Climate change impacts on tropical sponges and associated microbial communities

Climate change is causing rapid changes in reef structure, biodiversity, and function as a response to ocean warming and acidification. The negative impacts of climate change on corals are well-documented, but most sponges are predicted to tolerate conditions projected for 2100, making them a viable option for stable alternative reef states. Sponges maintain an intimate relationship with microbial communities, whose general stability in a given sponge species makes them suitable indicators of host responses to stressful environmental conditions such as ocean warming and acidification. The overall aim of this thesis is to examine the impacts of climate change on sponges and their associated microbial communities, with a focus on microbial community composition and abundance and sponge protein expression.

The first data chapter examines the results from a reciprocal transplantation of the coral reef sponges Coelocarteria singaporensis and Stylissa cf. flabelliformis between a control reef site and an adjacent CO2 vent site in Papua New Guinea to explore how the sponge microbiome responds to ocean acidification in situ. Microbial communities of C. singaporensis, which differed initially between sites, did not shift towards characteristic control or vent microbiomes. Microbial communities of S. cf. flabelliformis, which were initially stable between sites, did not respond specifically to transplantation but collectively exhibited a significant change over time, with a relative increase in Thaumarchaeota and decrease in Proteobacteria in all treatment groups. The lack of a community shift upon transplantation to the vent site suggests that microbial flexibility, at least in the adult life-history stage, does not necessarily underpin host survival under ocean acidification.

The second data chapter compares the symbiotic microbial community composition of tropical sponge Stylissa flabelliformis after an eight-week exposure to nine different treatments of three temperatures (28.5 °C, 30 °C, 31.5 °C) and three pH levels (8.1, 7.8, 7.6) based on ambient conditions and two IPCC predictions of future ocean conditions (RCP6.0 and RCP8.5). Bacterial communities differed significantly between temperature treatments, but not pH, with the highest temperature treatments showing increased relative abundances of Bacteroidia and Clostridia (commonly associated with sponge disease and thermal stress), and decreased relative abundances of Nitrospira (associated with nitrogen cycling). Similarly, archaeal communities differed significantly across temperature, with a relative decrease in Nitrososphaeria (associated with ammonia oxidation). Symbiotic eukaryotes were compared using three different reference databases and only two treatments (28.5 °C, pH 8.1 and 31.5 °C, pH 7.6) and exhibited a significant difference in community composition between the two treatments, but also highlighted the requirement for more thorough reference databases. Overall, there was a clear change with temperature across all three microbial groups, indicating increased stress and potential hindrance of nutrient cycling.

The third data chapter aims to determine the impact of temperature and pH on the abundance and spatial arrangement of sponge-associated microbes using droplet digital PCR (ddPCR) and fluorescence in situ hybridization (FISH). Total bacterial abundance was not significantly different across temperature or pH, but was unexpectedly high in sponge replicates with notable algal growth and tissue necrosis. Archaea differed significantly with temperature, decreasing in abundance with increasing temperature, but exhibited no changes due to pH. FISH was largely unsuccessful, due primarily to high sponge autofluorescence and a very low concentration of archaea in the sponge tissue (as shown with ddPCR). Regardless, shifts in bacterial abundance with reduced sponge health and archaeal abundance with temperature show signs of stress and potential functional implications.

The fourth data chapter uses proteomic analysis to examine shifts in protein expression due to temperature and pH. High-temperature treatments exhibited an increased expression of proteins associated with heat shock and a decreased expression of proteins associated with oxidative stress, actin-related processes, and smooth muscle contraction in comparison to low-temperature treatments. The comparison of high- and low-pH treatments resulted in only two significant and annotated proteins associated with biological processes. Oxidation stress exhibited higher expression at pH 7.6 while smooth muscle contraction exhibited lower expression at pH 7.6. Overall, a decrease in the expression of important functions such as reduction of oxidative stress and smooth muscle contraction indicate negative impacts of thermal stress on S. flabelliformis.

Overall, sponges are expected to be more resilient under climate change conditions than calcifying organisms such as corals. Although low pH produced little response in the sponge holobiont, S. flabelliformis exhibits a temperature threshold of approximately 31.5 °C. At this temperature, microbial community composition and protein expression shift with negative implications for the functional roles of sponges.