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Molecular Investigation of Australian Termites and Their Gut Symbionts

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Molecular Investigation of Australian Termites and Their Gut Symbionts Molecular Investigation of Australian Termites and their Gut Symbionts Nurdyana Abdul Rahman BBiotech (Hons), University of Queensland A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2015 School of Chemistry and Molecular Biosciences Abstract Termites are one of the most abundant and ecologically important eusocial insects in tropical and subtropical regions. Their success as lignocellulose decomposers is a result of a mutualistic relationship with their gut microbiota. Termites have evolved from wood-feeding cockroaches (lower termites) and expanded their dietary scope to soil, herbivore dung, grass and litter (higher termites). The introduction of high-throughput culture-independent molecular techniques has reinvigorated efforts to understand the termite gut microbiome and its involvement in symbiotic digestion. Yet, there remain significant unanswered or poorly answered questions regarding termite gut microbiome ecology and evolution such as the relative effect of diet vs vertical inheritance on shaping gut communities, the resilience of these communities under changing dietary regimes, the function of specific populations and the relative contributions of prokaryotic and eukaryotic symbionts to hydrolysis in lower termites. The aim of this thesis is to address these questions making use of Australia’s diverse but understudied termite species. In Chapter 2, a molecular survey using SSU rRNA amplicon pyrosequencing was conducted on 66 termite gut samples comprising seven higher termite genera and nine lower termite genera. Findings indicated that vertical inheritance is the primary force shaping the termite gut microbiome, with diet playing a more subtle role changing relative abundance of some populations. This suggested that gut community and structure may change in response to dietary changes as a short-term adaptive mechanism. To test this hypothesis, feeding experiments were performed on the polyphagous lower termite species, Mastotermes darwiniensis, and gut communities were monitored over time via SSU rRNA profiling, forming the basis of Chapter 3. Small shifts in relative abundance of gut populations were noted with compositionally different feedstocks (e.g. wood to grass) supporting the original hypothesis, but greater shifts are likely due to response to stress as an effect of smaller colony size. However, only small differences were noted in corresponding gut protein profiles, suggesting that gut function was maintained even though community composition altered. In Chapter 4, whole gut DNA samples of two lower (Mastotermes and Porotermes) and two higher (Nasutitermes and Microcerotermes) termite genera were shotgun sequenced. Gene-centric analysis of the shotgun data was performed to determine community-level functional similarities and differences. Despite conspicuous differences in community structure between these four wood- feeding genera (Chapter 2), they had similar gene family abundance profiles suggesting functional convergence in these communities. Differential coverage binning was also attempted to recover population genomes from the metagenomic datasets, but with limited success due to termite host DNA compromising the assemblies. However, three and one substantially complete population genomes belonging to the Fibrobacteres and TG3 phyla, respectively, were recovered from the two i higher termite genera, Microcerotermes and Nasutitermes. Currently only one sequenced isolate is publicly available for the Fibrobacteres (Fibrobacter succinogenes) and one for TG3 (Chitinivibrio alkaliphilus). In Chapter 5, a comparative genomics analysis of the Fibrobacteres/TG3 phyla was conducted using the four termite gut population genomes together with three from a cellulose-fed anaerobic digester, one from sheep rumen and the two isolate reference genomes. Genome-based phylogeny indicated a robust relationship between Fibrobacteres and TG3, thus we propose reclassifying TG3 as a class within the Fibrobacteres phylum. Polymer hydrolysing genes were found to be over-represented in all 10 genomes suggesting that this is a unifying characteristic of the Fibrobacteres, although additional ecosystems should be investigated to confirm this inference. Historically, the Fibrobacteres were thought to be non-motile based on extrapolation from F. succinogenes, however, our analysis suggests that flagella-based motility is an ancestral and widespread trait in this phylum and has been recently lost in F. succinogenes and related genera. The findings of this thesis contribute to the growing body of knowledge on termite gut microbiomes and in particular, Australian species. The Fibrobacteres genomes provide insight into the evolution of this understudied and underrepresented phylum, which are common constituents of anoxic fibrolytic communities. ii Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my research higher degree candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis. iii Publications during candidature Published peer-reviewed papers Abdul Rahman, N., Parks, D.H., Willner, D.L., Engelbrektson, A.L., Goffredi, S.K., Warnecke, F., Scheffrahn, R. H. and Hugenholtz, P. 2015. A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome 3: 5. Abdul Rahman, N., Parks, D.H., Vanwonterghem, I., Morrison, M., Tyson, G. W., Hugenholtz, P., 2015. A phylogenomic analysis of the bacterial phylum Fibrobacteres. Frontiers in Microbiology 6: 1469. Publications included in this thesis Abdul Rahman, N., Parks, D.H., Willner, D.L., Engelbrektson, A.L., Goffredi, S.K., Warnecke, F., Scheffrahn, R. H. and Hugenholtz, P. 2015. A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome 3: 5 – incorporated as Chapter 2. Contributor Statement of contribution Abdul Rahman, N. (Candidate) Designed experiments (35%) Performed experiment (40%) Analysed data (55%) Wrote and edited paper (55%) Parks, D.H. Analysed data (20%) Willner, D.L. Analysed data (5%) Engelbrektson, A.L. Performed experiment (30%) Goffredi, S.K. Performed experiment (10%) Warnecke, F. Designed experiments (30%) Performed experiment (10%) Scheffrahn, R. H. Performed experiment (10%) Hugenholtz, P. Designed experiments (35%) Analysed data (20%) Wrote and edited paper (45%) iv Abdul Rahman, N., Parks, D.H., Vanwonterghem, I., Morrison, M., Tyson, G. W., Hugenholtz, P., 2015. A phylogenomic analysis of the bacterial phylum Fibrobacteres. Frontiers in Microbiology – incorporated as Chapter 5. Contributor Statement of contribution Abdul Rahman, N. (Candidate) Designed experiments (30%) Performed experiment (55%) Analysed data (55%) Wrote and edited paper (50%) Parks, D.H. Analysed data (20%) Wrote and edited paper (5%) Vanwonterghem, I. Performed experiment (45%) Analysed data (5%) Wrote and edited paper (2%) Morrison, M. Designed experiments (5%) Analysed data (5%) Wrote and edited paper (5%) Tyson, G. W. Designed experiments (5%) Wrote and edited paper (8%) Hugenholtz, P. Designed experiments (60%) Analysed data (15%) Wrote and edited paper (30%) v Contributions by others to the thesis Chapter 3 – Effect of diet on microbial community composition in the gut of Mastotermes darwiniensis Study design and chapter review: Maria Chuvochina and Philip Hugenholtz Chapter 4 – Metagenome-based analysis of gut communities in lower and higher termites Study design and chapter review: Philip Hugenholtz Statement of parts of the thesis submitted to qualify for the award of another degree None vi Acknowledgements Alhamdullilah, all praises to Allah for the strengths and His blessings in completing this thesis. Without the help of the people, to whom I wish to express my gratitude, this thesis could not be completed. First and foremost, I’d like to thank my PhD advisors, Professors Philip Hugenholtz, Gene Tyson and David Merritt, for their consistent guidance, unparalleled knowledge, tutelage, and encouragement during my
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