DC7 - Phylogenomics and physiology of oomycete pathogens infecting red algae, brown algae and diatoms towards biocontrol and biosecurity

Advisors: Claire Gachon, Sigrid Neuhauser, Yacine Badis

Location: Muséum National d’Histoire Naturelle, Paris.

How to apply for this position
The submission deadline for this project was May 15th, 2024 and we are currently not accepting any new application.

Scientific context:

Red algae are commonly infected by intracellular oomycetes pathogens, most commonly known as Olpidiopsis, Pontisma or Sirolpidium spp. Their diversity, abundance and prevalence worldwide, both in farms and wild seaweed populations, has only started to be recognised a few years ago, via a combination of microscopy, laboratory cultivation and metabarcoding studies [1,2]. Unexpectedly, evidence has been accumulating over the past decade that these pathogens are phylogenetically related to equally diverse and little-known pathogens of diatoms, brown algae and dinoflagellates [e.g. 3]. The phylogenetic relationships and evolutionary history of this vast, presumably monophyletic, group of pathogens remain mostly unresolved [4].  The exponential growth of seaweed aquaculture, combine to the increasing reliance of mankind on marine resources and ever-growing anthropogenic pressures on coastal environments all raise many questions as to how to mitigate the impact of these pathogens on commercial production as well as their impact on wild seaweed  populations [5,6]. Thanks to a long-standing effort including field sampling and protocol development, laboratory cultures, preliminary transcriptomics and genome skimming data have been obtained for over 15 different of these organisms. Comparable to Ectocarpus for brown algae, the filamentous red alga Bangia sp. has been established as an excellent laboratory model to grow various pathogen species, investigate their virulence mechanisms, as well as the defence reactions of their red algal host. 

Objectives and expected results: 
Building on existing datasets and protocols, this PhD aims to:

1) Augment our current collection of “Olpidiopsis”-like oomycetes infecting commercially cultivated red algae, characterise them with validated microscopy, microbiology and phylogenomics methods, with a focus on commercially-important red algal hosts such as Porphyra spp., Palmaria palmata, Gracilaria spp. and Asparagopsis armata (collaboration with ALGA+ and HORTIMARE). 
2) Using Bangia as a laboratory model, investigate with transcriptomics and cell biology methods (e.g. FISH, ref. 7) the virulence strategies of selected oomycete strains and the defence responses of their red algal host with contrasting susceptibilities to infection. 
3) Integrate these novel datasets with similar datasets obtained by us on biotrophic oomycete pathogens of brown algae and diatoms to identify their shared virulence strategies and therefore identify potential targets for future biocontrol.

Newly-obtained knowledge on the phylogenomics, cell biology and physiology of novel oomycete pathogens infecting cultivated red algae shall directly inform the development of diagnostic tools in farms and contribute to the identification of potential biocontrol targets. Additionally, the planned characterisation of pathogen diversity with microscopy and next-generation sequencing parallels the work of other PHABB PhD students on microalgae, and thus holds the promise of complementary discoveries. A close interaction with seaweed hatcheries (via a secondment and summer schools) will ensure the relevance of the research to seaweed producers.

Planned secondment(s): 
At HORTIMARE to learn industrial algal cultivation and husbandry, and deploy microscopy and molecular diagnostic tools in an industrial setting
At CNRS-Roscoff with Yacine Badis to learn high-end custom bioinformatics scripting

Candidate profile: 

We would like to encourage applications from candidates with diverse backgrounds, and therefore shall welcome applications from candidates who may not fully meet all specifications below. 

Most important is an appetite for crossing disciplines, an ability to learn quickly a breadth of theoretical and practical skills, and a willingness to work on fundamental concepts towards their application to concrete situations. Essential qualifications are a Master degree in Microbiology, Molecular biology, Functional or evolutionary genomics, Plant physiology, or a related discipline, with demonstrable knowledge of biology. Some knowledge of host-pathogen interactions, next generation sequencing technologies would be an advantage. Relevant work or professional experience would be to have successfully completed (a) laboratory project(s), e.g. as part of a degree. Laboratory experience in microbiology, microscopy, molecular biology, or an omics technique (e.g. metabarcoding, genome annotation, transcriptomics), some fluency with statistics, scripting or programming skills would all be a plus. The applicant should be willing and able to perform secondments and participate in training programs at the facilities of other consortium members. Excellent interpersonal skills, the ability to think independently, the motivation and ability to work collaboratively in an international team, good oral and written communication skills, as well as strong organisational skills are also important for this position. 

References: 
[1] Y Badis, TA Klochkova, J Brakel, P Arce, M Ostrowski, SG Tringe, GH Kim, CMM Gachon. (2019) Hidden diversity in the oomycete genus Olpidiopsis is a potential hazard to red algal cultivation and conservation worldwide. European Journal of Phycology, doi: 10.1080/09670262.2019.1664769.
[2] Y Badis, TA Klochkova, M Strittmatter, A Garvetto, P Múrua, JC Sanderson, G-H Kim, CMM Gachon. (2018) Novel species of the oomycete Olpidiopsis potentially threaten European red algal cultivation. Journal of Applied Phycology, doi: 10.1007/s10811-018-1641-9. 
[3] A Garvetto, MM Perrineau, M Dreβler-Allame, E Bresnan, CMM Gachon. (2020) Ectrogella parasitoids of the diatom Licmophora sp. are polyphyletic. Journal of Eukaryotic Microbiology, 67 (1), 18-27.
[4]  GC Zuccarello, CMM Gachon, Y Badis, P Murúa, A Garvetto & GH Kim (2024) Holocarpic oomycete parasites of red algae are not Olpidiopsis, but neither are they all Pontisma or Sirolpidium (Oomycota). Algae, doi: 10.4490/algae.2024.39.3.8.  
[5] P Murúa, A Garvetto, S Egan & CMM Gachon (2023). The re-emergence of phycopathology: when algal biology meets ecology and biosecurity. Annual Reviews of Phytopathology  doi: 10.1146/annurev-phyto-020620-120425. 
[6] J Brakel, R Sibonga, R Dumilag, V Montalescot, I Campbell, E Cottier-Cook, G Ward, V Le Masson, T Liu, F Msuya, J Brodie, PE Lim, CMM Gachon. Exploring, harnessing, and conserving genetic resources towards a sustainable seaweed aquaculture. (2021) Plants, People, Planet doi: 10.1002/ppp3.10190. 
[7] J Badstöber, CMM Gachon, J Ludwig-Müller, AM Sandbichler, S Neuhauser.  Demystifying biotrophs FISHing for mRNAs to decipher plant and algal pathogen-host interactions at the single cell level. (2020) Scientific Reports  10: 14269.