Workshop for 'omics methodology development: use of secretome enriched meta-transcriptome sequencing for understanding interactions in diseased corals

Coral reefs are beautiful, unique and important ecosystems. Coral ecosystems are home to a huge range of biodiversity, conduct important ecosystem services and support many tropical fisheries and their associated human societies.

Coral reefs are dying at an unprecedented rate leading to catastrophic ecosystem collapse, which is threatening biodiversity conservation and reducing the sustainability of many tropical fisheries around the globe. Climate change, over-fishing and pollution are recognised as the major contributing factors to coral reef decline. Furthermore, the significant increase in coral infectious disease load and diversity are also recognised as critical threats to coral reef ecosystems. In many cases climate change, over-fishing and pollution are recognised as the drivers of increased coral disease load and diversity.

Corals rely on complex interactions with the microbes that live on and inside their bodies. The nature of these interactions, both beneficial and negative, are therefore dependant on numerous environmental factors and ecological interactions. These interactions are incredibly difficult to study in natural coral reef ecosystems and very difficult to reconstitute accurately in laboratory experiments. As such we drastically need new methods that make use of cutting edge large-scale DNA sequencing platforms so we can study these interactions directly in natural environments.

Many of the complex interactions that corals undergo, with the microbes that live on and inside their bodies, are mediated through genes that encode proteins that exit out of the cell into the external environment. These proteins are functional in the external environment, interacting with other microbes and the host coral cells. In some cases, these proteins function to cause disease, for example by killing or perturbing the coral cells.

The aim of this project is to bring together an international community of scientists to develop a new methodology for studying how microbes interact with coral (and vice versa) through specifically sampling and sequencing the genes that encode the specialised proteins that exit the cell and function in the external environment. By developing this protocol, we will have a new powerful and direct method that will enable us to study how microbes interact with coral to cause disease. Having established this method we will build public access resources and detailed protocols so that other scientists can then use this methodological approach to study a range of coral reef diseases and further adapt the approach for the study of additional infectious disease interactions in natural environments. This is important because it will unlock the door to studying a whole range of complex interactions in new ways directly from the environment, interactions which cannot be realistically recapitulated in a laboratory setting.

Findings from this project will provide a new 'omics tool for the analysis of natural environmental samples. As such, the communication of the methods developed, the detailed protocols and bioinformatic approaches to subsequent sequence analysis (including code), need to be communicated across a number of fields to facilitate uptake of this new approach. Additional communities and stakeholders that will benefit from the research are detailed below along with information regarding how we will engage these communities with our research findings.

Education and Outreach

The project provides the tools and resources for a number of education opportunities. As such the project, film and photography materials generated from the field workshop will be used to develop a number of opportunities for education and public engagement.

1) Consistent with our track record, we will undertake a range of public lectures and school trips to support outreach on the subject of coral decline and host parasite interactions, providing the foundation for greater understanding of the need for conservation, how it can be achieved and who is responsible. Such opportunities will be communicated in an inspirational manner focusing on the adventure of research with the aim of inspiring members of the public, especially school-aged children and young people, to take up science.

2) We will produce a short abstract film for the general public to report the themes of this project.

3) Working with Digital Explorer (CIC) we will develop curriculum materials for Key Stage 3 and GCSE Geography and Science students looking at the role of infectious disease in coral reef ecosystem health.

NGOs and governmental organisations charged with ecosystem protection and policy.

The project provides the tools and resources to understand coral ecosystem health in new ways, monitor infection states and provide data for planning conservation efforts. As such the results and application of this approach will be communicated with governmental organisations and coral reef conservation organisations.

1) We will produce a one-page briefing note focusing on the new scientific capability achieved and how it can be used for conservation planning and environmental health tracking.

2) We will send the one-page briefing note to a range of governmental organisations and NGOs charged with coral reef conservation.