Diurnal and seasonal host-symbiont interactions in the coral reef demosponge Amphimedon queenslandica

Animals and plants are not autonomous organisms but rather complex assemblages of different species in close association. Marine sponges are essential components of coral reefs ecosystems. As a result of physiological interactions performed by both the animal host and its symbiotic prokaryotes, sponges perform a wide range of ecologically relevant functions. However, many factors can affect the holobiont metabolic activity and alter the composition and diversity of the symbiont communities. The physico-chemical composition of the seawater can be subject to significant fluctuations over diurnal and seasonal periods. In particular, the sponges living in the intertidal waters of the inner reef flat can experience wide environmental fluctuations. The capacity of sponge-holobionts to cope with a fluctuating environment might rely both on metabolism modulation and inter-species interactions. However, our understanding of these symbiotic systems over temporal dynamics is limited. Here, I investigate the composition and transcriptional activity of the marine sponge holobiont Amphimedon queenslandica to identify factors that change over diurnal or seasonal time scales. This marine demosponge is a tractable study system because it harbours a low diversity and low abundance microbial community dominated by only three Gammaproteobacteria symbionts. In order of abundance, these symbionts are: AqS1 which is connected to free-living Ectothiorhodospiraceae, AqS2 which has recently been reclassified as Amphirhobacter heronislandensis, and AqS3 which belongs to the order OceanospirillalesThe seawater physico-chemical parameters in the habitat where A. queenslandica lives showed significant variations over diurnal and seasonal time scales (Chapter 2). These fluctuations can have potential repercussions on the composition and the stability of the microbial community in association with A. queenslandica over the same time scales. Here I have investigated this hypothesis using 16S rRNA genes and rRNA amplicon sequencing of the A. queenslandica microbial community, obtaining respectively snapshots of the sponge microbial community structure and relative activity over diurnal (day vs night) and seasonal (winter vs summer) time frames. Based on the permanence of the association with the sponge through time, I conceptualised the microbial community as composed of three categories: core microbial species, consistently conserved through diurnal and seasonal environmental variations, transient species fluctuating with the environment, and opportunistic species those highly fluctuating in both abundance and relative activity. Based on this definition, I found a core microbial community composed by the previously described AqS1, AqS2 and AqS3, and a fourth bacterium of the family Flavobacteriaceae, a group of 25 transient species, and a large variety of opportunistic species highly fluctuating through samples. Among these core species, AqS1 and AqS3 significantly fluctuate in abundance and relative activity between the two seasons. I show that their fluctuations appear to be more correlated with the presence of interactions between the symbiotic members of the holobiont rather than a direct response to the variations of the environment.I then explored if A. queenslandica and its three most abundant symbionts experience cyclical changes in gene expression that may reflect a response to diurnal (day vs night) fluctuations in water parameters in their intertidal habitat (Chapter 3). I examined their daily molecular fluctuations by quantifying global transcriptional changes in twelve holotranscriptomes from adults of A. queenslandica. I also characterised the adult sponges’ physiological responses to diurnal environmental fluctuations in the form of pumping activity. I show that the sponge A. queenslandica does not follow a clear circadian cycle. Instead, the holobiont shows high inter-individual variability even between adult sponges living just centimetres apart in their native habitat. Furthermore, I show that the activity of the AqS1 sulfur metabolism is not just a response to the cyclical seawater hypo-anoxic conditions, hypothesised to be a possible detoxicating function within the holobiont, but rather a core metabolic process.I then interrogated holotranscriptomes from adults of A. queenslandica holobiont for changes in gene expression that may reflect a response to the variations of the physico-chemical characteristics of the seawater between summer and winter (Chapter 4). I show that with 24% of its genes differentially expressed, AqS1 is the organism undergoing the broadest gene expression change between the seasons. This wide variation is consistent with the response to the combination of (i) the environmental fluctuations experienced by the holobiont, and (ii) the pathway complementation between the sponge host, AqS1, AqS2 and AqS3. I show that via pathway complementation, resource partitioning, and quorum sensing signals, AqS1 is able to interact and influence the sponge host, the other bacteria symbionts and its biotic and abiotic environment. In turn, I show that A. queenslandica might be able to influence AqS1 metabolism through the management of taurine and γ-aminobutyric acid (GABA) leaked to the symbiont. These amino acids can be uptaken and metabolised by the symbiont for energy production. Their rationing in periods of the year when the environmental nutrients are less abundant might affect AqS1 metabolic activity and reproductive output.In summary, this project shows the importance of the microbial community associated with the sponge A. queenslandica in supporting the holobiont life. Via microbial composition analysis, this project expands our understanding of the phylogenetic composition and the stability of the microbial community associated with A. queenslandica. The analysis of the gene expression variations of A. queenslandica and its most abundant bacterial symbionts show the pivotal role covered by AqS1 in buffering the environmental fluctuations that may impact the holobiont and the influence it exerts over the other members involved in the symbiosis. Furthermore, it increases the evidence indicating host-symbiont metabolism interdependence.