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Characterization of the diversity and function of plankton associated microbiota

Periodic Reporting for period 1 - DYNAMO (Characterization of the diversity and function of plankton associated microbiota)

Reporting period: 2016-10-03 to 2018-10-02

Ever since living organisms arose in the oceans, they have competed for resources and space. However, many planktonic species developed peaceful cooperation involving mutualistic interactions between two partners. Within unicellular eukaryotes, such symbiotic association between heterotrophic hosts and microalgae is widespread and sustain ecologically important taxa, such as the Rhizaria, in the open ocean. While knowledge of bipartite symbiosis has greatly improved, it is only recently that scientists disclosed more intricate relationships involving additional partners such as bacteria. Wherever bacterial communities (i.e. microbiota) have been found in tight association with other organisms (e.g. humans or plants), its critical role for the biology and ecology has been demonstrated. The DYNAMO project explored the diversity of multipartite symbiosis in the plankton and aimed at characterizing the cellular metabolites they produce. Radiolarians have been used as relevant model for marine ecology. An original combination of single-cell sorting and sequencing coupled with microscopy has been used to characterize and specifically localize the partners of the association. Then, a cutting-edge approach of single-cell genetics and of metabolomics, allowed us to better describe the bacterial diversity and better understand the role of the associations in the physiology of the holobiont. We tried to bridge the gap between a descriptive approach and the functional understanding of the biological processes involved in plankton associated microbiota. DYNAMO provided an innovative perspective on marine ecological research and represented an important step in my career development with the ambition to place me as one of the very few experts in the field of plankton metabolomics in Europe.
The project started in October 2016 at the Biological Sation of Roscoff (SBR) in the Diversity and Interaction within Oceanic Plankton team (DIPO, UMR7144). The first phase of the project was dedicated to the sampling of planktonic organisms on the field at the Laboratoire d´Océanographie de Villefranche-sur-Mer (LOV, France), cultivation of associated bacteria and metabarcoding of symbiotic bacterial partners (WP1). The second phase focused on the optimization of protocols for metabolite profiling of the partners taken separately and of the whole holobiont (WP2). Because of analysis issues faced by the project during the second phase, the WP2 was re-directed towards a more targeted metabolomics approach, with a special interest given to antimicrobial peptide extraction. This experiment was conducted at the University of Lille in collaboration with Aurélie Tasiemski. A total of three field sampling trips in Villefranche-sur-Mer were finally done to collect enough material for the different analyses. Labelling experiment using the CARD-FISH approach is planned in winter 2019. The results from WP1 allowed to describe a rich bacterial community associated to rhizarian representatives and particularly one strain of bacteroidetes that specifically interacts (possibly a symbiosis) with collodarians. I also developed a new protocol to sequence amplicons using nanopore sequencing. WP2 will give some insights about what mechanisms could explain special interactions between eukaryotic hosts and bacterial partners. The last months of the project involved the writing of two papers that are planned to be submitted first semester of 2019. Overall, results from the project were disseminated through the participation of three international conferences and information about symbiosis and the concept of holobiont was communicated to the general public through the creation of a scientific movie festival in Roscoff that took place in September 2018 for its first edition (Le Pourquoi du Comment?).
Symbiotic interactions between unicellular eukaryotes have received very little scrutiny despite being highly pertinent for the study of basic eukaryotic processes and thus for biomedicine and biotechnology. The models of this project between two single-celled eukaryotes and prokaryotes are not only ecologically relevant, but also fundamental to better understand how cells from very different lineages create tight relationships in the context of the holobiont concept. The results we obtained improved our knowledge about the diversity of partners that can be related in marine waters, not only for multicellular organisms but also for single-cell eukaryotes. We pinpointed the existence of one bacterial partner, found in association with a collodarian species but undetectable in the surrounding waters. This brings new insights on bacterial association with free-living planktonic organisms. During the last decade, high-throughput sequencing technologies have improved our knowledge of different types of symbioses. This descriptive study is another step forward and allow to compare current sequencing methods used by most of the labs in the world. However, the coupling of appropriate metabolomics description was not able to disentangle the role of each partner in the association/holobiont. In this context, the project DYNAMO proposed an original approach to investigate in situ the cellular metabolites exchanged in a multipartite association. Therefore, results of the project will very likely foster collaborations with oceanographers and biochemists in the near future.