Characterizing the microbiome associated with the gastric cavity of solitary cup corals

Master Thesis subject (30 ECTS)
The role of the gastric cavity of corals as hotspot for microbial mechanisms of ecosystem-scale relevance is still rather unexplored. Biochemical conditions within these semi-closed, often anoxic, microniches likely foster metabolic pathways not present in the well-oxygenated surrounding seawater environment. Solitary cup corals living off the south coast of Portugal will allow shedding light on the overlooked relations established between coral hosts and the microbial communities inhabiting their gastric cavity. As a first step to unravel such interactions, we propose to investigate the genetic variation of the microbial communities associated with the coral’s gastric cavity, both between distinct host species and across geographic locations. Solitary corals are often disregarded in comparison to their colonial homologs. Furthermore, azooxanthellate corals (without photoautotrophic endosymbionts) lack the capacity to build reefs and are not considered ecosystem keystone species. Solitary cup corals such as the ones living off the south coast of Algarve (Portugal) seem to accumulate a double jeopardy regarding their conservation and that of the habitats they occupy, because of being neither colonial nor zooxanthellate. With this study we ultimately aim at placing these corals in the conservation spotlight by using them as model systems to study the influence of the external environment as well as that of the host on the diversity of microbes inhabiting the gastric cavity. Because the coral’s gastric cavity is a semi-closed sub-environment, it experiences conditions divergent from the surrounding seawater environment, with permanent or temporary anoxic conditions, low but fluctuating pH and high nutrient concentrations. It is therefore possible that the gastric cavity functions as hotspot for biological activity and offers the necessary conditions for the presence of host-specific and habitat-specific prokaryotic communities which we hypothesize to be phylogenetically distinct from those inhabiting the surrounding environment. Exploring the coral gastric cavity in this project will contribute to characterize the uniqueness versus ubiquity of the microbial communities associated to it and to determine whether there is a core microbiome typical of the gastric cavity of all corals. The project aims at determining the influence of host and location on the in situ microbial community composition by comparing the microbiomes of the gastric cavity across geographical scales and between different coral hosts. SCUBA-diving will be used to collect coral samples off the south coast of Portugal (based at CCMAR) covering different locations and spatial scales. Target scleractinian species include Caryophyllia smithii and C. inornata, Leptopsammia pruvoti, Balanophyllia regia, Polycyathus muellerae, Phyllangia mouchezii, Hoplangia durotrix, Paracyathus pulchellus and Pourtalosmilia anthophyllites. Sample numbers will be kept low to reduce impact on the ecosystem. Microbiome characterization of the gastric cavity will be done by taking samples with blunt micro-needles to avoid epithelium perforation. Adjacent habitats (seawater, sediments and macroalgae) will be sampled as reference. All samples will be flash-frozen in liquid nitrogen. Intact representative specimens will be collected for taxonomic identification. Physicochemical parameters such as temperature, salinity, total OM, nutrient profile and pH, will be measured near the sampled corals. These sampling efforts will be complemented by underwater collections already available from rocky areas and inside caves near Sagres, Vilamoura and Tavira, in Algarve. Microbial community composition will be investigated for all samples (after DNA extraction optimized for small volumes) by 16S rRNA gene tag-amplicon sequencing using prokaryotic universal primers (targeting both Archaea and Bacteria). Analysis will follow the QIIME pipeline. Databases summarizing differences in community composition between distinct hosts and locations will be analyzed using specific R packages for multivariate statistics.
Relevant experience with molecular biology, excellent written and spoken English, demonstrated capacity to handle large datasets, motivation to do long working hours in the lab, willingness to work both independently and as part of a larger team.
Number of students: 
academic year: 
Contact person email: 
contact person first name: 
Dr. Pedro Frade
Other people involved: 
Prof. dr. Ester Serrão as promoter and Dr. Rodrigo Costa as co-supervisor.
Reference Number: RP-39961