) and Southern hybridization. We chose three target organisms, all potentially found in ballast water: a calicivirus, the bacterium Vibrio cholerae, and the photosynthetic protist Aureococcus anophagefferens. Here, we show simultaneous detection of multiple pathogens is possible, a result supporting the promising future use of microarrays for simultaneous detection of pathogens in ballast water.

Baines, SB, Fisher, NK, Doblin, MA, Cutter, GA, Cutter, LS & Cole, B 2004, 'Light dependence of selenium uptake by phytoplankton and implications for predicting selenium incorporation into food webs', Limnology and Oceanography, vol. 49, no. 2, pp. 566-578.
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The potentially toxic element selenium is first concentrated from solution to a large but highly variable degree by algae and bacteria before being passed on to consumers. The large loads of abiotic and detrital suspended particles often present in rivers and estuaries may obscure spatial and temporal patterns in Se concentrations at the base of the food web. We used radiotracers to estimate uptake of both selenite (Se(IV)) and C by intact plankton communities at two sites in the Sacramento/San Joaquin River Delta. Our goals were to determine (1) whether C and Se(IV) uptake were coupled, (2) the role of bacteria in Se(IV) uptake, and (3) the Se: C uptake ratio of newly produced organic material. Se(IV) uptake, like C uptake, was strongly related to irradiance. The shapes of both relationships were very similar except that at least 42-56% of Se(IV) uptake occurred in the dark, whereas C uptake in the dark was negligible. Of this dark Se(IV) uptake, 34-67% occurred in the 0.2-1.0-mum size fraction, indicating significant uptake by bacteria. In addition to dark uptake, total Se(IV) uptake consisted of a light-driven component that was in fixed proportion to C uptake. Our estimates of daily areal Se(IV): C uptake ratios agreed very well with particulate Se: C measured at a site dominated by phytoplankton biomass. Estimates of bacterial Se: C were 2.4-13 times higher than for the phytoplankton, suggesting that bacteriovores may be exposed to higher dietary Se concentrations than herbivores.

Beardall, J & Raven, JA 2004, 'The potential effects of global climate change on microalgal photosynthesis, growth and ecology', PHYCOLOGIA, vol. 43, no. 1, pp. 26-40.
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Belli, SI, Mai, K, Skene, C, Gleeson, M, Witcombe, DM, Katrib, M, Finger, A, Wallach, M & Smith, NC 2004, 'Characterisation of the antigenic and immunogenetic properties of bacterially expressed, sexual stage antigens of the coccidian parasite, Eimeria maxima', Vaccine, vol. 22, pp. 4316-4325.
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Benthien, M, Wieland, A, de Oteyza, TG, Grimalt, J & Kuhl, M 2004, 'Oil contamination on a hypersaline microbial mat community (Camargue, France) as studied with microsensors and geochemical analysis', OPHELIA, vol. 58, no. 3, pp. 135-150.
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Budel, B, Weber, B, Kuhl, M, Pfanz, H, Sultemeyer, D & Wessels, D 2004, 'Reshaping of sandstone surfaces by cryptoendolithic cyanobacteria: bioalkalization causes chemical weathering in arid landscapes', Geobiology, vol. 2, pp. 261-268.
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Carfrae, JA, Sheppard, LJ, Raven, JA, Leith, ID, Stein, W, Crossley, A & Theobald, M 2004, 'Early effects of atmospheric ammonia deposition on Calluna vulgaris (L.) hull growing on an ombrotrophic peat bog', Water, Air, and Soil Pollution: Focus, vol. 4, no. 6, pp. 229-239.
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This paper reports data from a field study investigating the impacts of elevated ammonia (NH3) deposition on Calluna vulgaris growing on an ombrotrophic peat bog in S.E. Scotland. Shoot extension, foliar N concentrations, chlorophyll concentration and chlorophyll fluorescence were measured during the second growing season of exposure to a gradient of ammonia concentrations. Results indicate that NH3 increases growth between 150-200 kg N ha-1y-1 cumulative deposition. Foliar N content increased significantly in response to NH3 cumulative deposition up to 400 kg N ha-1 y-1 whereas chlorophyll a content significantly decreased. Measurements of Fv/Fm suggest that although NH3 exposure altered the growth and reduced chlorophyll a, the efficiency of photosystem II was insensitive to NH3-N deposition at this stage. © Kluwer Academic Publishers 2004.

Caumette, P, Cohen, Y, Grimalt, J, Herbert, R & Kuhl, M 2004, 'Special Issue: Role of microbial mats in the bioremediation of oil polluted coastal zones - Preface', OPHELIA, vol. 58, no. 3, pp. 133-134.

Caumette, P, Cohen, Y, Grimalt, J, Herbert, R & Kühl, M 2004, 'Ophelia: Preface', Ophelia, vol. 58, no. 3, pp. 133-134.

Chen, M, Zeng, H, Larkum, AWD & Cai, ZL 2004, 'Raman properties of chlorophyll d, the major pigment of Acaryochloris marina: Studies using both Raman spectroscopy and density functional theory', Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, vol. 60, no. 3, pp. 527-534.
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The Raman spectroscopy of purified chlorophyll (Chl) d extracted from Acaryochloris marina has been measured over the wide region of 250-3200 cm -1 at 77 K following excitation of its Soret band at 488 nm and analyzed with the aid of hybrid density-functional vibrational analyses. A Raman peak specific to Chl d, which arises from the formyl group 31 C = O stretching, was clearly observed at 1659 cm-1 with medium intensity. Peaks due to other C = O stretching vibrations of the 131 keto-, 133 ester- and 173 groups were also observed. Four very strong peaks were observed in the range of 1000-1600 cm-1, assigned to the CC stretching and mixtures of the CH3 bend and CN stretching. CCC and NCC bending contribute to medium intensity peaks at 986 and 915 cm-1. Out-of-plane CH bending at Chl d methine sites 10, 5 and 20 contribute to observed peaks at 885, 864 and 853 cm-1, respectively. A few modes involving the MgN stretching and MgNC bending motions were observed in the very low frequency range. Density functional theory (DFT) calculations have been used to make assignments on the observed Raman spectrum and the DFT results have been found to be in good agreement with the experimental results. © 2003 Elsevier B.V. All rights reserved.

Cockell, CS & Raven, JA 2004, 'Zones of photosynthetic potential on Mars and the early Earth', Icarus, vol. 169, no. 2, pp. 300-310.
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Ultraviolet radiation is more damaging on the surface of Mars than on Earth because of the lack of an ozone shield. We investigated micro-habitats in which UV radiation could be reduced to levels similar to those found on the surface of present-day Earth, but where light in the photosynthetically active region (400-700 nm) would be above the minimum required for photosynthesis. We used a simple radiative transfer model to study four micro-habitats in which such a theoretical Martian Earth-like Photosynthetic Zone (MEPZ) might exist. A favorable radiation environment was found in martian soils containing iron, encrustations of halite, polar snows and crystalline rocks shocked by asteroid or comet impacts, all of which are known habitats for phototrophs on Earth. Although liquid water and nutrients are also required for life, micro-environments with favorable radiation environments for phototrophic life exist in a diversity of materials on Mars. This finding suggests that the lack of an ozone shield is not in itself a limit to the biogeographically widespread colonization of land by photosynthetic organisms, even if there are no other UV-absorbers in the atmosphere apart from carbon dioxide. When applied to the Archean Earth, these data suggest that even with the worst-case assumptions about the UV radiation environment, early land masses could have been colonized by primitive photosynthetic organisms. Such zones could similarly exist on anoxic extra-solar planets lacking ozone shields. © 2004 Elsevier Inc. All rights reserved.

Cooke, RRM, Hurd, CL, Lord, JM, Peake, BM, Raven, JA & Rees, TAV 2004, 'Iron and zinc content of Hormosira banksii in New Zealand', NEW ZEALAND JOURNAL OF MARINE AND FRESHWATER RESEARCH, vol. 38, no. 1, pp. 73-85.
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Cummins, SP, Roberts, DE, Ajani, PA & Underwood, AJ 2004, 'Comparison of assemblages of phytoplankton between open water and seagrass habitats in a shallow coastal lagoon.', Marine and Freshwater Research, vol. 55, no. 5, pp. 447-146.
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Patterns of phytoplankton in areas with seagrass (Zostera capricorni, Halophila ovalis, and Ruppia megacarpa) and areas without seagrass were quantified in an estuary near Sydney, NSW, Australia. Replicate samples (separated by metres) were collected on 20 randomly chosen occasions over almost 3 years, from two sites (separated by tens of metres) nested in both habitats, at four locations (separated by kilometres). Areas with seagrass often supported a significantly different assemblage of phytoplankton compared with areas without seagrass. Dissimilarities were due to small differences in the relative abundance of taxa, particularly the diatom Pseudonitzschia cf. pseudodelicatissima, rather than the presence or absence of specific taxa. In both habitats, abundances of phytoplankton were patchy at all of the spatial scales sampled, although most of the variation was among replicate samples. These findings emphasise the need to incorporate a hierarchy of scales in programs designed to understand processes that cause spatial and temporal patterns of phytoplankton or to detect changes in response to human activities.

Doblin, MA, Popels, LC, Coyne, K, Hutchins, DA, Cary, S & Dobbs, FC 2004, 'Transport of the harmful bloom alga Aureococcus anophagefferens by oceangoing ships and coastal boats', Applied and Environmental Microbiology, vol. 70, no. 11, pp. 6495-6500.
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It is well established that cyst-forming phytoplankton species are transported in ships' ballast tanks. However, there is increasing evidence that other phytoplankton species which do not encyst are also capable of surviving ballast transit. These species have alternative modes of nutrition (hetero- or mixotrophy) and/or are able to survive long-term darkness. In our studies of no-ballast-on-board vessels arriving in the Great Lakes, we tested for the presence of the harmful algal bloom species Aureococcus anophagefferens (brown tide) in residual (i.e., unpumpable) ballast water using methods based on the PCR. During 2001, the brown tide organism was detected in 7 of 18 ballast water tanks in commercial ships following transit from foreign ports. Furthermore, it was detected after 10 days of ballast tank confinement during a vessel transit in the Great Lakes, a significant result given the large disparity between the salinity tolerance for active growth of Aureococcus (>22 ppt) and the low salinity of the residual ballast water (similar to2 ppt). We also investigated the potential for smaller, recreational vessels to transport and distribute Aureococcus. During the summer of 2002, 11 trailered boats from the inland bays of Delaware and coastal bays of Maryland were sampled. Brown tide was detected in the bilge water in the bottoms of eight boats, as well as in one live-well sample. Commercial ships and small recreational boats are therefore implicated as potential vectors for long-distance transport and local-scale dispersal of Aureococcus.

Falkowski, PG, Katz, ME, Knoll, AH, Quigg, A, Raven, JA, Schofield, O & Taylor, FJR 2004, 'The evolution of modern eukaryotic phytoplankton', SCIENCE, vol. 305, no. 5682, pp. 354-360.
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Fourcans, A, de Oteyza, TG, Wieland, A, Sole, A, Diestra, E, van Bleijswijk, J, Grimalt, JO, Kuhl, M, Esteve, I, Muyzer, G, Caumette, P & Duran, R 2004, 'Characterization of functional bacterial groups in a hypersaline microbial mat community (Salins-de-Giraud, Camargue, France)', F E M S Microbiology Ecology, vol. 51, no. 1, pp. 55-70.
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A photosynthetic microbial mat was investigated in a large pond of a Mediterranean saltern (Salins-de-Giraud, Camargue, France) having water salinity from 70 to 150 (w/v). Analysis of characteristic biomarkers (e.g., major microbial fatty acids, hydrocarbons, alcohols and alkenones) revealed that cyanobacteria were the major component of the pond, in addition to diatoms and other algae. Functional bacterial groups involved in the sulfur cycle could be correlated to these biomarkers, i.e. sulfate-reducing, sulfur-oxidizing and anoxygenic phototrophic bacteria. In the first 0.5 mm of the mat, a high rate of photosynthesis showed the activity of oxygenic phototrophs in the surface layer. Ten different cyanobacterial populations were detected with confocal laser scanning microscopy: six filamentous species, with Microcoleus chthonoplastes and Halomicronema excentricum as dominant (73% of total counts); and four unicellular types affiliated to Microcystis, Chroococcus, Gloeocapsa, and Synechocystis (27% of total counts). Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments confirmed the presence of Microcoleus, Oscillatoria, and Leptolyngbya strains (Halomicronema was not detected here) and revealed additional presence of Phormidium, Pleurocapsa and Calotrix types. Spectral scalar irradiance measurements did not reveal a particular zonation of cyanobacteria, purple or green bacteria in the first millimeter of the mat. Terminal-restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA gene fragments of bacteria depicted the community composition and a fine-scale depth-distribution of at least five different populations of anoxygenic phototrophs and at least three types of sulfate-reducing bacteria along the microgradients of oxygen and light inside the microbial mat.

Grunwald, B & Kuhl, M 2004, 'A system for imaging variable chlorophyll fluorescence of aquatic phototrophs', Ophelia, vol. 58, no. 2, pp. 79-89.

Hill, R, Larkum, A, Frankart, C, Kuehl, M & Ralph, PJ 2004, 'Loss of functional Photosystem II reaction centres in zooxanthellae of corals exposed to bleaching conditions: using fluorescence rise kinetics', Photosynthesis Research, vol. 82, pp. 59-72.
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Hill, R, Schreiber, U, Gademann, R, Larkum, A, Kuehl, M & Ralph, PJ 2004, 'Spatial heterogeneity of photosynthesis and the effect of temperature-induced bleaching condition in three species of corals', Marine Biology, vol. 144, pp. 633-640.
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Huang, EP, Marquis, CP & Gray, PP 2004, 'Process development for a recombinant Chinese hamster ovary (CHO) cell line utilizing a metal induced and amplified metallothionein expression system', Biotechnology and Bioengineering, vol. 88, no. 4, pp. 437-450.
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Jermiin, LS, Ho, SYW, Ababneh, F, Robinson, J & Larkum, AWD 2004, 'The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated', Systematic Biology, vol. 53, no. 4, pp. 638-643.
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Jorgensen, MF, Murray, S & Daugbjerg, N 2004, 'Amphidinium revisited. I. Redefinition of Amphidinium (Dinophyceae) based on cladistic and molecular phylogenetic analyses (vol 40, pg 351, 2004)', JOURNAL OF PHYCOLOGY, vol. 40, no. 6, pp. 1181-1181.
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Jorgensen, MF, Murray, SA & Daugbjerg, N 2004, 'A new genus of athecate interstitial dinoflagellates, Togula gen. nov., previously encompassed within Amphidinium sensu lato: Inferred from light and electron microscopy and phylogenetic analyses of partial large subunit ribosomal DNA sequences', Phycological Research, vol. 52, no. 3, pp. 284-299.

Jorgensen, MF, Murray, SA & Daugbjerg, N 2004, 'Amphidinium revisited. I. Redefinition of Amphidinium (Dinophyceae) based on cladistic and molecular phylogenetic analyses', Journal of Phycology, vol. 40, pp. 351-365.
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Lenzen, M, Dey, CJ & Murray, SA 2004, 'Historical accountability and cumulative impacts: the treatment of time in corporate sustainability reporting', Ecological Economics, vol. 51, no. 3-4, pp. 237-250.
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Macinnis-Ng, CM & Ralph, PJ 2004, 'In situ impact of multiple pulses of metal and herbicide on the seagrass| Zostera capricorni', Aquatic Toxicology, vol. 67, pp. 227-237.
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Macintyre, H, Lomas, M, Cornwell, J, Suggett, DJ, Gobler, C, Koch, E & Kana, T 2004, 'Mediation Of Benthic-pelagic Coupling By Microphytobenthos: An Energy- And Material-based Model For Initiation Of Blooms Of Aureococcus Anophagefferens', Harmful Algae, vol. 3, no. 4, pp. 403-437.
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We present a conceptual model for initiation of blooms of the estuarine brown-tide pelagophyte Aureococcus anophagefferens. The model is based on the observation that in addition to its well-documented stimulation by organic nutrients, Aureococcus is pie

Murray, SA & Patterson, DJ 2004, 'Cabra matta, gen. nov., sp. nov., a new benthic, heterotrophic dinoflagellate', European Journal of Phycology, vol. 39, pp. 229-234.
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Murray, SA, Jorgensen, MF, Daugbjerg, N & Rhodes, L 2004, 'Amphidinium revisited. II. Resolving species boundaries in the Amphidinium operculatum species complex (Dinophyceae), including the descriptions of Amphidinium trulla sp. nov. and Amphidinium gibbosum comb. nov.', Journal of Phycology, vol. 40, pp. 366-382.
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Ostrowski, M, Fegatella, F, Wasinger, V, Guilhaus, M, Corthals, GL & Cavicchioli, R 2004, 'Cross-species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, Sphingopyxis alaskensis', PROTEOMICS, vol. 4, no. 6, pp. 1779-1788.
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Raven, JA 2004, 'Building botany in Cambridge', NEW PHYTOLOGIST, vol. 162, no. 1, pp. 7-8.
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Raven, JA & Waite, AM 2004, 'The evolution of silicification in diatoms: inescapable sinking and sinking as escape?', NEW PHYTOLOGIST, vol. 162, no. 1, pp. 45-61.
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Raven, JA, Handley, LL & Andrews, M 2004, 'Global aspects of C/N interactions determining plant-environment interactions', JOURNAL OF EXPERIMENTAL BOTANY, vol. 55, no. 394, pp. 11-25.
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Runcie, J, Larkum, A & Ritchie, RJ 2004, 'Uptake kinetics and assimilation of phosphorus by Catenella nipae and Ulva lactuca can be used to indicate ambient phosphate availability', Journal of Applied Phycology, vol. 16, no. 3, pp. 181-194.
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Uptake, assimilation and compartmentation of phosphate were studied in the opportunist green macroalgaUlva lactucaand the estuarine red algal epiphyteCatenella nipae. The MichaelisMenten model was used to describe uptake rates of inorganic phosphate (Pi) at different concentrations. Maximum uptake rates (V max) of P-starved material exceededV maxof P-enriched material; this difference was greater forC. nipae. Uptake and allocation of phosphorus (P) to internal pools was measured using trichloroacetic acid (TCA) extracts and32P. Both species demonstrated similar assimilation paths: when P-enriched, most32P accumulated as free phosphate. When unenriched,32P was rapidly assimilated into the TCA-insoluble pool.C. nipaeconsistently assimilated more32P into this pool thanU. lactuca, indicatingC. nipaehas a greater P-storage capacity. In both species,32P release data showed two internal compartments with very different biological half-lives.

Ryan, KG, Ralph, PJ & McMinn, A 2004, 'Acclimation of Antarctic bottom-ice algal communities to lowered salinities during melting', Polar Biology, vol. 27, pp. 679-686.
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Seymour, JR, Mitchell, JG & Seuront, L 2004, 'Microscale heterogeneity in the activity of coastal bacterioplankton communities', Aquatic Microbial Ecology, vol. 35, no. 1, pp. 1-16.
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Microscale sampling techniques and flow cytometry were employed to measure the distribution patterns of 8 subpopulations of bacteria separated according to variations in cell fluorescence and light scatter properties. Subpopulations of bacteria defined on the basis of these parameters have recently been shown to represent cells exhibiting dissimilar activity levels, and we therefore assume that the subpopulations of bacteria identified here represent metabolically diverse groups. Microscale distribution patterns of these subpopulations were measured at a resolution of 4.5 and 12 mm, within 2 dissimilar coastal habitats, A mean 2-fold change in the abundance of the total bacterial community across sample sets was observed. However, levels of spatial heterogeneity were consistently higher for the cytometrically defined subpopulations than total counts. In most samples, the population of bacteria exhibiting the highest levels of green fluorescence, or DNA content, and hence assumed to represent the most active bacteria in the community, also showed the highest levels of microscale spatial variability, with a maximum change in abundance of 14.5-fold observed across a distance of 9 nun. Where Zipf rank-size analysis was conducted, the microscale distributions of subpopulations differed significantly (p < 0.05) in 79% of cases, implying that bacterial communities are made up of physiologically distinct compartments, perhaps influenced by different microscale features of the environment. We suggest that these results provide the first evidence for the existence of microscale heterogeneity in the metabolic activity of aquatic bacterial communities.

Siboni, N, Fine, M, Bresler, V & Loya, Y 2004, 'Coastal coal pollution increases Cd concentrations in the predatory gastropod Hexaplex trunculus and is detrimental to its health', Marine Pollution Bulletin, vol. 49, no. 1-2, pp. 111-118.
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Parameters of environmental health, including paracellular permeability of external epithelia, functional state of lysosomes and the level of metallothioneins (MTs), were examined using fluorescent markers and vital microfluorometry in different tissues of the marine gastropod, Hexaplex trunculus, from a coal-polluted and coal-free site. Vital microfluorometrical examinations exhibited enhanced paracellular permeability of external epithelia to the anionic marker, fluorescein (FLU), lower lysosomal accumulation of neutral red (NR) as well as higher levels of MTs, when compared with epithelia of gastropods from the coal-free site. Those differences were particularly marked in the foot epithelium, which is in direct contact with the substrate. In addition, cadmium was measured by ICP-AES in the hepatopancreas of gastropods sampled from the coal-polluted site and two coal-free sites. Significantly higher levels of Cd were found in gastropod hepatopancreas from the coal-polluted site. In addition, two months feeding experiments conducted in aquaria containing: (a) coal pieces covered by barnacles; (b) natural rocks covered by barnacles; and (c) natural rocks with barnacles+bare coal pieces, demonstrated significant increase of Cd concentration in the hepatopancreas of the gastropods exposed to coal. We suggest that coal in the marine environment has detrimental effects on marine gastropods, both directly through contact with the organisms and indirectly through the food web. © 2004 Elsevier Ltd. All rights reserved.

Stewart, AR, Luoma, SN, Schlekat, CE, Doblin, MA & Hieb, KA 2004, 'Food web pathway determines how selenium affects aquatic ecosystems: A San Francisco Bay case study', Environmental Science & Technology, vol. 38, no. 17, pp. 4519-4526.
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Chemical contaminants disrupt ecosystems, but specific effects may be under-appreciated when poorly known processes such as uptake mechanisms, uptake via diet, food preferences, and food web dynamics are influential. Here we show that a combination of food web structure and the physiology of trace element accumulation explain why some species in San Francisco Bay are threatened by a relatively low level of selenium contamination and some are not. Bivalves and crustacean zooplankton form the base of two dominant food webs in estuaries, The dominant bivalve Potamocorbula amurensis has a 10-fold slower rate constant of loss for selenium than do common crustaceans such as copepods and the mysid Neomysis mercedis (rate constant of loss, k(e) = 0.025, 0.155, and 0.25 d(-1), respectively). The result is much higher selenium concentrations in the bivalve than in the crustaceans. Stable isotope analyses show that this difference is propagated up the respective food webs in San Francisco Bay. Several predators of bivalves have tissue concentrations of selenium that exceed thresholds thought to be associated with teratogenesis or reproductive failure (liver Se > 15 mug g(-1) dry weight). Deformities typical of selenium-induced teratogenesis were observed in one of these species. Concentrations of selenium in tissues of predators of zooplankton are less than the thresholds. Basic physiological and ecological processes can drive wide differences in exposure and effects among species, but such processes are rarely considered in traditional evaluations of contaminant impacts.

Suggett, DJ, MacIntyre, HL & Geider, RJ 2004, 'Evaluation of biophysical and optical determinations of light absorption by photosystem II in phytoplankton', Limnology And Oceanography-methods, vol. 2, pp. 316-332.
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Fast repetition rate (FRR) fluorescence can provide highly resolved estimates of light absorption by photosystem II ( PSII), a variable that is critical to bio-optical determinations of phytoplankton productivity. We compared estimates of chlorophyll a -

Thar, R & Kuhl, M 2004, 'Propagation of electromagnetic radiation in mitochondria?', Journal of Theoretical Biology, vol. 230, pp. 261-270.
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Witcombe, DM, Ferguson, DJ, Belli, SI, Wallach, M & Smith, NC 2004, 'Eimeria maxima TRAP family protein EmTFP250: subcellular localisation and induction of immune responses by immunisation with a recombinant C-terminal derivative', International Journal for Parasitology, vol. 34, pp. 861-872.
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Belli, SI, Ferguson, DJ, Luxford, C, Davies, MJ, Wallach, M, Finger, A & Smith, NC 2004, 'The molecular basis of the poultry coccidiosis vaccine, Coxabic', Proceedings of the 53rd Western Poultry Disease Conference, Proceedings of the 53rd Western Poultry Disease Conference, pp. 68-70.

Raven, JA 2003, 'Symbiosis, size and celerity', SYMBIOSIS, 4th International Symbiosis Congress, SPRINGER, Halifax, CANADA, pp. 281-291.

Salih, A, Larkum, A, Cronin, T, Wiedenmann, J, Szymczak, R & Cox, G 2004, 'Biological properties of coral GFP-type proteins provide clues for engineering novel optical probes and biosensors', Proceedings of SPIE - The International Society for Optical Engineering, pp. 61-72.
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In recent years, a variety of Green Fluorescent Protein (GFP)-like pigments have been discovered from corals and other marine organisms. They are widely used to expand the range of available GFP-type proteins in imaging applications, such as in vivo markers for gene expression and protein localization studies, FRET-based (Förster resonance energy transfer) multicolor imaging and biosensors. They have known diverse optical and biochemical properties but their in vivo spectral properties and biological function in marine organisms is only beginning to be understood We have investigated their spectral diversity, optical properties and cellular microstructure in corals of the Great Barrier Reef with the aim of elucidating their photo-biological function/s as well as to identify novel proteins suitable for GFP-based technologies. We found numerous spectral variants, with emissions covering almost the full range of the visible spectrum. Many of these GFP-like proteins, especially in corals from the more extreme habitats, such as sun-exposed shallows or in deep water, showed a range of light-related spectral characteristics: high photostability, spectral tuning for energy transfer and dynamic photo-induced transformation properties. Intra-cellularly they were organized into spectral donor-acceptor pairs or even arrays, tuned for FRET. Coral color proteins thus offer an exciting potential to expand the use of the available GFPs in bio-imaging applications and as a basis for improved protein engineering.

Seuront, L, Leterme, S, Seymour, JR & Mitchell, JG 2004, 'Sampling the sampling unit: A world in a bottle.', United States.

Seymour, JR & Mitchell, JG 2004, 'Microscale distributions of bacterioplankton and virus-like particles assessed using flow cytometry', United States.