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The First Insights into the Phylogeny, Genomics, and Ecology of the Novel Bacterial Phylum Armatimonadetes A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy in Biology at The University of Waikato by Chien-Yu Kevin Lee 2015 ii Executive Summary Currently, a large proportion of novel microbial evolutionary lineages is poorly understood due to limited coverage of representative species. These “candidate” lineages represent significant gaps in our understanding of microbial function and ecology. This study focused on Chthonomonas calidirosea, the earliest isolated species within Armatimonadetes, the most recently-recognised bacterial phylum. The overall aim of this research was to start to understand the ecology and phylogeny of Armatimonadetes, and provide a foundation for future research into the phylum, with the benefit of narrowing the current knowledge gaps on microbial diversity. This was achieved by integrating multiple data types (phylogenetics, genomics, and community profiling metagenomics). The initial stage of this research aimed to address and clarify conflicts in reported phylogeny of the phylum Armatimonadetes. This study generated a comprehensive reference phylogenetic tree of 16S rRNA genes for the phylum, so that the phylogenetic position of newly-identified phylotypes can be reliably associated across studies. Multiple robust statistical methods were used to arrive at a consensus on the partitioning of classes and neighbouring phyla. The process also helped to identify and exclude candidate phyla previously misattributed to Armatimonadetes, thus better defining the phylum for future studies. The deeply-branching phylogenetic relationship of Armatimonadetes with other bacterial phyla was resolved by the sequencing of C. calidirosea T49T genome and analysing concatenated amino acid sequences of conserved genes against homologs in other prokaryotic genomes. The phylogenomic analysis showed Chloroflexi to be the most closely related formal phylum to Armatimonadetes. This publication was the first analysis of a genome from the phylum Armatimonadetes, and provided evolutionarily- and genetically-distinct insights to the overall knowledge of microbial genetic diversity. Analysis of the genome showed a metabolism geared towards non-cellulosic carbohydrates as the carbon and energy source, which coincides with previous culture- based physiological experiments (Lee et al., 2011). Genetic mechanisms behind leucine auxotrophy and narrow pH growth range were also identified. These observations supported the theory that C. calidirosea T49T occupies the niche of a scavenger of diverse species of carbohydrates within geothermal environments, in association with cellulolytic community members. In addition, the genome exhibited an unusual disorganisation of functionally-related genes typically found in conserved operons. The relatively high abundance of sigma factors (relative to genome size) in strain T49T may play an important role in gene regulation and coordination of metabolic pathways to compensate for the scattering of operons. Overall, this research built upon the previous physiological iii characterisation C. calidirosea T49T (Lee et al., 2011), resulting in a more in-depth and integrated analysis of the bacterium through both phenotypic and genotypic information. Finally, to investigate the genome dynamics of the species (particularly in genome organisation and adaptation to various environments as a scavenger), and to provide ecological and evolutionary context beyond the single genome analysed, the genomes of three additional C. calidirosea isolates cultured from diverse locations across the Taupō Volcanic Zone were extracted, sequenced, and compared to T49T. The genomes exhibited higher within-species conservation than other thermophilic species such as Thermus thermophilus (Henne et al., 2004; Jiang et al., 2013; Oshima & Ariga, 1975) and Sulfolobus islandicus (Reno et al., 2009) isolated from similar geographical distance. No genomic rearrangements were identified between C. calidirosea isolates. The majority of variation was limited to single nucleotide polymorphisms, with a limited number of horizontally-transferred genes and differentially-present fast-evolving genes, such as restriction modification system. The phylogeny and carbohydrate utilisation profiles of the isolates correlated with the geographical relationship between the sample sites rather than with other factors, such as soil geochemistry or microbial communities of the sites. The correlation between geography and phylogeny, low abundance of C. calidirosea at all sample sites (ranging from 0.006 % to 0.3 %), and the high genomic conservation indicated rapid aeolian dispersal and localised extinction as the most probable causes of homogeneity between the populations. The findings contribute to a better understanding of the genome dynamics and ecology of C. calidirosea, as well as the dispersal possibilities of free-living bacteria between distinct and discrete habitats. These studies addressed the overarching aim to investigate the ecology and phylogeny of Armatimonadetes through the research outlined above. This body of work contributed greatly to our understanding of Armatimonadetes phylogeny, both by clarifying its internal taxonomy and its position relative to neighbouring clades. Furthermore, it contributed to understanding of Armatimonadetes ecology by richly describing the ecological niche, genome, and lifestyle of C. calidirosea. Not only does this work greatly increase our understanding of the newest of the 30 prokaryotic phyla (Euzéby, 2011, Retrieved in December 2014), it also provides a rich foundation for future study. iv Publications Resulting from this Thesis Dunfield, P. F., Tamas, I., Lee, K. C., Morgan, X. C., McDonald, I. R., & Stott, M. B. (2012). Electing a candidate: a speculative history of the bacterial phylum OP10. Environmental Microbiology, 14(12), 3069–80. doi:10.1111/j.1462- 2920.2012.02742.x Lee, K. C.-Y., Stott, M. B., & Dunfield, P. F. (2013). Phylum Armatimonadetes. In E. Rosenberg, E. F. DeLong, F. Thompson, S. Lory, & E. Stackebrandt (Eds.), The Prokaryotes (4th ed.). Springer. Lee, K. C. Y., Herbold, C. W., Dunfield, P. F., Morgan, X. C., McDonald, I. R., & Stott, M. B. (2013). Phylogenetic delineation of the novel phylum Armatimonadetes (former Candidate Division OP10) and definition of two novel candidate divisions. Applied and Environmental Microbiology, 79(7), 2484–7. doi:10.1128/AEM.03333- 12 Lee, K. C., Morgan, X. C., Dunfield, P. F., Tamas, I., McDonald, I. R., & Stott, M. B. (2014). Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes. The ISME Journal, 8, 1522–1533. doi:10.1038/ismej.2013.251 Lee, K. C., Stott, M. B., Dunfield, P. F., Huttenhower, C., McDonald, I. R., & Morgan, X. C. Comparative genomics and metagenomics of geographically-diverse Chthonomonas calidirosea isolates. Applied and Environmental Microbiology (In Revision). v Table of Contents Executive Summary ........................................................................................................... iii Publications Resulting from this Thesis .............................................................................. v Table of Contents ............................................................................................................... vi List of Figures ..................................................................................................................... x List of Tables ...................................................................................................................... xi Acknowledgements ........................................................................................................... xii Notes for the Readers ....................................................................................................... xiii List of Abbreviations ........................................................................................................ xiv Chapter 1 Introduction ..................................................................................................... 1 1.1 - The need to characterise the great prokaryotic unknown ....................................... 1 1.2 - A brief introduction to molecular and environmental microbiology ...................... 2 1.3 - The development of DNA sequencing technologies and community profiling ..... 5 1.4 - Extremophiles ......................................................................................................... 7 1.5 - Candidate Division OP10 and Phylum Armatimonadetes ...................................... 8 Chapter 2 Literature Review - “Phylum Armatimonadetes”.........................................