AUV-based classification of benthic communities of the Ningaloo shelf and mesophotic areas

Abstract

Despite a growing understanding of the importance of mesophotic ecosystems, they remain relatively unexplored globally, and particularly in the Indian Ocean. The composition of benthic communities of the Ningaloo Marine Park in deeper water (> 20 m) was determined using autonomous underwater vehicles (AUVs). Environmental variables collected by the AUVs as well as geomorphological variables derived from high-resolution multibeam bathymetry were used to explain the distribution of these communities. Imagery was classified for benthic biota, and non-hierarchical k-means clustering was used to identify community groups. Overall, 12 community groups were identified which fell into three broad categories: (1) coral-dominated, (2) CCA-dominated; and (3) macroalgae- and filter-feeder-dominated. Specific deeper water communities (> 50 m) were characterised by the presence of sponges or other non-photosynthetic filter feeders. Corals were confined to depths < 40 m, and cover was high (29–40%). Generalised additive models identified the importance of substrate (cover of sand, rock, and gravel/pebbles), geomorphological variables (slope and bathymetric position index) and temperature in the distribution of communities.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  1. Althaus F, Hill N, Ferrari R, Edwards L, Przeslawski R, Schonberg CH, Stuart-Smith R, Barrett N, Edgar G, Colquhoun J, Tran M, Jordan A, Rees T, Gowlett-Holmes K (2015) A Standardised Vocabulary for Identifying Benthic Biota and Substrata from Underwater Imagery: The Catami Classification Scheme. PLoS One 10:e0141039

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Althaus F, Hill N, Edwards L, Ferrari R, Case M, Colquhoun J, Edgar G, Fromont J, Gershwin L, Gowlett-Holmes K, Hibberd T, Jordan A, Kendrick G, Nichol S, Post A, Przeslawski R, Rees A, Schönberg C, Scott F, Tran M (2013) Catami Classification Scheme for Scoring Marine Biota and Substrata in Underwater Imagery – a Pictorial Guide to the Collaborative and Annotation Tools for Analysis of Marine Imagery and Video (Catami) Classification Scheme. Version 1

  3. Amado-Filho GM, Pereira-Filho GH, Bahia RG, Abrantes DP, Veras PC, Matheus Z (2012) Occurrence and Distribution of Rhodolith Beds on the Fernando De Noronha Archipelago of Brazil. Aquatic Botany 101:41–45

    Article  Google Scholar 

  4. Amado-Filho GM, Moura RL, Bastos AC, Francini-Filho RB, Pereira-Filho GH, Bahia RG, Moraes FC, Motta FS (2016) Mesophotic Ecosystems of the Unique South Atlantic Atoll Are Composed by Rhodolith Beds and Scattered Consolidated Reefs. Marine Biodiversity 46:933–936

    Article  Google Scholar 

  5. Aponte N, Ballantine D (2001) Depth Distribution of Algal Species on the Deep Insular Fore Reef at Lee Stocking Island, Bahamas. Deep Sea Research Part I: Oceanographic Research Papers 48:2185–2194

    Article  Google Scholar 

  6. Armstrong RA, Singh H, Rivero S, Gilbes F (2008) Monitoring Coral Reefs in Optically-Deep Waters. Proceedings of the 11th International Coral Reef Symposium, Ft Lauderdale, Florida, 7-11 July 2008

  7. Bak RPM, Nieuwland G, Meesters EH (2005) Coral Reef Crisis in Deep and Shallow Reefs: 30 years of Constancy and Change in Reefs of Curacao and Bonaire. Coral Reefs 24:475–479

    Article  Google Scholar 

  8. Baker EK, Puglise KA, Harris PT, (eds) (2016) Mesophotic Coral Ecosystems–a Lifeboat for Coral Reefs? The United Nations Environment Programme and GRID-Arendal, Nairobi and Arendal:98 p

  9. Barrett N, Meyer L, Hill N, Walsh P (2011) Methods for the Processing and Scoring of Auv Digital Imagery from South Eastern Tasmania. Institute for Marine and Antarctic Studies, University of Tasmania

  10. Bax NJ (2011) Marine Biodiversity Hub, Commonwealth Environment Research Facilities, Final Report 2007-2010. Report to Department of Sustainability, Water, Population and Communities Canberra, Australia

  11. Beckley LE, Lombard AT (2012) A Systematic Evaluation of the Incremental Protection of Broad-Scale Habitats at Ningaloo Reef, Western Australia. Marine and Freshwater Research 63:17–22

    Article  Google Scholar 

  12. Bell JJ (2008) The Functional Roles of Marine Sponges. Estuarine, Coastal and Shelf Science 79:341–353

    Article  Google Scholar 

  13. Bell JJ, Davy SK, Jones T, Taylor MW, Webster NS (2013) Could Some Coral Reefs Become Sponge Reefs as Our Climate Changes? Glob Chang Biol 19:2613–2624

    Article  PubMed  Google Scholar 

  14. Bewley M, Friedman A, Ferrari R, Hill N, Hovey R, Barrett N, Pizarro O, Figueira W, Meyer L, Babcock R, Bellchambers L, Byrne M, Williams SB (2015) Australian Sea-Floor Survey Data, with Images and Expert Annotations. Sci Data 2:150057

    Article  PubMed  PubMed Central  Google Scholar 

  15. Bongaerts P, Ridgway T, Sampayo EM, Hoegh-Guldberg O (2010) Assessing the ‘Deep Reef Refugia’ Hypothesis: Focus on Caribbean Reefs. Coral Reefs 29:309–327

    Article  Google Scholar 

  16. Brasileiro PS, Pereira-Filho GH, Bahia RG, Abrantes DP, Guimarães SMPB, Moura RL, Francini-Filho RB, Bastos AC, Amado-Filho GM (2015) Macroalgal Composition and Community Structure of the Largest Rhodolith Beds in the World. Marine Biodiversity 46:407–420

    Article  Google Scholar 

  17. Bridge TCL, Hughes TP, Guinotte JM, Bongaerts P (2013) Call to Protect All Coral Reefs. Nature Climate Change 3:528–530

    Article  Google Scholar 

  18. Bridge TCL, Done TJ, Beaman RJ, Friedman A, Williams SB, Pizarro O, Webster JM (2010) Topography, Substratum and Benthic Macrofaunal Relationships on a Tropical Mesophotic Shelf Margin, Central Great Barrier Reef, Australia. Coral Reefs 30:143–153

    Article  Google Scholar 

  19. Bridge TCL, Fabricius KE, Bongaerts P, Wallace CC, Muir PR, Done TJ, Webster JM (2011a) Diversity of Scleractinia and Octocorallia in the Mesophotic Zone of the Great Barrier Reef, Australia. Coral Reefs 31:179–189

    Article  Google Scholar 

  20. Bridge TCL, Done TJ, Friedman A, Beaman RJ, Williams SB, Pizarro O, Webster JM (2011b) Variability in Mesophotic Coral Reef Communities Along the Great Barrier Reef, Australia. Marine Ecology Progress Series 428:63–75

    Article  Google Scholar 

  21. Buhl-Mortensen L, Buhl-Mortensen P (2005) Distribution and Diversity of Species Associated with Deep-Sea Gorgonian Corals Off Atlantic Canada. In: Freiwald A, Roberts JM (eds), 2005, Cold-water Corals and Ecosystems Springer-Verlag Berlin Heidelberg:849–879

  22. Cassata L, Collins LB (2008) Coral Reef Communities, Habitats, and Substrates in and near Sanctuary Zones of Ningaloo Marine Park. Journal of Coastal Research 24:139–151

    Article  Google Scholar 

  23. Charrad M, Ghazzali N, Boiteau V, Niknafs A (2014) Nbclust: An R Package for Determining the Relevant Number of Clusters in a Data Set. UseR! 61:36

  24. Clarke KR, Warwick RM (2001) Change in Marine Communities: An Approach to Statistical Analysis and Interpretation. PRIMER-E: Plymouth, United Kingdom 2nd Edition

  25. Clarke KR, Gorley RN (2015) Primer V7: User Manual/Tutorial. PRIMER-E, Plymouth:296

  26. Collins LB, Twiggs E, Tecchiato S (2015) Final Report of Project 1.3.1 of the Kimberley Marine Research Program Node of the Western Australian Marine Science Institution. WAMSI, Perth, Western Australia:247

  27. Colquhoun J, Heyward A (2008) Ningaloo Reef Marine Park, Deepwater Benthic Biodiversity Survey, Annual Report 2007.Wamsi Node 3 Project 1 Subproject 3.1.1, Deepwater Communities at Ningaloo Marine Park. The Australian Institute of Marine Science, University of Western Australia, Curtin University of Technology, Western Australian Museum, and Western Australian Marine Science Institution:209

  28. Costa B, Kendall MS, Parrish FA, Rooney J, Boland RC, Chow M, Lecky J, Montgomery A, Spalding H (2015) Identifying Suitable Locations for Mesophotic Hard Corals Offshore of Maui. Hawai’i, Plos One, p 10

    Google Scholar 

  29. Davies HN, Beckley LE, Kobryn HT, Lombard AT, Radford B, Heyward A (2016) Integrating Climate Change Resilience Features into the Incremental Refinement of an Existing Marine Park. PLOS ONE 11:e0161094

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Englebert N, Bongaerts P, Muir PR, Hay KB, Pichon M, Hoegh-Guldberg O (2017) Lower Mesophotic Coral Communities (60-125 M Depth) of the Northern Great Barrier Reef and Coral Sea. PLOS ONE 12:e0170336

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Erftemeijer PL, Riegl B, Hoeksema BW, Todd PA (2012) Environmental Impacts of Dredging and Other Sediment Disturbances on Corals: A Review. Mar Pollut Bull 64:1737–1765

    Article  PubMed  CAS  Google Scholar 

  32. Fitzpatrick BM, Harvey ES, Heyward AJ, Twiggs EJ, Colquhoun J (2012) Habitat Specialization in Tropical Continental Shelf Demersal Fish Assemblages. PLoS One 7:e39634

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Fricke HW, Meischner D (1985) Depth Limits of Bermudan Scleractinian Corals: A Submersible Survey. Marine Biology 88:175–187

    Article  Google Scholar 

  34. Fulton CJ, Depczynski M, Holmes TH, Noble MM, Radford B, Wernberg T, Wilson SK (2014) Sea Temperature Shapes Seasonal Fluctuations in Seaweed Biomass within the Ningaloo Coral Reef Ecosystem. Limnology and Oceanography 59:156–166

    Article  Google Scholar 

  35. Garcia-Sais JR (2010) Reef Habitats and Associated Sessile-Benthic and Fish Assemblages across a Euphotic-Mesophotic Depth Gradient in Isla Desecheo, Puerto Rico. Coral Reefs 29:277–288

    Article  Google Scholar 

  36. Garcia-Sais JR, Castro R, Sabater-Clavell J, Carlo M, Esteves R (2007) Characterization of Benthic Habitats and Associated Reef Communities at Bajo De Sico Seamount, Mona Passage, Puerto Rico. Report to the Caribbean Fishery Management Council.

  37. Gilmartin M (1960) The Ecological Distribution of the Deep Water Algae of Eniwetok Atoll. Ecology 41:210–221

    Article  Google Scholar 

  38. Hanson CE, McKinnon AD (2009) Pelagic Ecology of the Ningaloo Region, Western Australia: influence of the Leeuwin Current. Journal of the Royal Society of Western Australia 92:129–137

    Google Scholar 

  39. Harris PT, Tsuji Y, Marshall JF, Davies PJ, Honda N, Matsuda H (1996) Sand and Rhodolith-Gravel Entrainment on the Mid- to Outer-Shelf under a Western Boundary Current: Fraser Island Continental Shelf, Eastern Australia. Marine Geology 129:313–330

    Article  Google Scholar 

  40. Hastie T, Tibshirani R (1986) Generalized Additive Models. Statist Sci 1:297–310

    Google Scholar 

  41. Heyward A, Fromont J, Schönberg CHL, Colquhoun J, Radford B, Gomez O (2010) The Sponge Gardens of Ningaloo Reef, Western Australia. The Open Marine Biology Journal 4:3–11

    Article  Google Scholar 

  42. Hiddink JG, Jennings S, Sciberras M, Szostek CL, Hughes KM, Ellis N, Rijnsdorp AD, McConnaughey RA, Mazor T, Hilborn R, Collie JS, Pitcher CR, Amoroso RO, Parma AM, Suuronen P, Kaiser MJ (2017) Global Analysis of Depletion and Recovery of Seabed Biota after Bottom Trawling Disturbance. Proceedings of the National Academy of Sciences 114:8301–8306

    Article  CAS  Google Scholar 

  43. Hinderstein LM, Marr JCA, Martinez FA, Dowgiallo MJ, Puglise KA, Pyle RL, Zawada DG, Appeldoorn R (2010) Theme Section on “Mesophotic Coral Ecosystems: Characterization, Ecology, and Management”. Coral Reefs 29:247–251

    Article  Google Scholar 

  44. Holmes KW, Van Niel KP, Radford B, Kendrick GA, Grove SL (2008) Modelling Distribution of Marine Benthos from Hydroacoustics and Underwater Video. Continental Shelf Research 28:1800–1810

    Article  Google Scholar 

  45. Hooper JN, Kennedy JA (2002) Small Scale Patterns of Sponge Biodiversity (Porifera) on Sunshine Coast Reefs, Eastern Australia. Invertebrate Systematics 16:637–653

    Article  Google Scholar 

  46. Hooper JN, Kennedy JA, Quinn RJ (2002) Biodiversity ‘Hotspots’, Patterns of Richness and Endemism, and Taxonomic Affinities of Tropical Australian Sponges (Porifera). Biodiversity & Conservation 11:851–885

    Article  Google Scholar 

  47. Huang Z, Brooke B, Li J (2011) Performance of Predictive Models in Marine Benthic Environments Based on Predictions of Sponge Distribution on the Australian Continental Shelf. Ecological Informatics 6:205–216

    Article  Google Scholar 

  48. Hughes TP, Barnes ML, Bellwood DR, Cinner JE, Cumming GS, Jackson JBC, Kleypas J, van de Leemput IA, Lough JM, Morrison TH, Palumbi SR, van Nes EH, Scheffer M (2017) Coral Reefs in the Anthropocene. Nature 546:82–90

    Article  PubMed  CAS  Google Scholar 

  49. Kahng SE, Copus JM, Wagner D (2014) Recent Advances in the Ecology of Mesophotic Coral Ecosystems (Mces). Current Opinion in Environmental Sustainability 7:72–81

    Article  Google Scholar 

  50. Kahng SE, Wagner D, Lantz C, Vetter O, Gove J, Merrifield M (2012) Temperature Related Depth Limits of Warm-Water Corals. Proceedings of the 12th International Coral Reef Symposium, Cairns, Australia

  51. Kahng SE, Garcia-Sais JR, Spalding HL, Brokovich E, Wagner D, Weil E, Hinderstein L, Toonen RJ (2010) Community Ecology of Mesophotic Coral Reef Ecosystems. Coral Reefs 29:255–275

    Article  Google Scholar 

  52. Kane C, Kosaki RK, Wagner D (2014) High Levels of Mesophotic Reef Fish Endemism in the Northwestern Hawaiian Islands. Bulletin of Marine Science 90:693–703

    Article  Google Scholar 

  53. Kassambara A, Mundt F (2017) Factoextra: Extract and Visualize the Results of Multivariate Data Analyses. R package version 104, https://CRANR-project.org/package=factoextra

  54. Krieger KJ, Wing BL (2002) Megafauna Associations with Deepwater Corals (Primnoa Spp.) in the Gulf of Alaska. Hydrobiologia 471:83–90

    Article  Google Scholar 

  55. Kutti T, Bannister RJ, Fosså JH (2013) Community Structure and Ecological Function of Deep-Water Sponge Grounds in the Traenadypet Mpa—Northern Norwegian Continental Shelf. Continental Shelf Research 69:21–30

    Article  Google Scholar 

  56. LeProvost Dames, Moore (2000) Ningaloo Marine Park (Commonwealth Waters) Literature Review Prepared for Environment Australia

  57. Lesser MP, Slattery M, Leichter JJ (2009) Ecology of Mesophotic Coral Reefs. Journal of Experimental Marine Biology and Ecology 375:1–8

    Article  Google Scholar 

  58. Linklater M, Carroll AG, Hamylton SM, Jordan AR, Brooke BP, Nichol SL, Woodroffe CD (2016) High Coral Cover on a Mesophotic, Subtropical Island Platform at the Limits of Coral Reef Growth. Continental Shelf Research 130:34–46

    Article  Google Scholar 

  59. Locker SD, Armstrong RA, Battista TA, Rooney JJ, Sherman C, Zawada DG (2010) Geomorphology of Mesophotic Coral Ecosystems: Current Perspectives on Morphology, Distribution, and Mapping Strategies. Coral Reefs 29:329–345

    Article  Google Scholar 

  60. Lozano-Montes HM, Keesing JK, Grol MG, Haywood MDE, Vanderklift MA, Babcock RC, Bancroft K (2017) Limited Effects of an Extreme Flood Event on Corals at Ningaloo Reef. Estuarine, Coastal and Shelf Science 191:234–238

    Article  Google Scholar 

  61. Magalhaes GM, Amado-Filho GM, Rosa MR, de Moura RL, Brasileiro PS, de Moraes FC, Francini-Filho RB, Pereira-Filho GH (2015) Changes in Benthic Communities Along a 0-60 M Depth Gradient in the Remote St. Peter and St. Paul Archipelago (Mid-Atlantic Ridge, Brazil). Bulletin of Marine Science 91:377–396

    Article  Google Scholar 

  62. Maldonado M, Young CM (1996) Bathymetric Patterns of Sponge Distribution on the Bahamian Slope. Deep-Sea Research 43:897–915

    Article  Google Scholar 

  63. Maldonado M, Young CM (1998) Limits on the Bathymetric Distribution of Keratose Sponges: A Field Test in Deep Water. Marine Ecology Progress Series 174:123–139

    Article  Google Scholar 

  64. Marouchos A, Muir B, Babcock R, Dunbabin M (2015) A Shallow Water Auv for Benthic and Water Column Observations. OCEANS:1-7

  65. Menza C, Kendall M, Hile S (2008) The Deeper We Go the Less We Know. Rev Biol Trop 56:11–24

    Google Scholar 

  66. Moore JAY, Bellchambers LM, Depczynski MR, Evans RD, Evans SN, Field SN, Friedman KJ, Gilmour JP, Holmes TH, Middlebrook R, Radford BT, Ridgway T, Shedrawi G, Taylor H, Thomson DP, Wilson SK (2012) Unprecedented Mass Bleaching and Loss of Coral across 12° of Latitude in Western Australia in 2010–11. PLOS ONE 7:e51807

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  67. Muir P, Wallace C, Bridge TC, Bongaerts P (2015) Diverse Staghorn Coral Fauna on the Mesophotic Reefs of North-East Australia. PLoS One 10:e0117933

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  68. Muir PR, Marshall PA, Abdulla A, Aguirre JD (2017) Species Identity and Depth Predict Bleaching Severity in Reef-Building Corals: Shall the Deep Inherit the Reef? Proceedings of the Royal Society B: Biological Sciences 284:20171551

    Article  PubMed  Google Scholar 

  69. Nichol SL, Brooke BP (2011) Shelf Habitat Distribution as a Legacy of Late Quaternary Marine Transgressions: A Case Study from a Tropical Carbonate Province. Continental Shelf Research 31:1845–1857

    Article  Google Scholar 

  70. Pereira-Filho GH, Amado-Filho GM, de Moura RL, Bastos AC, Guimarães SMPB, Salgado LT, Francini-Filho RB, Bahia RG, Abrantes DP, Guth AZ, Brasileiro PS (2012) Extensive Rhodolith Beds Cover the Summits of Southwestern Atlantic Ocean Seamounts. Journal of Coastal Research 279:261–269

    Article  CAS  Google Scholar 

  71. Pizarro O, Williams SB, Jakuba MV, Johnson-Roberson M, Mahon I, Bryson M, Steinberg D, Friedman A, Dansereau D, Nourani-Vatani N, Bongiorno D (2013) Benthic Monitoring with Robotic Platforms - the Experience of Australia. Underwater Technology Symposium (UT), 2013 IEEE International:1-10

  72. Przeslawski R, Alvarez B, Battershill C, Smith T (2014) Sponge Biodiversity and Ecology of the Van Diemen Rise and Eastern Joseph Bonaparte Gulf, Northern Australia. Hydrobiologia 730:1–16

    Article  Google Scholar 

  73. Przeslawski R, Alvarez B, Kool J, Bridge T, Caley MJ, Nichol S (2015) Implications of Sponge Biodiversity Patterns for the Management of a Marine Reserve in Northern Australia. PLoS One 10:e0141813

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  74. Puglise KA, Hinderstein LM, Marr JCA, Dowgiallo MJ, Martinez FA (2009) Mesophotic Coral Ecosystems Research Strategy: International Workshop to Prioritize Research and Management Needs for Mesophotic Coral Ecosystems, Jupiter, Florida, 12-15 July 2008. NOAA Technical Memorandum NOS NCCOS 98 and OAR OER 2

  75. Pyle RL, Boland R, Bolick H, Bowen BW, Bradley CJ, Kane C, Kosaki RK, Langston R, Longenecker K, Montgomery A, Parrish FA, Popp BN, Rooney J, Smith CM, Wagner D, Spalding HL (2016) A Comprehensive Investigation of Mesophotic Coral Ecosystems in the Hawaiian Archipelago. PeerJ 4:e2475

    Article  PubMed  PubMed Central  Google Scholar 

  76. Quinn GP, Keough MJ (2002) Experimental Design and Data Analysis for Biologists. Cambridge University Press, Cambridge, UK

    Book  Google Scholar 

  77. R Core Team (2010) R: A Language and Environment for Statistical Computing. Austria, Vienna

    Google Scholar 

  78. Rees M, Heyward A, Cappo M, Speare P, Smith L (2004) Ningaloo Marine Park - Initial Survey of Seabed Biodiversity in Intermediate and Deeper Waters Report to Australian Government Department of the Environment and Heritage http://ningaloo-atlas.org.au/content/ningaloo-marine-park-initial-survey-seabed-biodivers:1-45

  79. Richards Z, Bryce M, Bryce C (2013) New Records of Atypical Coral Reef Habitat in the Kimberley, Australia. Journal of Marine Biology 2013:1–8

    Article  Google Scholar 

  80. Roberts TE, Moloney JM, Sweatman HPA, Bridge TCL (2015) Benthic Community Composition on Submerged Reefs in the Central Great Barrier Reef. Coral Reefs 34:569–580

    Article  Google Scholar 

  81. Rooney J, Donham E, Montgomery A, Spalding H, Parrish F, Boland R, Fenner D, Gove J, Vetter O (2010) Mesophotic Coral Ecosystems in the Hawaiian Archipelago. Coral Reefs 29:361–367

    Article  Google Scholar 

  82. Rosa MR, Alves AC, Medeiros DV, Coni EOC, Ferreira CM, Ferreira BP, de Souza RR, Amado-Filho GM, Pereira-Filho GH, de Moura RL, Thompson FL, Sumida PYG, Francini-Filho RB (2015) Mesophotic Reef Fish Assemblages of the Remote St. Peter and St. Paul’s Archipelago, Mid-Atlantic Ridge, Brazil. Coral Reefs 35:113–123

    Article  Google Scholar 

  83. Ryan DA, Brooke BP, Collins LB, Kendrick GA, Baxter KJ, Bickers AN, Siwabessy PJW, Pattiaratchi CB (2007) The Influence of Geomorphology and Sedimentary Processes on Shallow-Water Benthic Habitat Distribution: Esperance Bay, Western Australia. Estuarine, Coastal and Shelf Science 72:379–386

    Article  Google Scholar 

  84. Schlacher TA, Schlacher-Hoenlinger MA, Williams A, Althaus F, Hooper JNA, Kloser R (2007) Richness and Distribution of Sponge Megabenthos in Continental Margin Canyons Off Southeastern Australia. Marine Ecology Progress Series 340:73–88

    Article  Google Scholar 

  85. Schönberg CHL (2015) Happy Relationships between Marine Sponges and Sediments – a Review and Some Observations from Australia. Journal of the Marine Biological Association of the United Kingdom 96:493–514

    Article  Google Scholar 

  86. Schönberg CHL, Fromont J (2011) Sponge Gardens of Ningaloo Reef (Carnarvon Shelf, Western Australia) Are Biodiversity Hotspots. Hydrobiologia 687:143–161

    Article  Google Scholar 

  87. Schönberg CHL, Fromont J (2014) Sponge Functional Growth Forms as a Means for Classifying Sponges without Taxonomy. The Ningaloo Atlas Available at http://ningaloo-atlas.org.au/content/sponge-functional-growth-forms-means-classifying-sponges-without-taxonomy

  88. Sherman C, Nemeth M, Ruíz H, Bejarano I, Appeldoorn R, Pagán F, Schärer M, Weil E (2010) Geomorphology and Benthic Cover of Mesophotic Coral Ecosystems of the Upper Insular Slope of Southwest Puerto Rico. Coral Reefs 29:347–360

    Article  Google Scholar 

  89. Shoham E, Benayahu Y (2017) Higher Species Richness of Octocorals in the Upper Mesophotic Zone in Eilat (Gulf of Aqaba) Compared to Shallower Reef Zones. Coral Reefs 36:71–81

    Article  Google Scholar 

  90. Smallwood CB, Beckley LE, Moore SA (2012) An Analysis of Visitor Movement Patterns Using Travel Networks in a Large Marine Park, North-Western Australia. Tourism Management 33:517–528

    Google Scholar 

  91. Smith TB, Glynn PW, Mate JL, Toth LT, Gyory J (2014) A Depth Refugium from Catastrophic Coral Bleaching Prevents Regional Extinction. Ecology 95:1663–1673

    Article  PubMed  Google Scholar 

  92. Spalding H (2012) Ecology of Mesophotic Macroalgae and Halimeda Kanaloana Meadows in the Main Hawaiian Islands. Honolulu, Hawaii: University of Hawaii PhD Dissertation:1–199

  93. Stafford-Smith MG (1993) Sediment-Rejection Efficiency of 22 Species of Australian Scleractinian Corals. Marine Biology 115:229–243

    Article  Google Scholar 

  94. Tibshirani R, Walther G, Hastie T (2001) Estimating the Number of Clusters in a Data Set Via the Gap Statistic. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 63:411–423

    Article  Google Scholar 

  95. Trembanis AC, Forrest AL, Keller BM, Patterson MR (2017) Mesophotic Coral Ecosystems: A Geoacoustically Derived Proxy for Habitat and Relative Diversity for the Leeward Shelf of Bonaire. Dutch Caribbean, Frontiers in Marine Science, p 4

    Google Scholar 

  96. Trussell GC, Lesser MP, Patterson MR, Genovese SJ (2006) Depth-Specific Differences in Growth of the Reef Sponge Callyspongia Vaginalis: Role of Bottom-up Effects. Marine Ecology Progress Series 323:149–158

    Article  Google Scholar 

  97. Turner JA, Babcock RC, Hovey R, Kendrick GA (2018) Can Single Classifiers Be as Useful as Model Ensembles to Produce Benthic Seabed Substratum Maps?. Estuarine, Coastal and Shelf Science

    Google Scholar 

  98. Turner JA, Babcock RC, Hovey R, Kendrick GA, Degraer S (2017) Deep Thinking: A Systematic Review of Mesophotic Coral Ecosystems. ICES Journal of Marine Science 74:2309–2320

    Google Scholar 

  99. Verfaillie E, Doornenbal P, Mitchell A, White J, Van Lancker V (2007) The Bathymetric Position Index (Bpi) as a Support Tool for Habitat Mapping. MESH Final Guidance, 14 pp

  100. Wickham H (2009) Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag, New York

    Book  Google Scholar 

  101. Williams SB, Pizarro O, Jakuba MV, Johnson CR, Barrett N, Babcock R, Kendrick GA, Steinberg PD, Heyward A, Doherty PJ, Mahon I (2012) Monitoring of Benthic Reference Sites Using an Autonomous Underwater Vehicle. Robotics & Automation Magazine 19:73–84

    Article  Google Scholar 

  102. Wilson SK, Depczynski M, Fulton CJ, Holmes TH, Radford BT, Tinkler P (2016) Influence of Nursery Microhabitats on the Future Abundance of a Coral Reef Fish. Proceedings of the Royal Society B: Biological Sciences 283:20160903

    Article  PubMed  Google Scholar 

  103. Wood SN (2011) Fast Stable Restricted Maximum Likelihood and Marginal Likelihood Estimation of Semiparametric Generalized Linear Models. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 73:3–36

    Article  Google Scholar 

  104. Wright DJ, Pendleton M, Boulware J, Walbridge S, Gerlt B, Eslinger D, Sampson D, Huntley E (2012) Arcgis Benthic Terrain Modeler (Btm), V. 3.0. Environmental Systems Research Institute, NOAA Coastal Services Center, Massachusetts Office of Coastal Zone Management Available online at http://esriurl.com/5754

Download references

Acknowledgements

We thank our funding agency BHP Billiton-CSIRO Ningaloo Outlook Marine Research Partnership for support of this work. The views expressed herein are those of the authors and do not necessarily reflect the views of BHP Billiton or CSIRO. Thanks go to the crew of the CSIRO vessel RV Linnaeus and Karl Forcey in particular for Starbug × AUV operations. We are also grateful to the IMOS AUV facility (http://imos.org.au/facilities/auv/) and the Squidle portal (http://squidle.acfr.usyd.edu.au/) for making additional data available and Claire Rafael for analysing these images. On behalf of all authors, the corresponding author states that there is no conflict of interest.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Joseph A. Turner.

Additional information

Topic editor Dr. Mark R. Patterson

Electronic supplementary material

Below is the link to the electronic supplementary material.

338_2018_1700_MOESM1_ESM.doc

Supplementary material 1 (DOC 36 kb)

Figure

Hierarchical visualisation of groups (data averaged by group) and significant SIMPROF groups (red). Contribution of each species/group to the cluster identified by shading. Circles = coral-dominated, triangles = CCA-/sponge-dominated, squares = filter feeder/macroalgae-dominated (TIFF 53 kb)

338_2018_1700_MOESM3_ESM.xlsx

Detailed results of SIMPER analysis, including within-group similarity and between-group dissimilarity and contributing species (XLSX 92 kb)

Appendix

Appendix

Broad groups and combined taxa (< 1% occurrence alone)

Broad group Combined category Contains
Brown macroalgae Dictyota spp. Dictyota spp.
Fine-branching Fine-branching
Filamentous/filiform Filamentous/filiform
Other Coarse branching
Globose/saccate
Laminate
Membranous
Red macroalgae Membranous Membranous
Fine-branching Fine-branching
Filamentous/filiform Filamentous/filiform
Crustose coralline algae Crustose coralline algae
Green macroalgae All green macroalgae Halimeda spp.
Filamentous/filiform
membranous
Hard coral Acropora spp. Acropora spp.
Favid spp. Favid spp.
Montipora spp. Montipora spp.
Porites spp. Porites spp.
Cycloseris spp. Cycloseris spp.
Encrusting—other Echinophyllia/Oxypora spp.
Echinopora spp.
Leptoseris spp.
Non-Acropora spp.
Foliose—other Echinophyllia/Oxypora spp.
Echinopora spp.
Merulina spp.
Pachyseris spp.
Pavona spp.
Pectinia spp.
Non-Acropora spp.
Other Branching: Seriatopora spp.
Branching: Non-Acropora spp.
Massive: Galaxea spp.
Massive: Lobophyllia spp.
Massive: Symphyllia spp.
Massive: Non-Acropora spp.
Mushroom coral: Fungia spp.
Submassive: Pocillopora spp.
Submassive: Stylophora pistillata
Submassive: Non-Acropora spp.
Soft coral Soft coral Branching
Lobophytum spp.
Massive
Non-photosynthetic filter feeders Non-photosynthetic filter feeders Ascidians: stalked: colonial
Ascidians: unstalked: colonial
Ascidians: unstalked: solitary
Black and octocorals: branching (3D)
Black and octocorals: fan (2D)
Black and octocorals: Whip
Bryozoa: hard: branching
Bryozoa: soft
Hydroids
Sponges Branching Branching
Encrusting Encrusting
Laminar Laminar
Massive Massive
Other Creeping/ramose
Barrels
Cups
Tubes and chimneys
Palmate
Simple
Stalked
Balls

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Turner, J.A., Babcock, R.C., Hovey, R. et al. AUV-based classification of benthic communities of the Ningaloo shelf and mesophotic areas. Coral Reefs 37, 763–778 (2018). https://doi.org/10.1007/s00338-018-1700-3

Download citation

Keywords

  • Benthic communities
  • Continental shelf
  • Coral
  • Invertebrates
  • Mesophotic
  • Ningaloo