Comparative genomics of marine algal microbiome

Type de poste
Niveau d'étude minimal
Dates
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce
Localisation
Adresse

Place Georges Teissier
29680 Roscoff
France

Contacts
Elham Karimi
Simon Dittami
Erwan Corre
Email du/des contacts
elham.karimi@sb-roscoff.fr
simon.dittami@sb-roscoff.fr
corre@sb-roscoff.fr
Description

Subject

Comparative genomics of marine algal microbiome: Pangenomes and Phylogenomics of marine Erythrobacter sp. in the context of host-symbiont interactions

Objectives

1. To perform a comparative genomics survey of Erythrobacter sp. with emphasis on pangenomic and accessory genes that govern different species/strains
2. To reveal the unique genes which differentiate pangenomes of symbiotic Erythrobacter from marine free-living Erythrobacter
3. To inspect the distinctive genes in host-associated Erythrobacter bacteria and their likely host fitness-enhancing value, within the marine algal holobiont

Dates
May 2020 to July 2020 (Adjustable)

Financial gratuity
568,76 Euro per month

Research plan and strategy
Marine algae are critical organisms in the intertidal zone due to their cultural, ecological, and economic importance. Like most organisms, algal fitness is dependent on their associated bacteria. The interactions between symbiotic prokaryotes and their multicellular hosts, together referred to as holobiont, have been the subject of hot discussions in the last decade. Although, the importance of the associated bacteria has been established by different researches, much remains unknown about their in situ ecological functions.
So far in our group, about 500 bacteria were cultivated from a small filamentous brown alga named Ectocarpus. This alga is a laboratory model and its genome was sequenced in 2010. Furthermore, we have recently accessed 72 draft genomes of bacteria associated with Ectocarpus. Among these genomes, Erythrobacter is of particular interest as this aerobic marine bacterium that has been isolated from seaweeds, sponges, and corals. In silico analyses of the metabolic network suggest its metabolism to be highly complementarity to that of Ectocarpus – its presence may thus enhance the fitness of alga. For instance, Erythrobacter is capable of producing pyridoxine (Vitamin B6), carotene (protection against reactive singlet oxygen and blue light radiations), and S-glutathione (protection against oxidative stress). Moreover, the consumption of methylmercury and arsenate (detoxification) has been observed by this genus. All of these features constitute potential benefits for the algal host.
In addition to the genome of Erythrobacter from Ectocarpus, there are112 publicly available marine genomes of Erythrobacter in Genbank. The aim of this internship is to determine what are the genomic features distinguish free-living form symbiotic members of the genus Erythrobacter and to interpret the results in light of algal bacteria interactions.

In the framework of stage M1, the trainee will accomplish the following tasks during her/his stay at ABIE and ABIMS groups:

1. Exploring and compile available genomes and metadata
2. Comparison of gene contents based on orthology
3. Analysis pan/core genome
4. Whole genome alignments/ pairwise alignments
5. Comparison of gene content in terms of function

Desired skills and interests
Familiar with R statistical analysis, interest in collaboration with different members of the group, working knowledge of English, organizational skills and detail-oriented.

Equipe adhérente personne morale SFBI
Equipe Non adhérente