Assessment of the Water Quality and Ecosystem Health of the Great Barrier Reef (Australia): Conceptual Models

Anonymous (2003) Reef water quality protection plan: for catchments adjacent to the Great Barrier Reef World Heritage Area. Queensland Department of Premier and Cabinet, Brisbane, Australia Anthony KRN (1999) Coral suspension feeding on fine particulate matter. Journal of Experimental Marine Biology and Ecology 232:85–106 Anthony KRN (2000) Enhanced particle-feeding capacity of corals on turbid reefs (Great Barrier Reef, Australia). Coral Reefs 19:59–67 Anthony KRN, Fabricius KE (2000) Shifting roles of heterotrophy and autotrophy in coral energy budgets at varying turbidity. Journal of Experimental Marine Biology and Ecology 252:221–253 Babcock R, Mundy C (1996) Coral recruitment: Consequences of settlement choice for early growth and survivorship in two scleractinians. Journal of Experimental Marine Biology and Ecology 206:179–201 Babcock R, Davies P (1991) Effects of sedimentation on settlement of Acropora millepora. Coral Reefs 9:205–208 Bell AM, Duke NC (2005) Effects of photosystem II inhibiting herbicides on mangroves—preliminary toxicology trials. Marine Pollution Bulletin 51:297–307 Bellwood DR, Hughes TP, Folke C, Nystrom CM (2004) Confronting the coral reef crisis. Nature 429:827–833 Berkelmans R, Oliver J (1999) Large-scale bleaching of corals on the Great Barrier Reef. Coral Reefs 18:55–60 Bewers JM, Blanton JO, Davies AM Gurbutt PA, Hofmann EE, Jamart BM et al. (1992) A conceptual model of contaminant transport in coastal marine ecosystems. Ambio 21:166–169 Birrell CL, McCook LJ, Willis BL (2005) Effects of algal turfs and sediment on coral settlement. Marine Pollution Bulletin 51:408–414 Bjôrk M, Mohammed SM, Bjôrklund M, Semesi A (1995) Coralline algae, important coral-reef builders threatened by pollution. Ambio 24:502–505 Bohl HP, Mitchell DC, Penny RS, Roth CH (2000) Nitrogen losses via subsurface flow from sugar cane on floodplain soils in the Australian wet tropics. Proceedings of the Australian Society of Sugar Cane Technologists 22:302–307 Brodie J, Furnas MJ (1996) Cyclones, river flood plumes and natural water quality extremes in the central Great Barrier Reef. In Hunter HM, Eyles AG Rayment GE (eds) Downstream effects of land use. Queensland Department of Natural Resources, Brisbane, Australia pp 367–374 Brodie J, Christie C, Devlin M, Haynes D, Morris S, Ramsay M et al. (2001a) Catchment management and the Great Barrier Reef. Water Science and Technology 43:203–211 Brodie J, Furnas M, Ghonim S, Haynes D, Mitchell A, Morris S et al. (2001b) Great Barrier Reef Catchment Water Quality Action Plan. Great Barrier Reef Marine Park Authority, Townsville, Queensland, Australia, 116pp Brodie J, Mitchell A (2005) Nutrients in Australian tropical rivers: changes with agricultural development and implications for receiving environments. Marine and Freshwater Research 56(3):279–302 Brodie J, Fabricius K, De’ath G, Okaji K (2005) Are increased nutrient inputs responsible for more outbreaks of crown-of-thorns starfish? An appraisal of the evidence. Marine Pollution Bulletin 51(1–4):266–278 Brodie J, De’ath G, Devlin M, Furnas M, Wright M (2007) Spatial and temporal patterns of near-surface chlorophyll a in the Great Barrier Reef lagoon. Marine and Freshwater Research 58:1–12 Cambell SJ, McKenzie JJ (2004) Flood related loss and recovery of intertidal seagrass meadows in southern Queensland, Australia. Estuarine, Coastal, and Shelf Science 60:477–490 Cloern JE (2001) Our evolving conceptual model of the coastal eutrophication problem. Marine Ecology Progress Series 210:223–253 Cox EF, Ward S (2002) Impact of elevated ammonium on reproduction in two Hawaiian scleractinian corals with different life history patterns. Marine Pollution Bulletin 44:1230–1235 DeVantier LM, De’ath G, Turak E, Done TJ, Fabricius KE (2006) Species richness and community structure of reef-building corals on the nearshore Great Barrier Reef. Coral Reefs 25:329–340 Devlin M, Waterhouse J, Taylor J, Brodie J (2001) Flood plumes in the Great Barrier Reef: spatial and temporal patterns in composition and distribution. GBRMPA Research Publication No 68, Great Barrier Reef Marine Park Authority, Townsville, Queensland, Australia Devlin M, Brodie J, Waterhouse A, Mitchell D, Audas D, Haynes D (2003) Exposure of Great Barrier Reef inner-shelf reefs to river-bourne contaminants. In Proceedings of the 2nd National Conference on Aquatic Environments: sustaining our aquatic environments, implimenting solutions. Queensland Department of Natural Resources and Mines, Brisbane, Australia Devlin M, Brodie J (2005) Terrestrial discharge into the Great Barrier Reef Lagoon: nutrient behaviour in coastal waters. Marine Pollution Bulletin 51:9–22 Dodge RE, Aller RE, Thomson J (1974) Coral growth related to resuspension of bottom sediments. Nature 247:574–576 Downs CA, Woodley CM, Richmond RH, Lanning LL, Owen R (2005) Shifting the paradigm of coral reef health assessment. Marine Pollution Bulletin 51:486–494 Duke NC, Bell AM, Pederson D, Roelfsema CM, Bengston Nash S (2005) Herbicides implicated as the cause of severe mangrove dieback in the Mackay region, NE Australia: consequences for marine plant habitats of the GBR World Heritage Area. Marine Pollution Bulletin 51:308–324 Fabricius KE (2005) Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis. Marine Pollution Bulletin 50:125–146 Fabricius KE, Wolanski E (2000) Rapid smothering of coral reef organisms by muddy marine snow. Estuarine, Coastal, and Shelf Science 50:115–120 Fabricius KE, De’ath G (2004) Identifying ecological change and its causes: A case study on coral reefs. Ecological Applications 14:1448–1465 Fabricius KE, Wild C, Wolanski E, Abele D (2003) Effects of transparent exopolymer particles (TEP) and muddy terrigenous sediments on the survival of hard coral recruits. Estuarine, Coastal and Shelf Science 57:613–621 Fabricius K, De’ath G, McCook L, Turak E, Williams DB (2005) Changes in algal, coral and fish assemblages along water quality gradients on the inshore Great Barrier Reef. Marine Pollution Bulletin 51(1–4):384–398 Faithful J, Finlayson W (2005) Water quality assessment for sustainable agriculture in the Wet Tropics—A community-assisted approach. Marine Pollution Bulletin 51:99–112 Ferrier-Pages C, Gattuso JP, Dallot S, Jaubert J (2000) Effect of nutrient enrichment of growth and photosynthesis of the zooxanthellate coral Stylophora pistillata. Coral Reefs 19:103–113 Ferrier-Pages C, Schoelzke V, Jaubert J, Muscatine L, Hoegh-Guldberg O (2001) Response of a scleractinian coral, Stylophora pistillata, to iron and nitrate enrichment. Journal of Experimental Marine Biology and Ecology 259:249–261 Finlayson CM, Lukacs GP (2003) Status of wetlands in northern Australia. In: Dawson N, Brodie J, (eds.) Proceedings of the 2nd National Conference on Aquatic Environments: Sustaining our aquatic environments—Implementing solutions. Queensland Department of Natural Resources and Mines, Brisbane, Australia Freeny JR, Denmead OT, Wood AW, Saffigna PG (1994) Ammonium loss following urea addition to sugarcane trash blankets. Proceedings of the Sugarcane Technologists 16:114–121 Furnas M (2003) Catchments and corals: terrestrial runoff to the Great Barrier Reef. Australian Institute of Marine Science, Townsville, Queensland, Australia Furnas MJ, Brodie J (1996) Current status of nutrient levels and other water quality parameters in the Great Barrier Reef. In: Hunter H, Eyles AG, Rayment GE, (eds.) Downstream effects of land use. Queensland Department of Natural Resources, Brisbane, Australia pp 9–23 Furnas M, Mitchell A, Skuza M, Brodie J (2005) In the other 90%: phytoplankton responses to enhanced nutrient availability in the Great Barrier Reef lagoon. Marine Pollution Bulletin 51:253–265 Gilbert M, Brodie J (2001) Population and major land use in the Great Barrier Reef Catchment area: spatial and temporal trends. Great Barrier Reef Marine Park Authority, Townsville, Queensland, Australia. pp 72 Gilmour J (1999) Experimental investigation into the effects of suspended sediment on fertilization, larval survival and settlement in a scleractinian coral. Marine Biology 135:451–462 Goreau TJ, MacFarlane AH (1990) Reduced growth rate of Montastrea annularis following the 1987–1988 coral-bleaching event. Coral Reefs 8:211–215 Greiner R, Herr A, Brodie A, Haynes D (2005) A multi-criteria approach to Great Barrier Reef catchment (Queensland, Australia) diffuse source pollution problem. Marine Pollution Bulletin 51:128–137 Gross JE (2003) Developing conceptual models for monitoring programs. Unpublished report. Available at: http://www.science.nature.nps.gov/im/monitor/docs/Conceptual_Modelling.pdf. Accessed: 20th August 2007 Hamilton D, Haydon G (1996) Pesticides and fertilisers in the Queensland sugar industry—Estimates of usage and likely environmental fate. Department of Primary Industries, Brisbane, Australia Harrington L, Fabricius K, Eaglesham G, Negri A (2005) Synergistic effects of diuron and sedimentation on photosynthesis and survival of crustose coralline algae. Marine Pollution Bulletin 51:415–427 Haynes D, Müller J, Carter S (2000a) Pesticide and herbicide residues in sediments and seagrass from the Great Barrier Reef World Heritage Area and Queensland coast. Marine Pollution Bulletin 41:279–287 Haynes D, Ralph P, Prange J, Dennison W (2000b) The impact of the herbicide diuron on photosynthesis in three species of tropical seagrass. Marine Pollution Bulletin 41:288–293 Haynes D, Brodie J, Christie C, Devlin M, Michalek-Wagner K et al. (2001) Great Barrier Reef water quality: current issues. Great Barrier Reef Marine Park Authority, Townsville, Queensland, Australia Haynes D, Carter S, Gaus C, Müller J, Dennison W (2005) Organochlorine and heavy metal concentrations in blubber and liver tissue collected from Queensland (Australia) dugong (Dugong dugon). Marine Pollution Bulletin 51:361–369 Haynes D, Brodie J, Furnas M, Waterhouse J, Hart B (2007) Assessment of the water quality and ecosystem health of the Great Barrier Reef (Australia), Part II: Long-term monitoring design (in review) Heyward A, Negri A (1999) Natural inducers for coral larval metamorphosis. Coral Reefs 18:273–279 Hodgson G (1990) Sediment and the settlement of larvae of the reef coral Pocillopora damicornis. Coral Reefs 9:41–43 Hoegh-Guldberg O (1999) Climate change, coral bleaching and the future of the world’s coral reefs. Marine and Freshwater Research 50:839–866 Hughes TP (1994) Catastrophes, phase shifts, and large-scale degradation of a Carribean coral reef. Science 265:1547–1551 Hughes TP, Baird AH, Bellwood DR, Card M, Connolly SR, Folke C (2003) Climate change, human impacts, and the resilience of coral reefs. Science 301:929–933 Hunte W, Wittenberg M (1992) Effects of eutrophication and sedimentation on juvenile corals. II. Settlement. Marine Biology 114:625–631 Hunter CL, Evans CW (1995) Coral reefs in Kaneohe Bay, Hawaii: two centuries of western influence and two decades of data. Bulletin of Marine Science 57:501–515 Johnson AKL, Ebert SP, Murray AE (1998) Spatial and temporal distribution of wetland and riparian zones and opportunities for their management in catchments adjacent to the Great Barrier Reef Marine Park. In: Haynes D, Kellaway D, Davis K (eds) Protection of wetlands adjacent to the Great Barrier Reef. Great Barrier Reef Marine Park Authority Workshop Series No 24, Great Barrier Reef Marine Park Authority, Townsville, Queensland, Australia pp 82–101 Jones R, Müller J, Haynes D, Schreiber U (2003) The effects of the herbicides diuron and atrazine on corals of the Great Barier Reef. Marine Ecology Progress Series 251:153–167 Jones R, Kerswell A (2003) Phytotoxicity evaluation of photosystem-II (PSII) herbicides in scleractinian coral. Marine Ecology Progress Series 261:149–159 Jones R (2005) The ecotoxicological effects of photosystem II herbicides on corals. Marine Pollution Bulletin 51:495–506 Jorgensen SE (1988) Fundamentals of ecological modelling. Developments in environmental modelling 9. Elsevier Kiene WE, Hutchings PA (1994) Bioerosion experiments at Lizard Island, Great Barrier Reef. Coral Reefs 13:91–98 Kleypus JA (1996) Coral reef development under naturally turbid conditions: fringing reefs near Broadsound, Australia. Coral Reefs 15:153–167 Kleypas JA, Buddemeier RW, Archer D, Gattuso JP, Langdon C, Opdyke BN (1999) Geochemical consequences of increased atmospheric carbon dioxide on coral reefs. Science 284:118–120 Koop K, Booth D, Broadbent A, Brodie J, Bucher D, Capone D et al. (2001) ENCORE: the effect of nutrient enrichment on coral reefs. Synthesis of results and conclusions. Marine Pollution Bulletin 42:91–120 Lambeck A, Woolfe KJ (2000) Composition and textural variability along the 10m isobath, Great Barrier Reef: evidence for pervasive northward sediment transport. Australian Journal of Earth Sciences 47:327–335 Longstaff BJ, Dennison WC (1999) Seagrass survival during pulsed turbidity events: the effects of light deprivation on the seagrasses Halodule pinifolia and Halophila ovalis. Aquatic Botany 65:105–121 Lukacs G (1998) Coastal freshwater wetlands of north Queensland—imperatives for their protection. In Haynes D, Kellaway D, Davis K (eds) Protection of wetlands adjacent to the Great Barrier Reef. Great Barrier Reef Marine Park Authority Workshop Series No 24, Great Barrier Reef Marine Park Authority, Townsville, Queensland, Australia pp 105–113 Lukacs P, Webb T, Valentine P, Marsh H (1997) The outstanding universal value of the Great Barrier Reef World Heritage Area. Great Barrier Reef Marine Park Authority, Townsville, Queensland, Australia Marubini F, Atkinson MJ (1999) Effects of lowered pH and elevated nitrate on coral calcification. Marine Ecology Progress Series 188:117–121 McIvor JG, Williams J, Gardner CJ (1995) Pasture management influences runoff and soil movement in the semi-arid tropics. Australian Journal of Experimental Agriculture 35:55–65 McKergow LA, Prosser IP, Hughes AO, Brodie J (2005) Regional scale nutrient modelling: exports to the Great Barrier Reef World Heritage Area. Marine Pollution Bulletin 51:186–199 McMahon K, Bengtson Nash S, Eaglesham G, Müller J, Duke N, Winderlich S (2005) Herbicide contamination and the potential impacts to seagrass meadows in Hervey Bay, Queensland. Marine Pollution Bulletin 51:325–334 McShane TJ, Reghenzani JR, Proove BG, Moody PW (1993) Nutrient balances and transport from sugarcane land—A preliminary report. In Proceedings of the Australian Sugar Cane Technologists 15th Conference. pp 268–275 Meesters EH, Bak RPM, Westmacott S, Ridgley M, Dollar S (1998) A fuzzy logic model to predict coral reef development under nutrient and sediment stress. Conservation Biology 12:957–965 Mellors J, Waycott M, Marsh H (2005) Variation in biogeochemical parameters across intertidal seagrass meadows in the central Great Barrier Reef region. Marine Pollution Bulletin 51:335–342 Mitchell A, Bramley R, Johnson A (1997) Export of nutrients and suspended sediments during a cyclone-mediated flood event in the Herbert River catchment, Australia. Marine and Freshwater Research 48:79–88 Mitchell C, Brodie J, White I (2005) Sediments, nutrients and pesticide residues in event flow conditions in streams of the Mackay Whitsunday Region, Australia. Marine Pollution Bulletin 51:23–36 Müller J, Duquesne S, Ng J, Shaw G, Krrishnamohan K, Manonmanii K et al. (2000) Pesticides in sediments from Queensland irrigation channels and drains. Marine Pollution Bulletin 41:294–301 Negri A, Vollhardt C, Humphrey C, Heyward A, Jones R, Eaglesham G et al. (2005) Effects of the herbicide diuron on early life stages of coral. Marine Pollution Bulletin 51:370–383 Neil DT, Orpin AR, Ridd PV, Yu B (2002) Sediment yield and impacts from river catchments to the Great Barrier Reef lagoon. Marine and Freshwater Research 53:733–752 Newton J, Mumford T, Dohrmann J, West J, Llanso R, Berry H et al. (1998) A conceptual model for environmental monitoring of a marine system developed for the Puget Sound ambient monitoring program. Puget Sound Research 98:23–33 Orpin AR, Ridd PV, Thomas S, Anthony KRN, Marshall P, Oliver J (2004) Natural turbidity variability and weather forecasts in risk management of anthropogenic sediment discharge near sensitive environments. Marine Pollution Bulletin 49:602–612 Pandolfi JM, Bradbury RH, Sala E, Hughes TP, Bjorndal KA, Cooke RG et al. (2003) Global trajectories of the long-term decline of coral reef ecosystems. Science 301:955–958 Pfitzner J, Brunskill G, Zagorskis I (2004) 137Cs and excess 210Pb deposition patterns in estuarine and marine sediment in the central region of the Great Barrier reef Lagoon, north-eastern Australia. Journal of Environmental Radioactivity 76:81–102 Philipp E, Fabricius KE (2003) Photophysiological stress in scleractinian corals in response to short-term sedimentation. Journal of Experimental Marine Biology and Ecology 287:57–78 Preen AR, Lee Long WJ, Coles RG (1995) Flood and cyclone related loss, and partial recovery, of more than 1000 km2 of seagrass in Hervey Bay, Queensland, Australia. Aquatic Botany 52:3–17 Ralph PJ (2000) Herbicide toxicity of Halophila ovalis assessed by chlorophyll a fluorescence. Aquatic Botany 66:141–152 Rasiah V, Armour JD (2001) Nitrate accumulation under cropping in the Ferrosols of Far North Queensland wet tropics. Australian Journal of Soil Research 39:329–341 Rayment G (2003) Water quality in sugar catchments of Queensland. Water Science and Technology 48:35–47 Reghenzani JR, Armour JD, Prove BG, Moody PW, McShane T (1996) Nitrogen balances for sugarcane plant and first ratoon crops in the wet tropics. In: Wilson JR, Hogarth DM, Campbell JA, Garside AL, (Eds.). Sugarcane research towards efficient and sustainable production. CSIRO Division of Tropical Crops and Pasture, Brisbane. pp 275–277 Riegl B (1995) Effects of sand deposition on sceractinian and alcyonacean corals. Marine Biology 121:517–526 Riegl B, Branch GM (1995) Effects of sediment on the energy budgets of four scleractinian (Bourne 1900) and five alcyonacean (Lamouroux 1816) corals. Journal of Experimental Marine Biology and Ecology 186:259–275 Robson BJ, Webster IT, Rosebrook U (2006) Biogeochemical modelling and nitrogen budgets for the Fitzroy Estuary and Keppel Bay. Technical Report No. 40, Cooperative Research Centre for Coastal Zone, Estuary and Waterway Management, Brisbane, Australia. 53 pp Rodhe K, Masters B, Noble R, Brodie J, Faithful J, Carroll C et al. (2005) Fresh and marine water quality in the Mackay Whitsunday Region, 2004/2005. Mackay Whitsunday Natural Resource Management Group, Mackay, Australia Rogers CS (1990) Responses of coral reefs and reef organisms to sedimentation. Marine Ecology Progress Series 62:185–202 Ruitenbeek J, Ridgley M, Dollar S, Huber R (1999) Optimization of economic policies and investment projects using a fuzzy logic based cost-effectiveness model of coral reef quality: empirical results for Montego Bay, Jamaica. Coral Reefs 18:381–392 Schaffelke B, Mellors J, Duke N (2005) Water quality in the Great Barrier Reef: responses of mangroves, seagrass and macroalgal communities. Marine Pollution Bulletin 51:279–298 Shaw M, Müller J (2005) Preliminary evaluation of the occurrence of herbicides and PAHs in the wet tropics region of the Great Barrier Reef, Australia, using passive samplers. Marine Pollution Bulletin 51:876–881 Stafford-Smith MG (1993) Sediment-rejection efficiency of 22 species of Australian scleractinian corals. Marine Biology 115:229–243 Stambler N, Popper N, Dubinsky Z, Stimson J (1991) Effect of nutrient enrichment and water motion on the coral Pocillopora damicornis. Pacific Science 45:299–307 Stambler N, Cox EF, Vago R (1994) Effects of ammonium enrichment on respiration, zooxanthellar densities and pigment concentrations in two species of Hawaiian corals. Pacific Science 48:284–290 Stimson J, Larned ST, Conklin E (2001) Effects of herbivory, nutrient levels, and introduced algae on the distribution and abundance of the invasive macroalga Dictyosphaeria cavernosa in Kaneohe Bay, Hawaii. Coral Reefs 19:343–357 Telesnicki GJ, Goldberg WM (1995) Effects of turbidity on the photosynthesis and respiration of two South Florida reef coral species. Bulletin of Marine Science 57:527–539 Thomas C, Hart B, Nicholson A, Grace M, Brodie J, Pollino C (2005) Development of criteria for simplifying ecological risk models. In: Zerger A, Argernt RM, (eds.) MODSIM 2005 International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand pp 772–778 Touchette BW, Burkholder JM (2000) Review of nitrogen and phosphorus metabolism in seagrasses. Journal of Marine Biology and Ecology 250:133–167 Udy JW, Dennison WC, Lee Long W, McKenzie LJ (1999) Responses of seagrass to nutrients in the Great Barrier Reef, Australia. Marine Ecological Progress Series 185:257–271 van Woesik R, Tomascik T, Blake S (1999) Coral assemblages and physico-chemical characteristics of the Whitsunday Islands: evidence of recent community changes. Marine and Freshwater Research 50:427–440 Walker D, Dennison W, Edgar G (1999) Status of Australian seagrass research and knowledge. In: Butler A, Jernakoff P (eds.) Seagrass in Australia. Strategic review and development of an R&D plan. CSIRO, Canberra Australia pp 1–24 Ward S, Harrison P (2000) Changes in gametogenesis and fecundity of acroporid corals that were exposed to elevated nitrogen and phosphorus during the ENCORE experiment. Journal Experimental Marine Biology and Ecology 246:179–221 Waycott M, Longstaff B Mellors J (2005) Seagrass population dynamics and water quality in the Great Barrier Reef: a review and future research directions. Marine Pollution Bulletin 51:335–342 Weber M, Lott C, Fabricius K (2006) Sedimentation stress in a scleractinian coral exposed to terrestrial and marine sediments with contrasting physical, organic and geochemical properties. Journal of Experimental Marine Biology and Ecology 336:18–32 Wittenberg M, Hunte W (1992) Effects of eutrophication and sedimentation on juvenile corals: I. Abundance, mortality, and community structure. Marine Biology 112:131–138 Wolanski E, van Senden D (1983) Mixing of Burdekin River floodwaters in the Great Barrier Reef. Australian Journal of Marine and Freshwater Research 34:49–63 Wolanski E, De’ath G (2005) Predicting the impact of present and future human land-use on the Great Barrier Reef. Estuarine, Coastal and Shelf Science 64:504–508 Wolanski E, Richmond RH, McCook L, Sweatman H (2003) Mud, marine snow and coral reefs. American Scientist 91:44–51 Wolanski E, Richmond RH, McCook L (2004) A model of the effects of land-based, human activities on the health of coral reefs in the Great Barrier Reef and in Fouha Bay, Guam, Micronesia. Journal of Marine Systems 46:133–144 Wooldridge S, Brodie J, Furnas M (2006) Exposure of inner-shelf reefs to nutrient enriched runoff entering the Great Barrier Reef Lagoon: Post-European changes and the design of water quality targets. Marine Pollution Bulletin 52:1467–1479