Alvarez-Filip, L, Gill, JA, Dulvy, N.K., Perry, A.L., Watkinson, A.R. and Côté, I.M. (2011) Drivers of region-wide declines in architectural complexity on Caribbean reefs. Coral Reefs 30, 1051–1060.
Anderson, M., Gorley, R. and Clarke, K. (2008) PERMANOVA for PRIMER: guide to software and statistical methods. Plymouth: PRIMER-E.
Bannister, R., Battershill, C. and de Nys, R. (2012) Suspended sediment grain size and mineralogy across the continental shelf of the Great Barrier Reef: impacts on the physiology of a coral reef sponge. Continental Shelf Research 32, 86–95.
Bautista-Guerrero, E., Carballo, J.L., Aguilar-Camacho, J.M. and Sifuentes-Romero, I. (2016) Molecular and morphological differentiation of sympatric larvae of coral excavating sponges of genus Thoosa. Zoomorphology 135, 159–165.
Bautista-Guerrero, E., Carballo, J.L. and Maldonado, M. (2010) Reproductive cycle of the coral-excavating sponge Thoosa mismalolli (Clionaidae) from Mexican Pacific coral reefs. Invertebrate Biology 129, 285–296.
Bell, J.J., Davy, S.K., Jones, T., Taylor, M.W. and Webster, N.S. (2013) Could some coral reefs become sponge reefs as our climate changes? Global Change Biology 19, 2613–2624.
Bell, J.J., McGrath, E., Biggerstaff, A., Bates, T., Bennett, H., Marlow, J. and Shaffer, M. (2015) Sediment impacts on marine sponges. Marine Pollution Bulletin 94, 5–13.
Bell, J.J. and Smith, D. (2004) Ecology of sponge assemblages (Porifera) in the Wakatobi region, south-east Sulawesi, Indonesia: richness and abundance. Journal of the Marine Biological Association of the United Kingdom 84, 581–591.
Bell, J.J. and Turner, J.R. (2000) Factors influencing the density and morphometrics of the cup coral Caryophyllia smithii in Lough Hyne. Journal of the Marine Biological Association of the United Kingdom 80, 437–441.
Bergman, K.M. (1983) Distribution and ecological significance of the boring sponge Cliona viridis on the Great Barrier Reef, Australia. MSc thesis. McMaster University, Hamilton, Ontario, Canada.
Biggerstaff, A., Smith, D.J., Jompa, J. and Bell, J.J. (2015) Photoacclimation supports environmental tolerance of a sponge to turbid low-light conditions. Coral Reefs 34, 1049–1061.
Biggerstaff, A., Smith, D.J., Jompa, J. and Bell, J.J. (2017) Metabolic responses of a phototrophic sponge to sedimentation supports transitions to sponge-dominated reefs. Scientific Reports 7, 2725.
Bruno, J.F. and Selig, E.R. (2007) Regional decline of coral cover in the Indo-Pacific: timing, extent, and subregional comparisons. PLoS ONE 2, e711.
Bruno, J.F., Sweatman, H., Precht, W.F., Selig, E.R. and Schutte, V.G. (2009) Assessing evidence of phase shifts from coral to macroalgal dominance on coral reefs. Ecology 90, 1478–1484.
Burke, L.M., Reytar, K., Spalding, M. and Perry, A. (2011) Reefs at risk revisited. Washington, DC: World Resources Institute.
Burnham, K.P. and Anderson, D.R. (2004) Multimodel inference: understanding AIC and BIC in model selection. Sociological Methods and Research 33, 261–304.
Büttner, E. and Siebler, F. (2013) The impact of simulated dredging on sponges from the East Australian coastal line. Habilitation thesis. University of Stuttgart, Germany.
Calcinai, B., Azzini, F., Bavestrello, G., Cerrano, C., Pansini, M. and Thung, D.C. (2006) Boring sponges from the Ha Long Bay, Tonkin Gulf, Vietnam. Zoological Studies 45, 201–212.
Calcinai, B., Bavestrello, G. and Cerrano, C. (2005) Excavating sponge species from the Indo-Pacific Ocean. Zoological Studies 44, 5–18.
Calcinai, B., Bavestrello, G., Cerrano, C. and Gaggero, L. (2008) Substratum microtexture affects the boring pattern of Cliona albimarginata (Clionaidae, Demospongiae). In Wisshak, M. and Tapanila, L. (eds) Current developments in bioerosion. Berlin: Springer, pp. 203–211.
Callahan, M.K. (2005) Distribution of clionid sponges in the Florida Keys National Marine Sanctuary (FKNMS), 2001–2003. MSc thesis. University of South Florida, Tampa, USA.
Carballo, J.L., Bautista-Guerrero, E. and Leyte-Morales, G.E. (2008) Boring sponges and the modelling of coral reefs in the east Pacific Ocean. Marine Ecology Progress Series 356, 113–122.
Carballo, J.L., Bautista, E., Nava, H., Cruz-Barraza, J.A. and Chávez, J.A. (2013) Boring sponges, an increasing threat for coral reefs affected by bleaching events. Ecology and Evolution 3, 872–886.
Carballo, J.L., Sanchez-Moyano, J.E. and García-Gómez, J.C. (1994) Taxonomic and ecological remarks on boring sponges (Clionidae) from the straits of Gibraltar (southern Spain): tentative bioindicators? Zoological Journal of the Linnean Society 112, 407–424.
Chaves-Fonnegra, A., Feldheim, K.A., Secord, J. and Lopez, J.V. (2015) Population structure and dispersal of the coral-excavating sponge Cliona delitrix. Molecular Ecology 24, 1447–1466.
Chaves-Fonnegra, A. and Zea, S. (2007) Observations on reef coral undermining by the Caribbean excavating sponge Cliona delitrix (Demospongiae, Hadromerida). In Custódio, M.R., Lôbo-Hajdu, G., Hajdu, E. and Muricy, G. (eds) Porifera research. Biodiversity, innovation and sustainability. Rio de Janeiro: National Museum, pp. 247–254.
Chaves-Fonnegra, A., Zea, S. and Gómez, M.L. (2007) Abundance of the excavating sponge Cliona delitrix in relation to sewage discharge at San Andrés Island, SW Caribbean, Colombia. Boletín de Investigaciones Marinas y Costeras 36, 63–78.
Cheal, A., MacNeil, M.A., Cripps, E., Emslie, M., Jonker, M., Schaffelke, B. and Sweatman, H. (2010) Coral-macroalgal phase shifts or reef resilience: links with diversity and functional roles of herbivorous fishes on the Great Barrier Reef. Coral Reefs 29, 1005–1015.
Clarke, K.R. and Gorley, R.N. (2006) PRIMER v6: user manual/tutorial. Plymouth: PRIMER-E.
Clarke, K.R., Somerfield, P.J. and Chapman, M.G. (2006) On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray–Curtis coefficient for denuded assemblages. Journal of Experimental Marine Biology and Ecology 330, 55–80.
Cooper, T.F., Ridd, P.V., Ulstrup, K.E., Humphrey, C., Slivkoff, M. and Fabricius, K.E. (2008) Temporal dynamics in coral bioindicators for water quality on coastal coral reefs of the Great Barrier Reef. Marine and Freshwater Research 59, 703–716.
Crabbe, J.M. and Smith, D.J. (2002) Comparison of two reef sites in the Wakatobi Marine National Park (SE Sulawesi, Indonesia) using digital image analysis. Coral Reefs 21, 242–244.
Crabbe, J.M. and Smith, D.J. (2005) Sediment impacts on growth rates of Acropora and Porites corals from fringing reefs of Sulawesi, Indonesia. Coral Reefs 24, 437–441.
Cullen, L.C., Pretty, J., Smith, D. and Pilgrim, S.E. (2007) Links between local ecological knowledge and wealth in indigenous communities of Indonesia: implications for conservation of marine resources. International Journal of Interdisciplinary Social Sciences 2, 289–299.
De'ath, G. and Fabricius, K.E. (2010) Water quality as a regional driver of coral biodiversity and macroalgae on the Great Barrier Reef. Ecological Applications 20, 840–850.
De'ath, G., Fabricius, K.E., Sweatman, H. and Puotinen, M. (2012) The 27-year decline of coral cover on the Great Barrier Reef and its causes. Proceedings of the National Academy of Sciences USA 109, 17995–17999.
Devlin, M.J., Da Silva, E.T., Petus, C., Wenger, A., Zeh, D., Tracey, D., Álvarez-Romero, J.G. and Brodie, J. (2013) Combining in-situ water quality and remotely sensed data across spatial and temporal scales to measure variability in wet season chlorophyll-a: Great Barrier Reef lagoon (Queensland, Australia). Ecological Processes 2, 31.
Doty, M.S. (1971) Measurement of water movement in reference to benthic algal growth. Botanica Marina 14, 32–35.
Edinger, E.N., Limmon, G.V., Jompa, J., Widjatmoko, W., Heikoop, J.M. and Risk, M.J. (1998) Reef degradation and coral biodiversity in Indonesia: effects of land-based pollution, destructive fishing practices and changes over time. Marine Pollution Bulletin 36, 617–630.
Edinger, E.N., Limmon, G.V., Jompa, J., Widjatmoko, W., Heikoop, J.M. and Risk, M.J. (2000) Normal coral growth rates on dying reefs: are coral growth rates good indicators of reef health? Marine Pollution Bulletin 40, 404–425.
Edinger, E.N. and Risk, M.J. (2013) Effect of land-based pollution on central Java coral reefs. Journal of Coastal Development 3, 593–613.
English, S.S., Wilkinson, C.C. and Baker, V.V. (1994) Survey manual for tropical marine resources. Line intercept transect. Townsville: Australian Institute of Marine Science, pp. 34–51.
Enochs, I.C. and Manzello, D.P. (2012) Species richness of motile cryptofauna across a gradient of reef framework erosion. Coral Reefs 31, 653–661.
Erftemeijer, P.L., Riegl, B., Hoeksema, B.W. and Todd, P.A. (2012) Environmental impacts of dredging and other sediment disturbances on corals: a review. Marine Pollution Bulletin 64, 1737–1765.
Fabricius, K.E. (2005) Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis. Marine Pollution Bulletin 50, 125–146.
Fabricius, K.E. (2011) Factors determining the resilience of coral reefs to eutrophication: a review and conceptual model. In Dubinsky, Z. and Stambler, N. (eds) Coral reefs: an ecosystem in transition. Dordrecht: Springer, pp. 493–505.
Fang, J.K.H., Schönberg, C.H.L., Hoegh-Guldberg, O. and Dove, S. (2017) Symbiotic plasticity of Symbiodinium in a common excavating sponge. Marine Biology 164, 104.
Fang, J.K.H., Schönberg, C.H.L., Mello-Athayde, M.A., Hoegh-Guldberg, O. and Dove, S. (2014) Effects of ocean warming and acidification on the energy budget of an excavating sponge. Global Change Biology 20, 1043–1054.
Glynn, P.W. (1997) Bioerosion and coral-reef growth: a dynamic balance. In Birkeland, C. (ed.) Life and death of coral reefs. New York, NY: Springer, pp. 68–95.
Golbuu, Y., Van Woesik, R., Richmond, R.H., Harrison, P. and Fabricius, K.E. (2011) River discharge reduces reef coral diversity in Palau. Marine Pollution Bulletin 62, 824–831.
González-Rivero, M., Yakob, L. and Mumby, P.J. (2011) The role of sponge competition on coral reef alternative steady states. Ecological Modelling 222, 1847–1853.
Graham, N.A. and Nash, K.L. (2012) The importance of structural complexity in coral reef ecosystems. Coral Reefs 32, 315–326.
Hennige, S.J., Smith, D.J., Perkins, R., Consalvey, M., Paterson, D.M. and Suggett, D.J. (2008) Photoacclimation, growth and distribution of massive coral species in clear and turbid waters. Marine Ecology Progress Series 369, 77–88.
Hennige, S.J., Smith, D.J., Walsh, S.J., McGinley, M.P., Warner, M. E. and Suggett, D.J. (2010) Acclimation and adaptation of scleractinian coral communities along environmental gradients within an Indonesian reef system. Journal of Experimental Marine Biology and Ecology 391, 143–152.
Holmes, K.E., Edinger, E.N., Limmon, G.V. and Risk, M.J. (2000) Bioerosion of live massive corals and branching coral rubble on Indonesian coral reefs. Marine Pollution Bulletin 40, 606–617.
Holmes, G., Ortiz, J.C. and Schönberg, C.H.L. (2009) Bioerosion rates of the sponge Cliona orientalis Thiele, 1900: spatial variation over short distances. Facies 55, 203–311.
Hughes, T., Szmant, A.M., Steneck, R., Carpenter, R. and Miller, S. (1999) Algal blooms on coral reefs: what are the causes? Limnology and Oceanography 44, 1583–1586.
Jokiel, P.L. and Morrissey, J.I. (1993) Water motion on coral reefs – evaluation of the clod card technique. Marine Ecology Progress Series 93, 175–181.
Kennedy, E.V., Perry, C.T., Halloran, P.R., Fine, M., Carricart-Ganivet, J.P., Iglesias-Prieto, R., Form, A., Wisshak, M., Schönberg, C.H.L. and Mumby, P.J. (2013) Avoiding coral structural collapse requires local and global action. Current Biology 23, 912–918.
Lapointe, B.E., Barile, P.J. and Matzie, W.R. (2004) Anthropogenic nutrient enrichment of seagrass and coral reef communities in the Lower Florida Keys: discrimination of local versus regional nitrogen sources. Journal of Experimental Marine Biology and Ecology 308, 23–58.
Lindgren, N.G. (1897) Beitrag zur Kenntniss der Spongienfauna des Malaiischen Archipels und der Chinesischen Meere. Zoologischer Anzeiger 547, 480–487.
López-Victoria, M. and Zea, S. (2004) Storm-mediated coral colonization by an excavating Caribbean sponge. Climate Research 26, 251–256.
López-Victoria, M. and Zea, S. (2005) Current trends of space occupation by encrusting excavating sponges on Colombian coral reefs. Marine Ecology 26, 33–41.
Mallela, J. and Perry, C. (2007) Calcium carbonate budgets for two coral reefs affected by different terrestrial runoff regimes, Rio Bueno, Jamaica. Coral Reefs 26, 129–145.
Mariani, S., Uriz, M.J. and Turon, X. (2000) Larval bloom of the oviparous sponge Cliona viridis: coupling of larval abundance and adult distribution. Marine Biology 137, 783–790.
Marlow, J., Smith, D., Werorilang, S. and Bell, J. (in press) Sedimentation limits the erosion rate of a bioeroding sponge. Marine Ecology e12483 doi: 10.1111/maec.12483.
McManus, J.W. and Polsenberg, J.F. (2004) Coral-algal phase shifts on coral reefs: ecological and environmental aspects. Progress in Oceanography 60, 263–279.
McMellor, S. and Smith, D.J. (2010) Coral reefs of the Wakatobi: abundance and biodiversity. In Clifton, J., Unsworth, R.K.F. and Smith, D.J. (eds) Marine research and conservation in the Coral Triangle: the Wakatobi National Park. New York, NY: Nova Publishers, pp. 11–26.
Mueller, B., de Goeij, J.M., Vermeij, M.J., Mulders, Y., van der Ent, E., Ribes, M. and van Duyl, F.C. (2014) Natural diet of coral-excavating sponges consists mainly of dissolved organic carbon (DOC). PLoS ONE 9, e90152.
Mumby, P.J. (2009) Phase shifts and the stability of macroalgal communities on Caribbean coral reefs. Coral Reefs 28, 761–773.
Muricy, G. (1991) Structure des peuplements de spongiaires autour de l'égout de Cortiou (Marseille, France). Vie et Milieu 41, 205–221.
Nava, H. and Carballo, J.L. (2008) Chemical and mechanical bioerosion of boring sponges from Mexican Pacific coral reefs. Journal of Experimental Biology 211, 2827–2831.
Nava, H. and Carballo, J.L. (2013) Environmental factors shaping boring sponge assemblages at Mexican Pacific coral reefs. Marine Ecology 34, 269–279.
Nava, H., Ramírez-Herrera, M.T., Figueroa-Camacho, A.G. and Villegas-Sanchez, B.M. (2014) Habitat characteristics and environmental factors related to boring sponge assemblages on coral reefs near populated coastal areas on the Mexican eastern Pacific coast. Marine Biodiversity 44, 45–54.
Norström, A.V., Nyström, M., Lokrantz, J. and Folke, C. (2009) Alternative states on coral reefs: beyond coral-macroalgal phase shifts. Marine Ecology Progress Series 376, 295–306.
Ogston, A.S., Storlazzi, C.D., Field, M.E. and Presto, M.K. (2004) Sediment resuspension and transport patterns on a fringing reef flat, Molokai, Hawaii. Coral Reefs 23, 559–569.
Pang, R.K. (1973) The ecology of some Jamaican excavating sponges. Bulletin of Marine Science 23, 227–243.
Perry, C.T., Spencer, T. and Kench, P. (2008) Carbonate budgets and reef production states: a geomorphic perspective on the ecological phase-shift concept. Coral Reefs 27, 853–866.
Pineda, M.C., Strehlow, B., Duckworth, A., Doyle, J., Jones, R. and Webster, N.S. (2016) Effects of light attenuation on the sponge holobiont – implications for dredging management. Scientific Reports 6, 39038.
Pineda, M.C., Strehlow, B., Kamp, J., Duckworth, A., Jones, R. and Webster, N.S. (2017a) Effects of combined dredging-related stressors on sponges: a laboratory approach using realistic scenarios. Scientific Reports 7, 5155.
Pineda, M.C., Strehlow, B., Sternel, M., Duckworth, A., Haan, J.D., Jones, R. and Webster, N.S. (2017b) Effects of sediment smothering on the sponge holobiont with implications for dredging management. Scientific Reports 7, 5156.
Pineda, M.C., Strehlow, B., Sternel, M., Duckworth, A., Jones, R. and Webster, N.S. (2017c) Effects of suspended sediments on the sponge holobiont with implications for dredging management. Scientific Reports 7, 4925.
Pollock, F.J., Lamb, J.B., Field, S.N., Heron, S.F., Schaffelke, B., Shedrawi, G., Bourne, D.G. and Willis, B.L. (2014) Sediment and turbidity associated with offshore dredging increase coral disease prevalence on nearby reefs. PLoS ONE 9, e102498.
Powell, A., Smith, D.J., Hepburn, L.J., Jones, T., Berman, J., Jompa, J. and Bell, J.J. (2014) Reduced diversity and high sponge abundance on a sedimented Indo-Pacific reef system: implications for future changes in environmental quality. PLoS ONE 9, e85253.
Ramsby, B.D., Hoogenboom, M.O., Whalan, S., Webster, N.S. and Thompson, A. (2017) A decadal analysis of bioeroding sponge cover on the inshore Great Barrier Reef. Scientific Reports 7, 2706.
Reis, M.A.C. and Leão, Z.M.A.N. (2000) Bioerosion rate of the sponge Cliona celata (Grant 1826) from reefs in turbid waters, north Bahia, Brazil. In Moosa, M.K., Soemodihardjo, S., Soegiarto, A., Romimohtarto, K., Nontji, A., Soekarno, and Suharsono, (eds) Proceedings of the 9th International Coral Reef Symposium, Bali, Indonesia 23–27 October 2000. Volume 1, pp. 273–278.
Reiswig, H.M. (1971) Particle feeding in natural populations of three marine demosponges. Biological Bulletin 141, 568–591.
Risk, M.J., Sammarco, P.W. and Edinger, E.N. (1995) Bioerosion in Acropora across the continental shelf of the Great Barrier Reef Coral Reefs 14, 79–86.
Rose, C.S. and Risk, M.J. (1985) Increase in Cliona delitrix infestation of Montastrea cavernosa heads on an organically polluted portion of the Grand Cayman fringing reef. Marine Ecology 6, 345–363.
Rosell, D. and Uriz, M.J. (1991) Cliona viridis (Schmidt, 1862) and Cliona nigricans (Schmidt, 1862) (Porifera, Hadromerida): evidence which shows they are the same species. Ophelia 33, 45–53.
Rützler, K. (2002) Impact of crustose clionid sponges on Caribbean reef corals. Acta Geologica Hispanica 37, 61–72.
Schönberg, C.H.L. (2000) Bioeroding sponges common to the central Australian Great Barrier Reef: descriptions of three new species, two new records, and additions to two previously described species. Senckenbergiana Maritima 30, 161–221.
Schönberg, C.H.L. (2001) Small-scale distribution of Great Barrier Reef bioeroding sponges in shallow water. Ophelia 55, 39–54.
Schönberg, C.H.L. (2002) Substrate effects on the bioeroding demosponge Cliona orientalis. 1. Bioerosion rates. Marine Ecology 23, 313–326.
Schönberg, C.H.L. (2008) A history of sponge erosion: from past myths and hypotheses to recent approaches. In Wisshak, M. and Tapanila, L. (eds) Current developments in bioerosion. Berlin: Springer, pp. 165–202.
Schönberg, C.H.L. (2015a) Monitoring bioeroding sponges: using rubble, quadrat, or intercept surveys? Biological Bulletin 228, 137–155.
Schönberg, C.H.L. (2015b) Self-cleaning surfaces in sponges. Marine Biodiversity 45, 623–624.
Schönberg, C.H.L. (2016a) Happy relationships of marine sponges with sediments – a review and some observations from Australia. Journal of the Marine Biological Association of the United Kingdom 96, 493–514.
Schönberg, C.H.L. (2016b) Project 6.1 – effects of dredging on filter feeder communities, with a focus on sponges. Final report of project 6.1 of the Dredging Science Node of the Western Australian Marine Science Institution, Perth: Australian Institute of Marine Science, 127 pp.
Schönberg, C.H.L., Fang, J.K.H. and Carballo, J.L. (2017a) Bioeroding sponges and the future of coral reefs. In Bell, J.J. and Carballo, J.L. (eds) Climate change, ocean acidification and sponges. Dordrecht: Springer.
Schönberg, C.H.L., Fang, J.K.H., Carreiro-Silva, M., Tribollet, A. and Wisshak, M. (2017b) Bioerosion: the other ocean acidification problem. ICES Journal of Marine Science 74, 895–925.
Schönberg, C.H.L. and Ortiz, J. (2009) Is sponge bioerosion increasing? Proceedings of the 11th International Coral Reef Symposium, Fort Lauderdale, Florida, 7–11 July 2008, Volume 1, pp. 520–523.
Soekarno, R. (1989) Comparative studies on the status of Indonesian coral reefs. Netherlands Journal of Sea Research 23, 215–222.
Tadjuddah, M., Mustafa, A., Pangerang, U.K. and Yasidi, F. (2012) Application of satellite multi-sensor techniques to detect upwellings and potential fishing grounds in Wakatobi Marine National Park, Southeast Sulawesi, Indonesia. Aquatic Ecosystem Health & Management 15, 303–310.
Tribollet, A., Decherf, G., Hutchings, P. and Peyrot-Clausade, M. (2002) Large-scale spatial variability in bioerosion of experimental coral substrates on the Great Barrier Reef (Australia): importance of microborers. Coral Reefs 21, 424–432.
Tribollet, A. and Golubic, S. (2005) Cross-shelf differences in the pattern and pace of bioerosion of experimental carbonate substrates exposed for 3 years on the northern Great Barrier Reef, Australia. Coral Reefs 24, 422–434.
Wisshak, M. and Tapanila, L. (2008) Current developments in bioerosion. Berlin: Springer.
Wyrtki, K. (1961) Physical oceanography of the Southeast Asian Waters. NAGA report volume 2. San Diego, CA: Scripps Institution of Oceanography, 195 pp.