Project 10: The influence of bacteria on the adaptation to changing environments in Ectocarpus: a systems biology approach

Based at the CNRS/UPMC in Roscoff, the objective of this research is to decipher the role of bacteria during the acclimation of the brown alga Ectocarpus subulatus to changing salinity using a three step approach:

1) Bacteria will be isolated from algal cultures in order to test the influence of specific bacteria on the E. subulatus holobiont and identify those important for freshwater acclimation.

The physiological state of the alga, e.g. survival, growth, as well as changes in the bacterial community, including their localization (FISH), will be monitored during the acclimation to low salinity (via a secondment at Marine Science Scotland); Alternatively, acclimation of the Ectocarpus holobiont with reduced microbiome will be examined.

2) The genomes of selected bacteria will be sequenced, assembled (via a secondment at VIB), annotated (automatically and manually), and used for the reconstruction of metabolic networks to assess bacterial metabolic capacities. Alternatively, metagenome analyses with a minimalized microbiome will be used for metabolic network reconstruction. Comparative genomics and metabolic network analysis between the bacteria/bacterial communities will enable the identification of key pathways in “beneficial” bacteria. Integrated analysis with a metabolic network for E. subulatus, which is currently under construction, will be carried out to highlight possible points of interaction and complementarities between algae and bacteria; and

3) These hypotheses will be tested by transcriptomic and metabolite profiling (via a secondment at FSU Jena) during the acclimation to low salinity. The data produced will be analysed in the context of the generated metabolic networks to understand the dynamics of algal/bacterial interactions during the acclimation.

This research is expected to deliver:

1) A model system to study algal-bacterial interactions along a salinity gradient. This includes genomic resources and metabolic networks for freshwater tolerance-conferring and non-freshwater tolerance-conferring bacteria.

2) Combined transcriptomic and metabolomics dataset during the acclimation to low salinity to highlight processes important during this transition.

3) Location of selected bacterial taxa in/on the alga using FISH experiments.

Hetty Kleinjan has been appointed Ph.D. researcher for this project at CNRS/UPMC. Originally from the Netherlands, she started her research in July 2015, after completing her training at the European Molecular Biology Laboratory in Heidelberg where she was able to build on her understanding of in vitro bacterial communities and the resilience of microbiota against disturbance by pathogens. This work also allowed Hetty to gain experience in the use of various molecular and microbiology techniques, such as bacterial cloning, culturing, high-throughput assays, sequencing, and fluorescent microscopy. Hetty completed an MSc degree in Biology in 2014 at the Wageningen University. For her thesis, she studied the expression of intestinal antimicrobial proteins in mice. With a strong interest in host-microbial interactions, Hetty’s research at CNRS/UPMC will allow her to better understand how symbionts can contribute to the wellbeing of algae.