Microbial Ecology and Biogeography of the Southern Ocean
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Microbial Ecology and Biogeography of the Southern Ocean David Wilkins Submitted in fulfillment of the requirements for the Degree of Doctor of Philosophy. School of Biotechnology and Biomolecular Sciences University of New South Wales,Sydney April 2013 PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: Wilkins First name: David Other name/s: Francis Abbreviation for degree as given in the University calendar: PhD School: Biotechnology and Biomolecular Sciences Faculty: Science Title: Microbial ecology and biogeography of the Southern Ocean Abstract 350 words maximum: (PLEASE TYPE) The biogeographic distribution of microorganisms is an important part of their ecology, as it is both a cause and a consequence of their interactions with environmental factors. In the Southern Ocean (SO), physical oceanographic features such as water masses and their circulation are closely associated with microbial biogeography, but this relationship has not been previously described on a large scale and at the whole-community level. As climate change continues to influence the physical structure of the SO, and as marine microorganisms are key drivers of many global ecosystem processes, the need to understand this system has become increasingly important. This study used shotgun metagenomic sequencing and bioinformatic analysis to describe the taxonomic composition and functional potential of surface microbial communities along a latitudinal transect of the SO, and test the hypothesis that the Polar Front (PF), a major oceanographic feature of the SO, is a biogeographic barrier. This hypothesis was confirmed on both the taxonomic and functional levels. Confirming and extending previous findings, microbial communities south of the PF reflected greater nutrient availability, particularly in the form of high molecular weight phytoplankton byproducts, while communities to the north suggested a more oligotrophic lifestyle. Further analysis of samples associated with this study suggested a role for advection (physical transport) of microbes by ocean circulation in shaping their biogeographic distribution, a mechanism frequently invoked to explain observations in microbial ecology but never directly tested. To test this hypothesis, microorganisms were sampled on a second latitudinal transect including samples from the surface to 5800 m depth, representing all major water masses of the SO. Tag pyrosequencing of 16S rRNA genes was used to construct taxonomic profiles for each sample, and these were compared to the computer-simulated advection of inertial particles, with the effects of environmental selection and spatial separation controlled for. Advection and taxonomic distance were well correlated, suggesting advection contributes to the variance in community composition across the SO. This study provides the first direct and quantitative support for an “advection effect”, and indicates that “everything is everywhere, but, the environment selects” is an incomplete description of marine microbial biogeography. 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 in part in the University 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 authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstracts International (this is applicable to doctoral theses only). .. ... Signature Witness Date 23/8/2013 The University recognises that there may be exceptional circumstances requiring restrictions on copying or conditions on use. Requests for restriction for a period of up to 2 years must be made in writing. Requests for a longer period of restriction may be considered in exceptional circumstances and require the approval of the Dean of Graduate Research. FOR OFFICE USE ONLY Date of completion of requirements for Award: THIS SHEET IS TO BE GLUED TO THE INSIDE FRONT COVER OF THE THESIS ii Originality Statement “I hereby declare that this submission is my own work and to the best of my knowl- edge 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.” August 29, 2013 Parts of this thesis that have been previously published are clearly marked with a statement in a sans-serif typeface preceding the relevant section. Where experimental work has been performed by a person or people other than the author, this is indicated in a footnote. iii Copyright Statement “I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary 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 authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstract International (this is applicable to doc- toral theses only). I have either used no substantial portions of copyright material in my thesis or I have obtained permission to use copyright material; where permission has not been granted I have applied/will apply for a partial restriction of the digital copy of my thesis or dissertation.” Authenticity Statement “I certify that the Library deposit digital copy is a direct equivalent of the final offi- cially approved version of my thesis. No emendation of content has occurred and if there are any minor variations in formatting, they are the result of the conversion to digital format.” August 29, 2013 Abstract The biogeographic distribution of microorganisms is an important part of their ecology, as it is both a cause and a consequence of their interactions with environmental factors. In the Southern Ocean (SO), physical oceanographic features such as water masses and their circulation are closely associated with microbial biogeography, but this relationship has not been previously described on a large scale and at the whole-community level. As climate change continues to influence the physical structure of the SO, and as marine microorganisms are key drivers of many global ecosystem processes, the need to understand this system has become increasingly important. This study used shotgun metagenomic sequencing and bioinformatic analysis to describe the tax- onomic composition and functional potential of surface microbial communities along a latitudinal transect of the SO, and test the hypothesis that the Polar Front (PF), a major oceanographic feature of the SO, is a biogeographic barrier. This hypothesis was confirmed on both the taxonomic and func- tional levels. Confirming and extending previous findings, microbial communities south of the PF reflected greater nutrient availability, particularly in the form of high molecular weight phytoplankton byproducts, while communities to the north suggested a more oligotrophic lifestyle. Further analysis of samples associated with this study suggested a role for advection (physical transport) of microbes by ocean circulation in shaping their biogeographic distribution, a mechanism frequently invoked to explain observations in microbial ecology but never directly tested. To test this hypothesis, microorganisms were sampled on a second latitudinal transect including samples from the surface to 5800 m depth, representing all major water masses of the SO. Tag pyrosequencing of 16S rRNA genes was used to construct taxonomic profiles for each sample, and these were compared to the computer-simulated advection of inertial particles, with the effects of environmental selection and spatial separation controlled for. Advection and taxonomic distance were well correlated, suggesting advection contributes to the variance in community composition across the SO. This study provides the first direct and quantitative support for an “advection effect”, and indicates that “everything is everywhere, but, the environment selects” is an incomplete description of marine microbial biogeography. v Acknowledgements This work was supported by funding from the Australian Research Council and the Australian Antarc- tic Division science program. Funding for sequencing described in Chapter 3 was provided by the Gordon and Betty Moore Foundation to the J. Craig Venter Institute. Many thanks to Captain Murray Doyle as well as the crew, science support teams and most impor- tantly the caterers of the RSV Aurora Australis for keeping us afloat, productive and well-fed through two long voyages. Special thanks are due to Steve Rintoul for his voyage