The Planktonic Microbiome of Coral Reefs: Community Structure and Function in the context of Reef Health

Name of applicant

Herdís Guðlaug Rabølle Steinsdóttir




Inter-University Institute for Marine Sciences in Eilat


DKK 700,000



Type of grant

Internationalisation Fellowships


This project will investigate the community structure and metabolic function of the microbes that live in the waters surrounding coral reefs: the planktonic microbiome. The microbes that constitute this planktonic microbiome of coral reefs can grow at rates up to 50-times faster than what is seen in similarly nutrient-poor waters of the open ocean, and we, therefore, have strong evidence that individual coral reefs sustain a unique planktonic microbiome. But we still know little about what such a microbiome looks like and how it relates to coral health, resilience and stress. With this project, I will study the planktonic microbiome in both healthy and stressed coral reefs, explore their temporal dynamics and investigate the differences between them.


The health and functioning of marine ecosystems are critically dependent on microbes. They are major primary producers, drivers of biogeochemical cycles and agents of disease. Coral reefs are areas of high biodiversity and productivity that offer great ecological and cultural value, as well as significant economical benefits to the nearby communities. By linking the planktonic microbiome with changes in the benthic coral reef community, the project will go a long way in understanding how stress, for example from rising temperatures and local pollution, translates into wholesale shifts in biogeochemistry.


The project will be carried out at the Inter-University Institute of Marine Sciences in Eilat (IUI), Israel, in close collaboration with Derya Akkaynak, an expert in underwater computer vision from the University of Haifa, and Miguel Frada, an expert in marine microbial ecology from the Hebrew University of Jerusalem. We will study the relationship between the planktonic microbiome and the benthic community by unifying three state-of-the-art methods, namely an advanced underwater computer vision algorithm to characterize the benthic communities, flow cytometry to visualize and count individual planktonic cells, and high-throughput DNA sequencing to analyze phylogeny and metabolic function of the planktonic microbes. The Gulf of Eilat is an ideal location to pursue this project as it harbors diverse coral reef systems, from thriving ones in protected nature reserves to heavily stressed areas near rapidly developing urban and tourist districts.

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