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Optical Detection and Quantification of Trichodesmium Spp. Within the Great Barrier Reef

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Optical Detection and Quantification of Trichodesmium Spp. Within the Great Barrier Reef ResearchOnline@JCU This file is part of the following reference: McKinna, Lachlan I.W. (2010) Optical detection and quantification of Trichodesmium spp. within the Great Barrier Reef. PhD thesis, James Cook University. Access to this file is available from: http://eprints.jcu.edu.au/29747/ The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owner of any third party copyright material included in this document. If you believe that this is not the case, please contact [email protected] and quote http://eprints.jcu.edu.au/29747/ Optical Detection and Quantification of Trichodesmium spp. within the Great Barrier Reef Thesis Submitted by: Lachlan I.W. McKinna BSc. (Hons) in November 2010 for the degree of Doctor of Philosophy in the School of Engineering and Physical Sciences James Cook University Copyright © 2010 by Lachlan I.W. McKinna BSc. (Hons) All rights reserved In loving memory of Nancy McKinna (1915 – 2009) “Do just once what others say you can't do, and you will never pay attention to their limitations again.” Captain James Cook Explorer and Navigator (1728 – 1779) “Both yesterday and today vast quantities of the sea Sawdust was seen; some of our people observd that on passing through a bed of it much larger than common they smelt an uncommon stink which they supposd to proceed from it.” 30 August 1770 Sir Joseph Banks Naturalist (1743 – 1820) Statement of Contribution of Others Research Funding Australian Postgraduate Award (stipend 3.5 years) $ 73,000 AIMS@JCU Project Funding $ 15,000 School of Engineering and Physical Sciences $ 2000 Graduate Research School $ 4600 The Oceanography Society Student Travel Grants $ 1200 Great Barrier Reef Marine Park Authority $ 1000 Australian Institute of Marine Science in-kind support (NA) Thesis Committee Prof. Peter Ridd, School of Engineering and Physical Sciences, James Cook University Prof. Miles Furnas, Australian Institute of Marine Science Dr. Yvette Everingham, School of Engineering and Physical Sciences, James Cook University Statistical and Analytical Assistance Prof. Peter Ridd Prof. Miles Furnas Dr. Yvette Everingham Mr. Matthew Slivkoff Editorial Support Prof. Peter Ridd Prof. Miles Furnas Acknowledgements I would first and foremost like to thank my supervisor Prof. Miles Furnas. Miles, your knowledge regarding the Great Barrier Reef seems inexhaustible and your enthusiasm for developing new scientific gadgetry has been inspiring. To my second supervisor Prof. Peter Ridd, I wholeheartedly thank you for your assistance during this undertaking. Your passion for physics and scientific research has ingrained upon me. To my third supervisor Dr. Yvette Everingham, thank you for your guidance. You have greatly contributed to my skills as a scientist. I would like to acknowledge the efforts of the external examiners who kindly reviewed my work. Your comments and feedback have improved the final form of this PhD thesis. My sincere thanks are also extended to those who assisted during the field component of my PhD. The Masters and crew of the RV Lady Basten and RV Cape Ferguson were always willing to assist me in all aspects of in situ sampling, equipment maintenance and repair, and always seemed to have just the right spare part available somewhere in the hold. During AIMS research cruises I was fortunate to have worked with Irena Zagorskis, John Carelton, Britta Schaffelke, Dave McKinnon and many other fine marine scientists. I thank you all for your guidance, assistance and cheerful spirits which made long journeys at sea together memorable. I am grateful to the James Cook University and Australian Institute of Marine Science academic and administrative staff for their support including Paula Rodger (JCU), Leanne Ashmead (JCU), Thomas Stieglitz (JCU), Ian and Anne Whittingham (JCU), Sue Bird (Graduate Research School), Barbara Pannach (Graduate Research School), Helene Marsh (Graduate Research School) and Michelle Heupel (AIMS@JCU). In addition, thank you to Michelle Devlin, Jon Brodie, Steve Lewis and Zoe Bainbridge of the Australian Centre for Tropical Freshwater Research for giving me the opportunity to work with your amazing team. To Matt Slivkoff and Wojciech Klonowski of Curtin University, your extensive knowledge of marine optics and the DALEC instrument has been an important resource for me. In particular I thank Matt for our many conversations which have helped develop this thesis. To my fellow PhD students with whom I have shared office spaces with over the past few years, Daniel Zamykal, Josh Davidson, Arnold Akem, Danny Cocks and Severine Choukroun, I thank you for your comradeship. I also apologise for the never ceasing cascade of scientific papers that are always flowing from my desk onto the floor. To my parents Ian and Carol McKinna, and my extended family, I thank you for your undivided love and support over these last few years and fostering my interest in learning from a young age. To my feline companion Hamish thanks for sitting up late at night with me whilst I have been madly typing. To you I say, “meow.” Finally, to my partner Jamie Coull, you have been my rock over these last few years and I love you dearly. Thank you so much for your never ceasing understanding and patience. Abstract The primary purpose of this PhD project was the development of suitable methods for the optical detection and quantification of the diazotrophic, marine cyanobacteria Trichodesmium within the Great Barrier Reef (GBR), Australia. Within the GBR, Trichodesmium is likely to contribute quantities of new-nitrogen of similar magnitude to that of rivers. However, due to uncertainties regarding the spatial and temporal abundance of Trichodesmium , there is an order of magnitude uncertainty associated with these nitrogen fixation estimates. Thus, improved methods for quantifying Trichodesmium within the GBR are essential. The key objectives of this PhD thesis were to: Study the bio-optical properties of Trichodesmium , Develop a binary flag for its detection using MODIS imagery and Examine hyperspectral radiometric data as a means of positively discriminating and quantifying Trichodesmium . In addition, the bio-optical properties of a senescing surface aggregation of Trichodesmium were studied. Within this PhD thesis, the bio-optical properties of Trichodesmium were studied primarily with discrete water samples analysed using a benchtop spectrophotometer. Particulate and coloured dissolved organic matter (CDOM) absorption coefficients were measured. From this research component, a relationship between the magnitude of the spectral absorption coefficient of Trichodesmium and chlorophyll-a (Chla) specific concentration was established. Results were comparable with those of the literature. The Chla-specific Trichodesmium absorption coefficients were later used as inputs for radiative transfer simulations with Hydrolight. In situ above-water hyperspectral radiometric measurements of Trichodesmium were also collected. A Trichodesmium-specific binary classification algorithm was developed using quasi-250 m MODIS data. Above-water hyperspectral radiometric measurements of dense Trichodesmium surface aggregations (> 30 mg Chla m -3) showed that the water leaving radiance at wavelengths greater than 700 nm were i much higher in magnitude (> 0.05 W m -2 sr -1) relative to the visible wavelengths 400 - 700 nm (< 0.03 W m - 2 sr -1). This “red-edge” effect agreed with observations of others from the literature. The binary classification algorithm was based on three criteria. The first criteria relied on the difference in magnitude between the MODIS normalised water-leaving radiance (nLw) of band 2 (859 nm) and band 15 (678 nm). The magnitudes of the nLw of band 4 (555 nm) and band 1 (645 nm) relative to band 15 formed the second and third criteria respectively. The classification algorithm was tested on a small subset of 13 MODIS images with corresponding Trichodesmium sea-truths and yielded an 85 % accuracy. Fine scale features consistent with dense Trichodesmium surface aggregations such as eddy swirls and windrows were well represented within the algorithm results. The algorithm was also found to be robust in the presence of highly reflective, potentially confounding affects such as coral reefs, shallow bathymetry and riverine sediment plumes. The suitability of the quasi-analytical algorithm (QAA) for inverting (λ) hyperspectral remote sensing reflectance, Rrs , and quantitatively discriminating Trichodesmium was examined. A technique combining the QAA and a similarity (λ) index measure (SIM) was developed using Rrs data simulated for examples of Case 1 and Case 2 waters. Hydrolight radiative transfer software was used to model (λ) Rrs with Trichodesmium Chla specific absorption inherent optical properties. The (λ) QAA was used to invert the simulated Rrs spectra to yield an estimate of the QAA phytoplankton absorption coefficient aφ (λ) . To ascertain the presence of QAA Trichodesmium , seven SIM values were derived by comparing aφ (λ) with a known ref (λ ) Trichodesmium reference absorption spectrum atri , and also with the absorption spectra of six other phytoplankton types. The results found that the SIM could discriminate Trichodesmium from the six other phytoplankton types for concentrations as low as 0.2 mg Chla m -3 and 3 mg Chla m -3 for the Case 1 and Case (λ) 2 scenarios considered. The QAA-SIM method was tested on along-transect Rrs data collected within the GBR. Upon identifying the presence of Trichodesmium
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