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Nitrogen Fixing Potential in Extreme Environments

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Nitrogen Fixing Potential in Extreme Environments Nitrogen fixing potential in extreme environments Reut Sorek Abramovich A thesis in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney, Australia March 2013 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 ……………………………………………........... 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 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.' Signed ……………………………………………........................... Date ……………………………………………........................... 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.’ Signed ……………………………………………........................... Date ……………………………………………........................... iv Abstract Biological nitrogen fixation is a key process in providing accessible nitrogen to Earth’s biosphere. This process has been studied in various habitats yet extreme environments still remain relatively unexplored. The nifH gene codes for the Fe protein component in the nitrogenase, which facilitates the nitrogen fixation. Our aims in this study were to assess diazotrophic diversity, richness and community structure in three unique environments and analyse potential adaptations in the Fe protein composition and structure. Our methods included a terminal-restriction fragment length polymorphism (T- RFLP) analysis on 16S rDNA, PCR amplification of the nifH gene, statistical t-test analysis of amino acid compositions, a novel evolutionary analysis and 3D modelling with the I-TASSER web server. Boulder Clay and Amorphous Glacier are two ice-free areas in Terra Nova Bay, Antarctica, which differ in their geological origins and physio-chemical properties. DNA yields from ice- core samples ranged from 0.29 ng PL-1 in Amorphous Glacier to 88 ng PL-1 in Boulder Clay. Bray-Curtis cluster analysis suggested Boulder Clay bacterial profiles were similar to each other, but cluster separately from Amorphous Glacier. The hypersaline (>70 ppt) bays of Shark Bay, Western Australia, are home to the stromatolites microbial mats. The microbial diversity of diazotrophs from two different years, 1996 and 2004, was investigated. Our analysis indicated columnar stromatolites included a common persisting cyanobacterial diazotroph, a Cyanothece or Xenoccocous. Both samples contained novel nifH gene sequences of low similarity to uncultured nifH clones from saline to hypersaline environments, and their inferred NifH amino acid sequences were highly similar to unicellular, non-heterocystous Cyanobacteria and γ,G-Proteobacteria sequences. Paralana’s hot radon springs (PHS, 57 C°) are situated in South Australia. Phylogenetic analysis indicated a rich and diverse group of amino acid NifH sequences from α-, γ-, and δ- Proteobacteria, Chloroflexi and Cyanobacteria phyla. These results suggested aerobic and anaerobic bacteria with conventional Mo nitrogenase might be involved in nitrogen fixation. Our bioinformatic analysis suggested that halophilic adaptations, with an increase in salt bridges, acidic residues and a decrease in bulkier hydrophobic amino acids, did occur in stromatolite diazotrophs and that partial thermophilic adaptations, mainly an increase in salt bridges, Pro and charged residues, did occur in the PHS diazotrophs. These studies provide new insight on the ongoing evolution of nitrogen fixation in extreme environments. v Acknowledgments I would like to thank my supervisors - Prof. Brett A. Neilan, Dr. Michelle Gehringer and Dr. Brendan P. Burns, for their support and advice during my PhD studies. I have benefited from their advice, and followed their wise council. I would like to thank Dr. Sohail Siddiqui, Prof. Aharon Oren and Prof. Nir Ben Tal, for their support and invaluable suggestions. The Australian Centre for Astrobiology was a creative hub for me and other students, a place to exchange ideas, thoughts and avenues of exploration into the biggest mysteries of life. I would like in particular to thank the director, Prof. Malcolm Walter, for his ongoing support of my efforts, and thank Carol, Jessica, Maria, Tamsyn, David and Ivan for creative conversations during my research career at the centre. I would also like to thank my friends and colleagues at the Blue Green Groove Machine lab, for their patience, help and suggestions. I could not have come this far without their knowledge. My special thanks go to: Anne D.J., Michelle A, Kristin, Falicia, Alex, Hannah, Ivan, Jasper, Troco, Shane, Stefan, Jae, Frank, Tim, Maria, Sarah, Tamsyn, Angie, Rati, Julia, Shauna, Leanne, Will and Alper. The Mars Society of Australia (MSA) is a group of intelligent and devoted people. My 2009 field trip to the Paralana Hot Springs in South Australia, with NASA’s Spaceward Bound program, was very special thanks to their efforts and hard work. I salute you: David Cooper, David Wilson, Jon Clarke, Guy Murphy, Mark Gargano, Eriita Jones, Marcia Tanner and Shaun Strong. I am also indebted to Dr. Chris McKay and Prof. Penelope Boston for enlightened conversations and field trip advice & help. Thank you my coffee break friends: Rhea, Shahar, Nitzan, Eldad and Mikayla. To my ever loving husband, Aviv - Thank You, my No. 1. To my parents & brother, Aryeh & Channa & Shachar - Thank you for inspirational stories. To my first born daughter, Eleanor - You were the best surprise I’ve have ever received. May your life be interesting and filled with joy. One last statement if I may - “The time has come for humanity to journey to Mars.” (The Mars Society founding declaration, University of Colorado, Boulder, Colorado, United States, 1998) vi List of Publications Abramovich, R.S., Pomati, F., Jungblut, A.D., Guglielmin, M., and Neilan, B.A. (2012) T- RFLP Fingerprinting Analysis of Bacterial Communities in Debris Cones, Northern Victoria Land, Antarctica. Permafrost and Periglacial Processes 23: 244-248. Contributions to academic conferences Abramovich, R.S., Burns, B.P., and Neilan, B.A. Temporal Biodiversity of Potential Diazotrophs in Stromatolites, Shark Bay, Western Australia. Australian Mars Exploration Conference. July, 17-19th 2009, Adelaide, South Australia. Abramovich, R.S., Burns, B.P., and Neilan, B.A. Nitrogen fixation potential in stromatolites, Shark Bay, Western Australia. The 9th Australian Space Science Conference. 28 - 30th, September 2009, Sydney, Australia. Abramovich, R.S., Gehringer, M.M., and Neilan, B.A. Biodiversity of Potential Diazotrophs in Microbial Communities of Stromatolites at Shark Bay, Western Australia. Sydney Astronomy and Astrophysics Student Symposium. 18th, June 2010, Sydney, Australia. Abramovich, R.S., Gehringer, M.M., and Neilan, B.A. Biodiversity of Potential Diazotrophs in Microbial Communities of a Radon Hot Spring in the Flinders Ranges and Stromatolites at Shark Bay. The 8th International Congress on Extremophiles. 12-14th, September 2010, Azores, Portugal. Abramovich, R.S., Gehringer, M.M., and Neilan, B.A. Biological nitrogen fixation potential in stromatolites, Shark Bay, Western Australia. The 16th SUNFix Symposium. 25th of June 2010, Sydney, Australia. Abramovich, R.S., Gehringer, M.M., Burns, B.P., and Neilan, B.A. Biodiversity of Potential Diazotrophs in Stromatolites of Shark Bay and a Radon Hot Spring. The Australian Society for Microbiology, Annual Scientific Meeting. 4-8th, July 2010, Sydney, Australia. vii List of Acronyms and Abbreviations ARA Acetylene reduction assay ATCC American Type Culture Collection ATP Adenosine triphosphate BLAST Basic local alignment search bp Base pairs BSA Bovine serum albumin cDNA Complementary Deoxyribonucleotide acid Chla Chlorophyll a DMSO Dimethyl sulfoxide DNA Deoxyribonucleotide acid dNTP Deoxyribonucleotide triphosphate DTT Dithiothreithol EDTA Ethylenediaminetetraacetic
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