Theme 1 Project 2 Analysis of Approaches for Monitoring Biodiversity in Commonwealth Waters - Field work report Althaus, F., Barrett, N., Dambacher, J. M., Davies, P., Ferrari, R., Ford, J., Hayes, K. R., Hill, N., Hosack, G., Hovey, R., Huang, Z., Hulls, J., Ingleton, T., Jordan, A., Kendrick, G., Kool, J., Lawrence, E., Leeming, R., Lucieer, V., Malcolm, H., Meyer, L., Monk, J., Nichol, S., Peel, D., Perkins, N., Siwabessy, J., Sherlock, M., Martin, T., Tran, S. M. , Walsh, A., Williams, A. May 2016 www nerpmarine edu au Enquiries should be addressed to: Keith Hayes [email protected] Copyright © 2016 NERP Marine Biodiversity Hub. To the extent permitted by law, all rights are reserved and no part of this publication covered by copyright may be reproduced or copied in any form or by any means except with the written permission of NERP Marine Biodiversity Hub. Acknowledgement This work was undertaken for the Marine Biodiversity Hub, a collaborative partnership supported through funding from the Australian Government’s National Environmental Research Program (NERP). NERP Marine Biodiversity Hub partners include the Institute for Marine and Antarctic Studies, University of Tasmania; CSIRO Wealth from Oceans National Flagship, Geoscience Australia, Australian Institute of Marine Science, Museum Victoria, Charles Darwin University and the University of Western Australia. Important Disclaimer The NERP Marine Biodiversity Hub advises that the information contained in this publication comprises general statements based on scientific research. The reader is advised and needs to be aware that such information may be incomplete or unable to be used in any specific situation. No reliance or actions must therefore be made on that information without seeking prior expert professional, scientific and technical advice. To the extent permitted by law, the NERP Marine Biodiversity Hub (including its employees and consultants) excludes all liability to any person for any consequences, including but not limited to all losses, damages, costs, expenses and any other compensation, arising directly or indirectly from using this publication (in part or in whole) and any information or material contained in it. Contents EXECUTIVE SUMMARY.............................................................................................. 1 Flinders CMR ......................................................................................................................... 3 Solitary Islands KEF............................................................................................................. 11 Houtman-Abrolhos KEF ....................................................................................................... 14 Overall Conclusion ............................................................................................................... 16 Additional Information .......................................................................................................... 17 1. INTRODUCTION ............................................................................................... 19 2. FLINDERS COMMONWEALTH MARINE RESERVE ....................................... 23 2.1 Background and objectives..................................................................................... 23 2.2 Sample design ........................................................................................................ 23 2.2.1 Phase I ................................................................................................................ 23 2.2.2 Phase II ............................................................................................................... 24 2.3 Data processing, scoring and analysis ................................................................... 30 2.3.1 Multi-beam sonar ................................................................................................ 30 2.3.2 Towed video and AUV ........................................................................................ 32 2.3.3 Baited Remote Underwater Video ....................................................................... 42 2.4 Summary of initial results ........................................................................................ 45 2.4.1 Multi-beam sonar survey ..................................................................................... 45 2.4.2 Towed video and AUV ........................................................................................ 45 2.4.3 Baited remote video ............................................................................................ 50 3. SOLITARY ISLANDS KEF ............................................................................... 53 3.1 Background and objectives..................................................................................... 53 3.2 Sample design ........................................................................................................ 53 3.3 Data processing, scoring and analysis ................................................................... 55 3.3.1 Multibeam sonar ................................................................................................. 55 3.3.2 Towed video and AUV ........................................................................................ 56 3.3.3 Baited remote underwater video ......................................................................... 57 3.4 Summary of initial results ........................................................................................ 58 3.4.1 Multi-beam sonar survey ..................................................................................... 58 3.4.2 Towed video and AUV ........................................................................................ 61 3.4.3 Baited remote video ............................................................................................ 66 4. HOUTMAN-ABROLHOS ISLANDS KEF .......................................................... 70 4.1 Background and objectives..................................................................................... 70 4.2 Data collection, processing and scoring ................................................................. 70 4.2.1 Drop camera ....................................................................................................... 70 4.2.2 Multibeam sonar ................................................................................................. 71 4.2.3 AUV .................................................................................................................... 71 4.2.4 Compound specific isotopes ............................................................................... 73 4.3 Summary of initial results ........................................................................................ 74 4.3.1 Drop camera ....................................................................................................... 74 4.3.2 Multi-beam sonar survey ..................................................................................... 76 4.3.3 AUV .................................................................................................................... 76 4.3.4 Compound specific isotopes ............................................................................... 84 REFERENCES ........................................................................................................... 85 APPENDIX A - AUV AND TSCS FILE REPOSITORIES ............................................ 88 APPENDIX B - BRUV FILE REPOSITORIES ............................................................ 90 APPENDIX C - IMAGE SCORING EXAMPLES ......................................................... 92 APPENDIX D - GRTS CELLS MULTIBEAM VALIDATION ....................................... 95 APPENDIX E - TSCS DEPLOYED AT THE SOLITARY ISLANDS ......................... 101 List of Figures – Executive Summary Figure A - Summary of the habitat classification of the 40 GRTS sites based on the drop camera survey and the multibeam sonar survey, illustrating the capacity of this approach to provide comprehensive habitat descriptions of unsurveyed areas where resources would not support a complete census. .......................................................................................................................... 3 Figure B - Bathymetric map of the continuously mapped area of the Flinders CMR and resulting GRTS design for AUV sampling on the shelf and towed video on the slope. ............................... 4 Figure C - Summary of shelf and slope habitats classifications for the multiple use zone of the Flinders CMR ................................................................................................................................ 5 Figure D - Spatial distribution of A) species richness B) fish assemblage groups on the Flinders CMR shelf (shaded grey). Increasing size of symbols in A) indicate increasing species richness. Symbols are colour coded according to the observed substratum type in BRUV footage: yellow = sediment; orange = mixed; red = reef. Assemblages in B) are coded by colour, with predominantly sediment-associated assemblages coloured green and predominantly reef- associated assemblages coloured blue. doi:10.1371/journal.pone.0110831.g005 ...................... 8 Figure E - Interpreted 3-class habitat layer based on swath bathymetry and backscatter data collected in the Solitary Islands survey. The light blue line shows the boundary