GENOmics of Marine Algae and their Pathogens: a transcriptomic picture of pathogenicity, disease and resistance using the Ectocarpus-Eurychasma model

Lead Research Organisation: Scottish Association For Marine Science
Department Name: Scottish Association For Marine Science

Abstract

DO ALGAE EVER GET SICK, AND WHY DOES IT MATTER?
Brown algae make up over 70% of the biomass of our rocky seashores. As the seaweed aquaculture industry grows exponentially worldwide, their economic importance is increasing rapidly. In the UK and other Western countries, algae are being considered as a potential sustainable biofuel source. The development of experimental aquaculture facilities is currently attracting considerable investment in the context of the ongoing transition towards a low carbon economy.
Like any other living organism, brown algae are plagued by diseases caused by fungi, bacteria or viruses. Among them, Eurychasma dicksonii - the parasite that I am studying - is very common and widespread. However, very little is known about its biology, or indeed the biology of similar algal pathogens. This lack of information hampers our capacity to comprehend the impact of diseases in natural algal populations, and more broadly, on marine ecosystem functioning. Additionally, the interplay between natural populations, crops and their pathogens, which are central to the design of management policies concerning any agricultural production, remain entirely unknown for marine seaweeds.
For these reasons, I have developed a laboratory model between Eurychasma and the filamentous brown alga Ectocarpus siliculosus, which I suggest to use in GenoMAP to help tackle these questions.

PATHOGENICITY AND IMMUNITY, THE YIN AND YANG OF DISEASE
In GenoMAP, I propose to apply cutting-edge genomics techniques to identify the gene repertoire of Eurychasma and elucidate the molecular basis of its pathogenicity. Since Eurychasma is also related to many other pathogens that have a devastating effect in agriculture (e.g. potato blight, grape mildew), aquaculture (fish saprolegniosis, crayfish plague), and on natural populations (sudden oak death), a cross-species comparative genomic analysis will have wide-ranging implications for understanding the biology and evolution of this group of pathogens (so-called oomycetes).
Secondly, I propose to conduct a large scale transcriptomic experiment to follow the expression of Ectocarpus and Eurychasma genes in infected disease-susceptible and disease resistant algal strains. This will give us information on the molecular basis of disease resistance in the brown alga Ectocarpus, whilst also shedding light on the strategies used by Eurychasma to defeat the immune system of its host. Indeed, and although not always successful, algae actually do have an immune system and try to defend themselves against pathogens. My results so far show that some of them indeed resist Eurychasma infection attempts by inducing the early death of infected cells, which prevents reproduction of the pathogen and subsequently, the spread of infection.
Finally, this dataset will provide a first insight on the natural variation between disease-susceptible and disease-resistant algal strains. In particular, In particular, I will investigate the variation in the so-called LRR-ROCO and NB-ARC-TPR gene families. Both display striking structural and evolutionary features that make them excellent candidates for being involved in pathogen perception.

Overall, GenoMAP will help us understand some of the fundamental biological mechanisms underpinning algal-host pathogen interactions. In the future, this new knowledge will be invaluable to address ecologically-relevant questions from a position of strength and novelty. Thus, in conjunction with ongoing parallel work, GenoMAP will go one step further towards the development of new evidence-based concepts on the fundamental - yet largely overlooked - impact of eukaryotic algal pathogens in marine ecosystems.

Planned Impact

Besides the academic beneficiaries detailed elsewhere, other groups will benefit from the research undertaken in GenoMAP.

1) The most important long term beneficiaries are government bodies and policy makers, in charge of designing science-informed environmental management policies. Scottish and UK laws are currently being reviewed to cover seaweed aquaculture activities. New policies will need to take into account the environmental impact of these new activities on natural algal populations and marine ecosystems as a whole.

2) The Asiatic seaweed aquaculture sector, which has undergone a drastic transition towards intensive production over the last few decades, is an eloquent example of forthcoming difficulties for Western countries: whilst mostly regarded as anecdotal in the past, diseases are now responsible of large-scale epidemic outbreaks in seaweed farms, cause massive economic loss, with hardly any control method in place. GenoMAP will develop the national capacity to support the nascent UK seaweed culturing industry, by creating relevant expertise and anticipating forthcoming difficulties. This aspect directly addresses NERC's mission to deliver a highly-skilled workforce and generate transferrable skills for the UK economy.

3). We think that NERC will also benefit from GenoMAP. The recent NERC NEOMICS consultation has clearly spelled out the need for NERC to develop a coordinated genomics strategy and build up its capacity in order to deliver world-class leadership (NEOMICS report, Oct 2010). In parallel, the NERC Oceans 2025 Advisory Board recently identified marine genomics as an area the potential of which should be better addressed, in the view of its relevance to NERC's missions and priority areas (O2025 PAB recommendations, May 2010).

GenoMAP's comprehensive impact plan has been designed to efficiently disseminate the results of the project to academics, end users and the general public through a diversity of complementary undertakings, and with the support of communication professionals.

Publications

10 25 50
 
Title Creative fashion design based on marine science 
Description Joint project undertaken with the start-up Crubag (www.crubag.co.uk) to communicate scientific outputs of a NERC New Investigator grant on algal diseases to the general public. Microscopy pictures of diseased seaweed were used as the basis for the creative design of a fashion collection. 
Type Of Art Artefact (including digital) 
Year Produced 2014 
Impact This work has already earned Crubag local and regional recognition in several business events (e.g. BEST festival in Inverarray) and fashion shows (Festada festival in Oban). 
URL http://www.crubag.co.uk
 
Description Our objective was to explore disease and immunity in marine seaweeds, harnessing the experimental power of next generation sequencing technologies. A high impact paper has already been published (doi: 10.1093/molbev/msv049) based on the data generated and at least two others are in preparation. Additionally, this New Investigator award has supported the establishment of a broad knowledge body on the molecular and cell biology of marine oomycete pathogens.
Exploitation Route Whilst the grant had a strong blue sky emphasis, our findigs are relevant to the ongoing development of seaweed aquaculture in the UK, and elsewhere in the world. Unexpectedly, we have also described a new family of higly unusual proteins potentially involved in pathogen recognition. This serendipitous discovery has far-reaching conceptual implications in our understanding of adaptive immunity, which relates for example to widely-used vaccination. Overall, the results of this New Investigator award have enabled me to aggregate a dynamic research community around little-studied algal parasites, especially consortia, notably ALFF and GENIALG. Note that the IOF GLOBALSEAWEED pump-priming networking grant is also a spin-off of this award, with a particular focus not only on cutting-edge research, but also on science-into-policy and interaction with the private sector.
Sectors Agriculture, Food and Drink,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

URL http://www.sams.ac.uk/claire-gachon/copy_of_genomap
 
Description In line with the strong blue-sky emphasis of this grant, the findings of the grant have initially been used as a support to further research work. In this respect, it is worth noting that this award enabled us to leverage several other major projects from blue-sky and applied funders. These subsequent grants, especially GlobalSeaweed, and the GCRF GlobalSeaweed-STAR have now started to enable take-up of these results beyond the scientific community. Please see the corresponding reports for details on our policy-making, community-building and other activities.
Sector Agriculture, Food and Drink
Impact Types Cultural

 
Description CNRS EC2CO
Amount € 18,000 (EUR)
Organisation National Center for Scientific Research (Centre National de la Recherche Scientifique CNRS) 
Sector Academic/University
Country France
Start 01/2014 
 
Description Elite early career travel award
Amount £500 (GBP)
Organisation Association for the Sciences of Limnology and Oceanography (ASLO) 
Sector Charity/Non Profit
Country Global
Start 07/2012 
End 07/2013
 
Description GCRF GlobalSeaweed* - Safeguarding the future of seaweed aquaculture in developing countries
Amount £5,419,059 (GBP)
Funding ID BB/P027806/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 12/2021
 
Description GENetic diversity exploitation for Innovative macro-ALGal biorefinery
Amount € 10,885,817 (EUR)
Funding ID 727892 
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 01/2017 
End 12/2020
 
Description Genomia Fund Pilot project
Amount £60,000 (GBP)
Organisation Genomia fund 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2014 
 
Description Genomia Fund Pilot project
Amount £50,000 (GBP)
Organisation Genomia fund 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2014 
 
Description H2020-MSCA-ITN-2014
Amount € 3,796,000 (EUR)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2015 
End 12/2018
 
Description IOF pump-priming plus networking call
Amount £414,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 04/2014 
End 12/2017
 
Description International Exchanges 2014 NSFC
Amount £5,200 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 02/2015 
End 03/2017
 
Description NERC Big Data Capital call
Amount £338,000 (GBP)
Funding ID NE/L013029/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 11/2013 
End 03/2014
 
Description PEER funding
Amount £800 (GBP)
Organisation Marine Alliance for Science and Technology for Scotland 
Sector Academic/University
Country United Kingdom
Start 06/2014 
End 07/2014
 
Description Visiting fellowship
Amount £4,800 (GBP)
Organisation Marine Alliance for Science and Technology for Scotland 
Sector Academic/University
Country United Kingdom
Start 01/2016 
End 07/2016
 
Title Prevention or treatment in algae of diseases induced by protistan pathogens 
Description The present invention relates to the use of a pyrenocine compound or a pyrenochaetic acid compound for the prevention or the treatment in algae of diseases induced by protistan pathogens. The present invention also relates to a new pyrenocine compound. 
IP Reference WO2017125775 
Protection Patent application published
Year Protection Granted 2017
Licensed No
Impact This patent application describes what is essentially the first-ever phytosanitary compound applicable to marine algal cultivation worldwide. Efforts are ongoing to licence the molecules. However, we believe that the main impact of this patent application is to provide a proof-of-concept for the feasibility and applicability of discovering and using phytosanitary products in open sea, and will accrodingly stimulate further research and investment into this novel market.
 
Description Invited seminar at University Innsbruck (Austria) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk: Gachon et al. "Pathogens of red and brown algae insights into genomes and transcriptomes"
Year(s) Of Engagement Activity 2017
 
Description Media Coverage of Crubag initiative 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact BBC coverage of Sic-art initiative by the start-up Crubag, with support by NERC to develop a fashion collection using images of diseases seaweeds
Year(s) Of Engagement Activity 2016
URL http://www.bbc.co.uk/news/uk-scotland-highlands-islands-35380323
 
Description Media Coverage of Crubag initiative 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Media coverage of the Crubag initiative, targeted at business professional
Year(s) Of Engagement Activity 2016
URL http://www.europeanmarinesciencepark.co.uk/news-events/2016/fabulous-phycological-fashion-a-top-draw...
 
Description Oral presentations & poster at the International Seaweed Symposium (Copenhagen, Denmark) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation: Gachon et al. "Pythium porphyrae, the agent of the red seaweed rot disease: a reformed plant pathogen?"
Oral presentation: Gachon et al."Introducing nephelometry for non-invasive biomass and growth monitoring macroalgae"
Poster: Strittmatter et al. "Mechanisms and heritability of disease resistance in brown algae"
Year(s) Of Engagement Activity 2016
URL https://www.iss-2016.org/ehome/index.php?eventid=130925&