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Molecular Studies on the Role of Bacteria in a Marine Algal Disease

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Molecular Studies on the Role of Bacteria in a Marine Algal Disease Molecular Studies on the Role of Bacteria in a Marine Algal Disease Neil Daniel Fernandes A thesis in fulfillment of the requirements for the degree of Doctor of Philosophy School of Biotechnology and Biomolecular Sciences Faculty of Science The University of New South Wales Sydney, Australia April, 2011 PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name Femandes First name Neil Other name/s Daniel Abbrev1at1on for degree as given in the Un1versity calendar PhD School School of Biotechnology and Biomolecular Sciences Faculty Science Title. Molecular Studies on the Role of Bacteria in a Marine Algal Disease Abstract 350 words maximum: {PLEASE TYPE) Disease is increasingly viewed as a major factor in marine ecology and its impact is expected to increase with environmental change such as global wanning. This thesis focuses on understanding a "bleaching" disease. which affects the temperate-water red macroalga Delisea pulchra, particularly in summer when sea water temperatme.., are elevated. The bleaching disease could be reproduced in vitro by a combination of increased temperature and the presence of bacterial pathogens. which are phylogenetically affiliated with the genera Microbulhljer. Alteromonas, Cellulophaga and the marine Roseobacter lineage. Since only a fraction of environmental bacteria are cultivable by standard laboratory techniques, a culture-independent metagenomics approach was used ll' characterize the ph) logenetic and functional shifts induced by bleaching in the surface-associated. bacterial community. Phylogenetic shifts mainly reflected relative changes in the genera Tha/assomonas. Thioc/a\'tl and Parvularcula. while changes in gene composition were mainly due to functions associated with transcriptional regulation. cation/multidrug efflux and non-ribosomal peptide synthesis. To obtain an enhanced understanding of the molecular mechanisms of pathogenicity. the genome sequence of strain R 11. a pre\ iousl) ic.lenti lied Rosebacrer-clade pathogen of D. pulchra. was analyzed. In addition to the metabolic versatilit~ that is characteristic of the Roseobacter lineage, the R 11 genome revealed specific adaptations that may aiiO\\ lor switching between free-living. surface-associated and pathogenic lifestyles. Of particular interesl to algal pathogenicity is the synthesis by strain R I I of plant hormone indole acetic acid. a known effector of\ irulence in phyto-pathogens. Comparative genomics including pathogenic and non-pathogenic Roseohacter strams. led to the identification of a unique quorum sensing (QS) dependent transcriptional regulator that may co-ordinate expression of virulence genes. This virulence regulator also provides a direct link to the furanone-based ~.:hemical defense system of D. pulchra. which is known to suppress QS and hence would prevent strain R II from expressing virulence genes. The outcomes of this thesis support the model that indigenous members of the alga\ epiphytic microbial community can become opportunistic pathogens under environmental condition~. \\hen innate host defense mechanisms are compromised and virulence genes are expressed. Declaration relating to disposition of project thesis/dissertation I hereby grant to the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or rn part 1n the Universrty libraries in all forms of media. now or here after known, subject to the provisions of the Copyright Act 1968 I retain all property rights such as patent rights. I also retain the right to use in future works {such as articles or books) all or part of this thesis or dissertation I also authorrse Un1versity Mrcrofilms to use the 350 word abstract of my thesrs in Dissertation Abstracts International (this rs applicable to doctoral theses only) . .~- ~''. >~ . A-G. lk 1;-! 6! " _ _..-- Signature Witness . ' Date The Unrversity~ecognises that there may be exceptronal crrcumstances requiring restrictrons on copyrng or conditrons on use Requests for restrrction for a penod of up to 2 years must be made 1n wntrng Requests for a longer period of restnction may be consrdered 10 except ronal Circumstances and require the approval of the Dean of Graduate Research FOR OFFICE USE ONLY Date of completion of requirements for Award· ( 7/0f/ 11 THIS SHEET IS TO BE GLUED TO THE INSIDE FRONT COVER OF THE THESIS ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed…………………………………………….............. Date…………………………………………….................. 1 "In all things of nature there is something of the marvelous." ~Aristotle 2 Abstract Disease is increasingly viewed as a major factor in marine ecology and its impact is expected to increase with environmental change such as global warming. This thesis focuses on understanding a "bleaching" disease, which affects the temperate-water red macroalga Delisea pulchra, particularly in summer when sea water temperatures are elevated. The bleaching disease could be reproduced in vitro by a combination of increased temperature and the presence of bacterial pathogens, which are phylogenetically affiliated with the genera Microbulbifer, Alteromonas, Cellulophaga and the marine Roseobacter lineage. Since only a fraction of environmental bacteria are cultivable by standard laboratory techniques, a culture-independent metagenomics approach was used to characterize the phylogenetic and functional shifts induced by bleaching in the surface-associated, bacterial community. Phylogenetic shifts mainly reflected relative changes in the genera Thalassomonas, Thioclava and Parvularcula, while changes in gene composition were mainly due to functions associated with transcriptional regulation, cation/multidrug efflux and non- ribosomal peptide synthesis. To obtain an enhanced understanding of the molecular mechanisms of pathogenicity, the genome sequence of strain R11, a previously identified Rosebacter-clade pathogen of D. pulchra, was analyzed. In addition to the metabolic versatility that is characteristic of the Roseobacter lineage, the R11 genome revealed specific adaptations that may allow for switching between free- living, surface-associated and pathogenic lifestyles. Of particular interest to algal 3 pathogenicity is the synthesis by strain R11 of plant hormone indole acetic acid, a known effector of virulence in phyto-pathogens. Comparative genomics including pathogenic and non-pathogenic Roseobacter strains, led to the identification of a unique quorum sensing (QS) dependent transcriptional regulator that may co-ordinate expression of virulence genes. This virulence regulator also provides a direct link to the furanone-based chemical defense system of D. pulchra, which is known to suppress QS and hence would prevent strain R11 from expressing virulence genes.The outcomes of this thesis support the model that indigenous members of the alga's epiphytic microbial community can become opportunistic pathogens under environmental conditions, when innate host defense mechanisms are compromised and virulence genes are expressed. 4 Publications Neil Fernandes, Rebecca Case, Peter Steinberg, Staffan Kjelleberg, Torsten Thomas "Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchra” Submitted for review. Neil Fernandes, Melissa Gardiner, Peter Steinberg, Staffan Kjelleberg, Torsten Thomas "Quorum-sensing regulators control virulence gene expression in Nautella italica R11, a bacterial pathogen of the red alga Delisea pulchra” Manuscript in preparation. Neil Fernandes, Alexandra Campbell, Peter Steinberg, Staffan Kjelleberg, Torsten Thomas "Phylogenetic and functional characterization of the bacterial community associated with healthy and diseased tissue of the marine red alga Delisea pulchra” Manuscript in preparation. Neil Fernandes, Torsten Thomas, Staffan Kjelleberg, "Characterization of infectious diseases of marine macroalgae by culture independent molecular approaches” Manuscript in preparation. Neil Fernandes, Onder Kimyon, Peter Steinberg, Staffan Kjelleberg, Torsten Thomas “Novel pathogens of the red alga Delisea pulchra show diverse phylogenetic affiliations” Manuscript in preparation. 5 Conference Presentations Neil Fernandes, Rebecca Case, Alexandra Campbell, Tilmann Harder, Peter Steinberg, Staffan Kjelleberg, Torsten Thomas "The Role of Bacteria in the Bleaching of a Marine Red Macroalga" at the Australian Society for Microbiology Conference Sydney, Australia, 4 - 8 July 2010 (oral) Neil Fernandes “Climate Change and Emerging Disease - The Role of Bacteria in the Bleaching of a Marine Red Macroalga" UNSW-Competition for Excellence in Postgraduate Research at UNSW Sydney, Australia, 19 August 2010 (oral) Neil Fernandes, Rebecca Case, Peter Steinberg, Staffan Kjelleberg, Torsten
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