The microbial diversity and function of Arctic supraglacial biomes. Stefanie Lutz Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds School of Earth & Environment December 2015 2 3 Declaration The candidate confirms that the work submitted is her own, except where work which has formed part of jointly authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. The work in Chapter 4 of the thesis has appeared in publication as follows: Lutz, S., Anesio, A. M., Villar, S. E. J. & Benning, L. G. (2014) Variations of algal communities cause darkening of a Greenland glacier. FEMS Microbiology Ecology, 89(2), 402-414. Field work was carried out by SL, LGB and AMA. All analyses, data interpretation, writing and production of figures and tables were completed by SL. SEJV carried out the Raman spectroscopic analyses. Manuscript was written by SL and discussions with all co-authors helped improve it. The work in Chapter 5 of the thesis has appeared in publication as follows: Lutz, S., Anesio, A. M., Edwards, A. & Benning, L. G. (2015) Microbial diversity on Icelandic glaciers and ice caps. Frontiers in Microbiology, 6, 307. Field work was carried out by SL and LGB. All analyses, data interpretation, writing and production of figures and tables were completed by SL. All DNA work was carried out by SL at Aberystwyth University. Manuscript was written by SL and discussions with all co-authors helped improve it. The work in Chapter 6 of the thesis has appeared in publication as follows: Lutz, S., Anesio, A. M., Field, K. & Benning, L. G. (2015) Integrated ‘omics’, targeted metabolite and single-cell analyses of Arctic snow algae functionality and adaptability. Frontiers in Microbiology, 6, 1323. Field work was carried out by SL and LGB. All analyses, data interpretation, writing and production of figures and tables were completed by SL. Metabolomics work was carried out by SL at the University of Sheffield under supervision of KF. Manuscript was written by SL and discussions with all co-authors helped to improve it. 4 The work in Chapter 7 of the thesis reproduces a manuscript in review with Nature Communications (since 09.09.2015): Lutz, S., Anesio, A. M., Raiswell, R., Edwards, A., Newton, R. J., Gill, F. & Benning, L. G. (in review) Algae Melt Arctic Glaciers: The Biogeography and Function of Snow Microbiomes. Field work was carried out by SL, AMA and LGB. All analyses, data interpretation, writing and production of figures and tables were completed by SL. All DNA work was carried out by SL at Aberystwyth University. CNP work was carried out by SL under supervision of RJN. Fatty acid analyses were carried out by SL under supervision of FG. Albedo model was developed by RR with data provided by SL. Manuscript was written by SL and discussions with all co-authors helped to improve it. The work in Chapter 8 of the thesis reproduces a manuscript in the final stages of preparation for submission to the ISME Journal: Lutz, S., Anesio, A. M., Edwards, A, Newton, R. J. & Benning, L. G. (in prep) Linking microbial diversity and functionality of Arctic glacial surface habitats. Field work was carried out by SL, AMA and LGB. All analyses, data interpretation, writing and production of figures and tables were completed by SL. All DNA work was carried out by SL at Aberystwyth University. CNP work was carried out by SL under supervision of RJN. Manuscript was written by SL and discussions with all co-authors helped to improve it. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. © 2015 The University of Leeds and Stefanie Lutz The right of Stefanie Lutz to be identified as Author of this work has been asserted by her in accordance with the Copyright, Designs and Patents Act 1988. 5 Acknowledgements I would like to thank Liane G. Benning for always being immensely supportive and encouraging, for giving me endless opportunities to gain new experiences and enlarge my knowledge and for her endless optimism. Special thanks to Alexandre M. Anesio for great support, his always encouraging words and for many hilarious moments in the field that I will never forget. I would like to thank the whole Cohen geochemistry group for a great time and a lot of fun. Massive thanks goes also to our IT guys who are absolute heroes. I am grateful to SEE and a Vice Chancellor Fellowhsip Contribution to LGB for funding my PhD and the following societies for additional grants awarded during my PhD: National Geographic, the European Association for Geochemistry, the Society for General Microbiology, the Royal Geographical Society, and the European Astrobiology Network Association. I am very grateful for my family, who has always supported me, no matter what I decided to do. Without them I would not be who I am today. I am also very grateful to Aleš, Andrea and all my friends for distracting me from work with climbing, caving, squash (thanks Ekbal!), coffee and tea breaks (thanks James!), after-work G&T (thanks again James!), and Catan (thanks Andy, Pieter, Adam!). 6 7 Abstract The main aim of this research project was to improve our understanding of the diversity, function and ecology of glacial microbiomes. Snow and ice algae are critical players in supraglacial habitats and form extensive blooms in spring and summer. Here I present results on the diversity and the function of snow and ice algae on 21 glaciers in 4 Arctic settings: Greenland, Iceland, Svalbard and Sweden. For the first time, I have evaluated the full microbial community composition (i.e., algae, bacteria, archaea) in the main supraglacial habitats, namely green snow, red snow, biofilms, dirty ice, and cryoconite holes. I have cross-correlated these data with metabolic analyses (i.e., metabolomics, pigments, fatty acids) and critical physico-chemical parameters. I found that snow and ice algae were the first communities to appear after the onset of melting and they showed positive net photosynthetic rates indicating accumulation of organic matter. Furthermore, for the first time I have described these communities in Iceland. My data reveal that red pigmented snow algae are cosmopolitan, and independent of location specific geochemical and mineralogical factors. Only six taxa made up >99% of the algal communities: two uncultured Chlamydomonadaceae, Chloromonas polyptera, Chloromonas nivalis, Chloromonas alpina and Raphidonema sempervirens. In contrast, the composition of green snow varied between the studied locations with higher relative abundance of Raphidonema sempervirens and Microglena sp. in Svalbard, and Chloromonas polyptera in Sweden. Furthermore, I show that green and red snow are not successive stages but two independent phenomena with different adaptation strategies. In all sites, bacteria were mostly represented by the phyla Bacteriodetes, Proteobacteria and Cyanobacteria. The bacterial community composition varied between the different habitats on the phylum level, whereas on the class level they also showed strong biogeography. Archaea showed overall low species diversity. The synthesis of pigments and fatty acids in snow and ice algae were mainly driven by nitrogen and less so by phosphorus limitation. This is especially important for pigments which cause a darkening of glacial surfaces. I show that snow and ice algae dramatically decrease surface albedo which will eventully result in higher melting rates of glaciers. 8 List of contents Declaration................................................................................................................3 Acknowledgements...................................................................................................5 Abstract.....................................................................................................................7 List of contents..........................................................................................................8 List of figures..........................................................................................................11 List of tables............................................................................................................17 List of abbreviations ...............................................................................................25 Chapter 1: Introduction...........................................................................................26 1.1 Background...................................................................................................26 1.2 Research hypotheses .....................................................................................28 1.3 Thesis outline................................................................................................29 Chapter 2: Literature review ...................................................................................32 2.1 Introduction...................................................................................................32 2.2 Stress factors of snow and ice environments ................................................32 2.3 Snow fields....................................................................................................34 2.4 Supraglacial ice.............................................................................................45