Exploring the function and behaviour of natural populations of coral reef microbes

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Microorganisms live in tight associations with corals, but the ecological interactions and microbial functions and behaviours underpinning these relationships are not yet fully understood. The goal of this thesis is to define coral-microbe interactions by exploring how the composition, behaviour and function of microbial communities vary throughout a coral reef and how increasing sea water temperatures can affect coral-microbial relationships. As a first step to achieving this aim, In Chapter 1 we used metagenomics to characterise patterns in microbial composition and metabolic capacity across different niches, including coral-associated and non-coral associated microenvironments, on Heron Island, the Great Barrier Reef (GBR). We found that the composition and metabolic potential of coral reef bacteria is highly heterogeneous across a coral reef ecosystem, with a shift from an oligotrophy-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. Among the major functional patterns observed were significant increases in genes associated with bacterial motility and chemotaxis in samples associated with the surfaces of coral colonies. The observation of increased motility and chemotaxis near to coral surfaces is notable given previous evidence that these phenotypes may be involved in coral disease processes. The research presented in this chapter was published in Microbial Ecology (2014 67 (3): 540-552) To investigate these patterns in chemotaxis further we next (Chapter 2) directly examined the potential ecological role of chemotaxis among coral-associated bacteria, by using laboratory based and in situ chemotaxis assays to test levels of chemotaxis among natural communities of coral reef microbes. We examined the behavioural responses towards several chemoattractants known to be released by corals and their symbiotic dinoflagelletes including amino acids, carbohydrates, ammonium chloride, and dimethylsulfonopropionate (DMSP). Using these approaches we found that bacteria associated with the surfaces of the corals exhibited high levels of chemotaxis, particularly towards DMSP and several amino acids. Levels of chemotaxis by coral-associated bacteria were consistently higher than those demonstrated by non-coral associated bacteria. This work was published in the ISME Journal (doi: 10.1038/ismej.2014.261) We next extended the in situ chemotaxis assays to examine the chemotactic behaviour of bacteria associated with other important coral reef organisms, sponges. These results redefine the sponge-symbiont acquisition paradigm whereby we show for that bacteria use chemotaxis to locate their sponge host on a coral reef. This work is in preparation for submission to the ISME Journal. After defining some of the functions and behaviours involved in coral reef microbiology, we next examined how these processes may shift under changing environmental conditions, associated with climate change. To determine how environmental variability, specifically thermal stress, influences bacterial community composition, behaviour and metabolic capacity, manipulation experiments were conducted using the coral Pocillopora damicornis. To investigate the dynamics of coral-associated vibrios under heat stress, in Chapter 4 we used Vibrio-specific amplicon sequencing approaches and qPCR to quantify shifts in the abundance and composition of natural populations of Vibrio, with a specific focus on the putative coral pathogen V. coralliilyticus. These experiments revealed that increasing seawater temperatures can favour the proliferation of potential coral pathogens among a natural mixed microbial community. This work has been published in Frontiers in Microbiology (6:432.doi: 10.3389/fmicb.2015.00432). In Chapter 5, we decided to explore the entire coral-associated community by using metagenomics and metatranscriptomics to investigate how the phylogeny and function of coral associated microbes shift resulting from increasing seawater temperatures. We found a dramatic shift in the community from Endozoicomonaceae being dominant in the control corals, while there was an appearance of the vibrios under increasing sea water temperatures in line with our findings from chapter 4. We also observed functional shifts that involved an upregulation of chemotaxis and motility genes at higher temperatures and were shown to be affiliated with vibrios, a genus which contains several putative coral pathogens. Taken together our data demonstrate that coral reef bacterial communities are highly dynamic and that key groups of copiotrophic bacteria have the capacity to use behaviours such as chemotaxis to use nutrient gradients to potentially locate and colonize benthic host animals including corals and sponges. Increasing seawater temperatures causes dramatic changes in the coral-associated bacterial community, allowing for the proliferation of potential coral pathogens and increased expression of behavioural phenotypes that may promote successful infection of corals.
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