The effect of environmental factors on the dynamics of bacterial populations associated with coral colonies and the implications for holobiont health

Abstract

The coral holobiont is comprised of a diverse community of microbial partners, including bacteria living within microhabitats, such as the coral tissue’s and surface mucus layer (SML). However, little is known about the interactions between the bacterial communities in the various compartments of the coral holobiont. Furthermore, although we know that water flow can serve as an ameliorator of thermal stress in corals, there is a lack of information about how water flow affects the bacterial community structure during stressful times. Research described in this thesis aimed to understand, using laboratory and in situ experiments, the interaction between the coral host and bacterial communities in the tissues and SML, as well as how water flow affects the bacterial community structure when the coral is under thermal stress. The bacterial community structure in thermally-stressed individuals of the coral Acropora muricata highlighted the potential for a bacterial community shift between the coral surface mucus and tissues. Nubbins of A. muricata were subjected to increasing water temperatures of 26°C to 33°C, to explore the bacterial diversity in the SML and tissues by 16S rRNA gene amplicon sequencing. Photochemical efficiency (FV/Fm) of symbiotic dinoflagellates within the corals declined above 31°C, suggesting that the corals were under thermal stress. Both the mucus and tissues of healthy A. muricata were dominated by γ-Proteobacteria, but under thermal stress there was a shift towards bacteria from the classes Verrucomicrobiaceae and α- Proteobacteria. Members of the classes Cyanobacteria, Flavobacteria and Sphingobacteria also started to become more prominent at higher temperatures. The relative abundance of sequences affiliated with Vibrio spp. in the coral mucus increased at 29°C, but at 31°C there was a drop in the relative abundance of Vibrio spp. in the mucus, with a reciprocal increase of Vibrio spp. in the tissues. In contrast, during bleaching, the relative abundance of Endozoicomonas montiporae affiliated sequences decreased in the tissues, with a reciprocal increase in the coral mucus. This study provided evidence for a change in the relative abundance of the native microbiota and potentially pathogenic bacteria in both the SML and tissues of corals in response to stress. This shift could result both from a direct change in the resident bacterial population, as well as the migration of bacteria between the SML and tissues. To investigate the influence of mucus chemical composition on bacterial community structure in the SML, the mucus carbohydrate composition of A. muricata was characterised when subjected to increasing thermal stress from 26°C to 31°C, and correlated with any changes in the bacterial community. Results showed that, at lower temperatures, the main components of mucus were N-acetyl glucosamine and C6 sugars, but these constituted a significantly lower proportion of the mucus in thermally-stressed corals. The change in mucus composition coincided with a shift from a γ-Proteobacteria- to a Verrucomicrobiae- and α-Proteobacteria-dominated community in the coral mucus, while Cyanobacteria also started to appear in the mucus as the coral host became thermally stressed. Changes in mucus composition and the bacterial community in the mucus layer occurred at 29°C, which was prior to visual signs of coral bleaching at 31°C. A compositional change in the coral mucus, induced by thermal stress could therefore be a key factor leading to a shift in the associated bacterial community. This, in turn, has the potential to impact the physiological function of the coral holobiont. A study using laboratory and in situ field experiments was conducted to observe changes in the bacterial community composition in the SML when thermally-stressed A. muricata colonies were exposed to different flow regimes. The deterioration of coral health and an associated change in the coral holobiont’s bacterial community are often a result of different environmental stressors acting synergistically. There is evidence that water flow is important for a coral’s resistance to elevated seawater temperatures, but until now there has been no information about how water flow affects the coral-associated bacterial community under these conditions. Laboratory and in situ field experiments were employed to assess whether the bacterial community composition of the surface mucus layer of the coral Acropora muricata was impacted by thermal stress, and how any effect was ameliorated by increased water flow. In the laboratory experiments, Acroproa muricata coral nubbins, each measuring about 2 cm, were subjected to interactive effects of seawater temperature and water flow. Seawater temperatures in the treatment tanks were raised 1°C per day from 27°C to 31°C, after which it was kept constant, while control temperature tanks were kept at a constant temperature of 27°C. Tanks which had high water flow had a pump attached, which moved the water at a speed of ~ 0.20 m s-1, while tanks which had low water flow had a diffuser which slowed down the water flow to ~ 0.03 m s-1. In the in situ field experiments, water flow manipulation was conducted on three colonies of A. muricata, each at depth 8 – 10 m, on December 03,2013 (winter season) and June 18 2014 (summer season), with each experiment lasting 10 days. Each coral colony was partially enclosed in a clear plastic mesh box to reduce the water flow past the enclosed portion of the colonies. Both laboratory and in situ approaches showed that elevated water flow could buffer changes to the bacterial community towards a population being dominated by pathogens. The phylogenetic composition of the bacterial community, characterized with 16S rRNA amplicon pyrosequencing, showed an increase in the relative abundance of Flavobacteriales, Rhodobacterales in the laboratory experiments and Vibrio spp. in the in situ experiments, when corals were exposed to elevated temperature and slow water flow. In contrast, corals that were exposed to low temperature or faster water flow under laboratory conditions had a stable bacterial community, dominated by Acanthopleuribacterales, Acidimicrobiales and Actinomycetales. In the summer and winter field experiments, Oceanospirillales, Alteromonadales and Rhodobacterales were prominent in the coral mucus of both enclosed and un-enclosed portion of the coral colonies. These findings indicate that water flow plays an important role in the maintenance of specific coral-bacteria associations during times of elevated thermal stress, and that high flow may ultimately aid the health of the coral holobiont under these circumstances. This study gives new insights into the dynamics of bacterial communities within the different compartments, such as surface mucus and tissue layer of the coral host, and how water flow can affect the complex bacteria-coral host relationship in times of thermal stress. These findings will be valuable for future research on microbe-coral host as well as microbe-microbe interaction within the coral host, and their role within the coral holobiont.