The characterisation of the microbiome of the demosponge Amphimedon queenslandica reveals host immune responses to changes in the symbiotic bacterial community

Bayes, Joanne Marie (2013). The characterisation of the microbiome of the demosponge Amphimedon queenslandica reveals host immune responses to changes in the symbiotic bacterial community MPhil Thesis, School of Biological Sciences, The University of Queensland.

       
Attached Files (Some files may be inaccessible until you login with your UQ eSpace credentials)
Name Description MIMEType Size Downloads
s4189970_mphil_finalthesis.pdf Thesis full text application/pdf 10.81MB 17
Author Bayes, Joanne Marie
Thesis Title The characterisation of the microbiome of the demosponge Amphimedon queenslandica reveals host immune responses to changes in the symbiotic bacterial community
Formatted title
The characterisation of the microbiome of the demosponge Amphimedon queenslandica reveals host immune responses to changes in the symbiotic bacterial community
School, Centre or Institute School of Biological Sciences
Institution The University of Queensland
Publication date 2013
Thesis type MPhil Thesis
Supervisor Sandie Degnan
Bernie Degnan
Phil Hugenholtz
Total pages 150
Total colour pages 28
Total black and white pages 122
Language eng
Subjects 0603 Evolutionary Biology
0605 Microbiology
0608 Zoology
Formatted abstract
Microbial-metazoan interactions have almost certainly existed since the dawn of the animal kingdom and it is becoming increasingly clear that the extent of their ecological and evolutionary effects is enormous. In marine invertebrates, these interactions underpin diverse biological and ecological processes, with bacteria acting variously as settlement cues, food, symbionts and pathogens. In order to detect pathogens whilst allowing useful relationships with bacteria to persist animals rely on the immediate and proficient responses of their innate immune system.

To elucidate some of the host mechanisms that may be used to mediate relationships with microbes, I have linked changes in the microbiome of the coral reef demosponge Amphimedon queenslandica – a basal metazoan with a fully sequenced genome - with the transcriptional responses of sponge innate immune genes. The presence of large numbers of phylogenetically diverse sponge-associated microbial communities has been well documented and the phylogenetic position of sponges as a sister group to the Eumetazoa makes them ideal for exploring the origin and evolution of animal innate immunity. This is because traits shared between sponges and animals likely reflect shared inheritance from the last common animal ancestor.

Using 16S amplicon sequencing to profile the bacterial and archaeal community in A. queenslandica embryos, larvae, postlarvae and adults I have identified five putative vertically transmitted bacterial OTUs that are present throughout the sponge lifecycle. The most abundant symbiont contributes between 30 - 90% of the total microbiome and belongs to the order Chromatiales. Only one other of the dominant symbionts could be confidently assigned a taxonomy; with a 99% match to Pseudoalteronomas. The three remaining symbionts have low (< 90%) sequence similarities to their closest relatives and likely represent new orders of the Proteobacteria. It has been suggested that changes in the microbiomes of marine invertebrates, including sponges, are associated with a decline in health and increased mortality of affected animals. I compared the microbiome of healthy A. queenslandica adults collected from their natural habitat with compromised A. queenslandica adults from the same environment and with individuals maintained in aquaria for a period of 2 weeks. The differences in community composition between healthy and immune-compromised sponges are characterised by: (i) an increase in microbial diversity, (ii) a significant decrease or, in some individuals, a total loss of the vertically transmitted symbionts, and (iii) a complete community shift from the Proteobacteria-dominated community present in sponges collected from their natural habitat to a community dominated by representatives of the Chlamydiae in the sponges maintained in aquaria.

Despite the ubiquitous nature of microbial-metazoan interactions and the high microbial diversity and concentration in the oceans, we have almost no grasp of the underlying molecular mechanisms that govern the cross-talk between the different kingdoms. From the microbial perspective, quorum sensing likely plays an important role in managing these relationships, whereas animal hosts rely on the innate immune system. All animals have an innate immune system that differentiates between self and non-self by using diverse pattern recognition receptors (PRRs). The sequencing of the A. queenslandica genome has resulted in the identification of a number of innate immune genes, including Toll-like receptors (TLRs), Immunoglobulin (Ig) domain-containing genes, Scavenger receptors (SRs), Aggregation factors (AFs) and Lipopolysachharide-binding-like genes (LBLs). Here, I add to the knowledge of the sponge innate immune system with the annotation of A. queenslandica Nucleotide-binding domain and Leucine-rich repeat containing genes (AmqNLRs). I have identified 11 putative AmqNLRs in the sponge genome; nine of these display the typical tripartite architecture - consisting of an N-terminal Death domain, a central NACHT domain and C-terminal LRR domains - that appears to be conserved across multiple invertebrate and vertebrate phyla. The presence of conventional NLRs in A. queenslandica implies that an ancestral NLR gene already existed in the last common metazoan ancestor. A wider taxa search that included a number of species of plants, fungi, protozoa and invertebrates revealed that the NACHT domain, which is central to NLRs, originated before the divergence of the opisthokonts. I used quantitative PCR (qPCR) to measure the transcriptional response of AmqNLRs throughout the sponge lifecycle and in healthy and immune-compromised adults. The results of these experiments highlight the response of AmqNLRs to changes in the A. queenslandica microbiome.
Keyword Porifera
Symbiosis
Evolution (biological)
Immunity
Nucleotide- binding domain and leucine-rich repeat containing genes

 
Citation counts: Google Scholar Search Google Scholar
Created: Sat, 19 Oct 2013, 03:22:18 EST by Joanne Bayes on behalf of Scholarly Communication and Digitisation Service