Molecular microbial ecology of Antarctic lakes Sheree Yau A thesis in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biotechnology and Biomolecular Sciences Faculty of Science University of New South Wales, Australia February, 2013 PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesla/Dissertation Sheet Surname or Family name: Yau First name: Sheree Other namels: Abbreviation fcx degree as given in the University calendar· PhD School: Biotechnology and Biomolecular Sciences Faculty: Faculty of Science Tltte: Molecular microbial ecology of Antarctic lakes Abs1Tac:t 350 words maximum: (PLEASE TYPE) The Vestfold Hills is a coastal Antarctic oas1s, a rare ic&-free region containing a high density of meromictic (permanently stratifice<l) lakes. These lakes are ideal model ecosystems as their microbial communities exist along physico-chemical gradients, allowing populations tc) be correlated with geochemical factors. As extensive historic, physico-chemical and biological datasets exist for Ace Lake and Organic Lake. two marine-derived meromictic lakes, they were chosen as study sites for molecular-based analysis·of their microbial communities. Analysis of genetic material randomly sequenced from the environment (metagenomlcs) was performed to determine taxonomic composition and metabolic potential. To support metagenomic inferences, methods were developed for performing microscopy on lake water samples and for the identification of proteins from the environment (metaproteomics). Metaproteomic analysis Indicated active community members, while microbial/viral abundances were determined by microscopy. An integrative approach combining metagenomic, metaproteomic and physico­ chemical data enabled comprehensive descriptions of the lake ecosystems.This included the Identification of taxa not previously known to inhabit the lakes and determination of biogeochemical cycles. A complete genome was reconstructed of a member of the virophage viral family and near complete genomes of phycodnaviruses. The virophage likely preys on phycodnaviruses that infect eucaryotic phytoflagellates. A model of virophag&-phycodnavirus-algae population d)lflamics predicted the presence of a virophage Increases the frequency of algal blooms and thus overall nutrient release. Virophage signatures wetre detected in other aquatic envcronments indicating they play a previously unrecognised role in other environments. In Organic Lake, genes a:;sociated with heterotrophic bacteria involved in OMSP cleavage. photoheterotrophy, llthoheterotrophy and nitrogen remineralisallon were abutndanl, indicating these processes are adaptations to nutnent constraints. Photo- and lithoheterotrophy enables carbon to be used for bios)lflthesis rather than energy generation thereby conseNing carbon in the lake, while recycling of nitrogen limits its loss. DMSP appears to be significc10t carbon and energy source and also the origin of high OMS in Organic Lake. These molecular-based discoveries shed light on the rote of previously unrecognised taxa and metabolic processes In unique Antarctic lake environments. 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 dissertc:ltron In whole ar 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 app11lcable to doctoral theses only) . .. ~~- :.ff~ ..... .. ......... ... 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FOR OFFICE USE ONLY Date of completion of requirements fcx Award: ~ ._______ _____j 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 ... ~0.---1'-/1--~(_~~.. >:W-; ••••• •••• $'1-'1~ .•••••• •.•.. • •.• .. .•••• . •. .? Date ...... &') ..~/. ... (._,. .'2.... , I . ...2.. 0.. ..I ....3 ..... ...... ................ 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 vxorks (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 doctoral 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.' / . ...-~-/ ,.. -~f/ ... f /~ Signed ..-r::<r. ol(: 'f'?:-:'~.<~? : ./ -~~·: :-:-: .. 0 •••••••••••••••• o··o·o·········· ..... o... -1 ') I;J -z I 7 ;] · /) Date ... -!::: ·/·: .. /· .. f:·:t:'L ;~?... ......... 0 ................ ................ AUTHENTICITY STATEMENT 'I certify that the Library deposit digital copy is a direct equivalent of the final officially 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.' ?-;.- ~·7/ ·? ,# "'(?'/? .gned ,.../;;;>; t;.-..· wv;·,.)/ - i... t"A..--· / '"-.. t-4.... Sl ... · -·· ... .. 000 .I: ..... '/('" 00 0 ... .... .. ................. ....... .... " } ....-; /. .. Date ... .. .-:::: ~.;. ~. ?-: 0 .. Jv .t?. C~.... ....... 0 .. .. 0 0 00 0 00 00 00 ...... 00 0 ....... Abstract The Vestfold Hills is a coastal Antarctic oasis, a rare ice-free region containing a high density of meromictic (permanently stratified) lakes. These lakes are ideal model ecosystems as their microbial communities exist along physico-chemical gra- dients, allowing populations to be correlated with geochemical factors. As extensive historic, physico-chemical and biological datasets exist for Ace Lake and Organic Lake, two marine-derived meromictic lakes, they were chosen as study sites for molecular-based analysis of their microbial communities. Analysis of genetic material randomly sequenced from the environment (metage- nomics) was performed to determine taxonomic composition and metabolic poten- tial. To support metagenomic inferences, methods were developed for performing microscopy on lake water samples and for the identification of proteins from the environment (metaproteomics). Metaproteomic analysis indicated active commu- nity members and processes, while microbial/viral abundances and morphology were determined by microscopy. An integrative approach combining metagenomic, metaproteomic and physico-chemical data enabled comprehensive descriptions of the lake ecosystems. This included the identification of taxa not previously known to inhabit the lakes and determination of biogeochemical cycles. A complete genome was reconstructed of a member of the newly described virophage viral family and near complete genomes of phycodnaviruses. The vi- rophage likely ‘preys’ on phycodnaviruses that infect eucaryotic phytoflagellates. A model of virophage–phycodnavirus–algae population dynamics predicted the pres- ence of a virophage increases the frequency of algal blooms and thus overall nutrient release. Virophage signatures were detected in other aquatic environments indi- cating they play a previously unrecognised role in other environments. In Organic Lake, genes associated with heterotrophic bacteria involved in DMSP cleavage, photoheterotrophy, lithoheterotrophy and nitrogen remineralisation were abun- dant, indicating these processes are adaptations to nutrient constraints. Photo- and lithoheterotrophy enables carbon to be used for biosynthesis rather than en- ergy generation thereby conserving carbon in the lake, while recycling of nitrogen limits its loss. DMSP apppears to be significant carbon and energy