Molecular investigation of Australian termites and their gut symbionts

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 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.