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Reference : UMR8227-SOPLAB-023
Workplace : ROSCOFF
Date of publication : Saturday, June 5, 2021
Scientific Responsible name : DITTAMI Simon
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 September 2021
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly
Description of the thesis topic
The Ascophyllum nodosum holobiont – evaluation of the impact of season, origin, and microbial communities on the biological properties of extracts
Ascophyllum nodosum is a common brown alga found along the coasts of the North Atlantic Ocean. A unique feature of this alga is its mutualistic association with the fungal endophyte “Mycophycias ascophylli” and other fungi and bacteria. Very little is known so far about the importance of these symbionts for the alga, except that they are believed to protect A. nodosum germlings from desiccation and benefit their fitness. A. nodosum also constitutes a prominent raw material used for many years to produce plant biostimulants. Different bioactive molecules such as original polysaccharides (laminarin, fucoidans, alginates), mannitol, betaines, polyamines, and polyphenolic compounds could be involved in these properties, but the exact active molecules and their origin remain unknown. Furthermore, we still have no information about how interactions with symbionts may impact the biosynthesis of these compounds, and thus also the biostimulant properties of A. nodosum extracts. This thesis will contribute to filling these aforementioned gaps in knowledge combining multi-omics and systems biology approaches:
- By evaluating the seasonal changes of the A. nodosum-associated microbiome at two sites, one in Brittany, and one in Ireland. This will involve regular sampling for barcoding experiments to identify fungal and bacterial symbionts.
- By analyzing functions encoded by the microbiome via metagenome sequencing for both sites. Assembly and annotation will be carried out for all components of the holobiont: the algal host, as well as the algal and bacterial symbionts.
- By in silico predictions of metabolic complementarities between partners, specific metabolic compounds of interest, as well as simplified microbial communities based on these assembled metagenomes.
- By testing the effects of bacteria and fungi via co-culture experiments with A. nodosum on the metabolic properties of the holobiont and later on biostimulant properties of algal extracts.
This work will be carried out in the context of the SEABIOZ ANR project with both academic partners (Roscoff Biological Station, IRISA Rennes, Natural History Museum Paris) and an industrial partner (Agro Innovation International, CMI Roullier, St. Malo). This doctoral contract is part of a multidisciplinary approach at the crossroads between massive sequence data mining, metabolomics and system biology. The thesis work will cover primarily fundamental research, but there will be links to potential industrial application. The candidate will carry out his/her experimental work at the Laboratoire de Biologie Integrative des Modèles Marins at Roscoff (LBI2M, UMR8227, SU/CNRS) using the tools of the Genomer and ABIMS platforms (FR2424, Illumina Mi-Seq, Nanopore MiniION, Galaxy suite for data processing) as well as the competency networks of the EMBRC-Fr infrastructure. The collection of biological samples will be carried out in the field in Brittany and Ireland. The expertise in bioinformatics will be provided by the Institute of Research in Informatics of Rennes (IRISA, UMR6074, Anne Siegel group) and by the ABIMS platform at Roscoff. The research will be supervised by Simon Dittami (CRCN CNRS, UMR8227, LBI2M) and Catherine Leblanc (DR CNRS-HDR, LBI2M). The candidate will be enrolled at the doctoral school 227 of Sorbonne University and Natural History Museum in Paris.
Constraints and risks
The PhD student will handle organic solvents under fume hoods, conduct microbiological experiments using non-pathogenic strains for humans while complying best laboratory practices and quality standards (ISO 9001 and NFX 50-900).
Applications should include a detailed CV; at least two references (persons we can contact); a one-page cover letter; a one-page summary of the Master's thesis; Master's or engineering school grades obtained to date. Please applied via the
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