Cross-scale analysis of adaptation to iron depletion in a key phytoplanktonic organism, in the context of global change – CINNAMON

The CINNAMON project used a systems biology approach to characterize the main acclimation (physiology) and adaptation (evolution) mechanisms involved in the differential response of Synechococcus ecotypes to iron deficiency and temperature variations. On the one hand, we studied the physiological response of 3 strains of CRD1 as well as representative strains of 4 other major lineages of Synechococcus, acclimated to different temperatures or to iron-limited conditions, in order to highlight and better understand the differential response of the different lineages of the Synechococcus genus. In parallel, comparative studies of the available Synechococcus genomes have made it possible to better understand the genetic bases of the response to these environmental factors. Finally, the combination of these genomic analyses with metagenomics and metatranscriptomics data from the Tara Oceans expedition allowed us to identify genes specifically present or absent in iron-depleted areas of the global ocean, and/or differentially regulated in response to iron deficiency.

The CINNAMON project made it possible to validate the existence of distinct thermotypes within the CRD1 clade, i.e. strains presenting different thermal tolerance ranges, and to highlight i) physiological specificities, in particular their low growth rate and photosynthetic activity and their high repair rate of the damage generated at the level of photosystem II, and ii) genomic specificities of the CRD1 and EnvB ecotypes compared to the Synechococcus ecotypes colonizing other ecological niches, which could be involved in cell adaptation to iron deficiency and/or temperature variations.

Understanding the impact of Fe limitation responds to a societal claim, as the general public is increasingly aware of the importance of preserving ecosystems, especially marine areas, and decision-makers need effective tools for oceans management. In this context, the results of the CINNAMON project should provide a better understanding of the ability of marine phytoplankton to cope with ongoing climate changes and how they will affect the structure and population dynamics of this basal compartment of marine ecosystems. Another perspective of the CINNAMON project is the possibility of using the Synechococcus CRD1 ecotypes and/or their specific genes as biomarkers for monitoring the expansion of iron-poor regions, iron limitation being particularly difficult to assess by chemical approaches.

The CINNAMON project is a fundamental research project coordinated by Laurence Garczarek. It also associates the LOMIC laboratory (UMR7621) of Banyuls-sur-mer, as well as the LS2N laboratories (UMR6004 and UMR6074) of Nantes Université and the ABIMS platform (FR2424) of the Roscoff biological station. The project started in January 2018 and lasted 57 months. It benefited from ANR aid of €450,000 for an overall cost of around €1,627 million.

CINNAMON's results have given rise to 20 scientific articles in A-ranked journals (4 others in progress) and 23 communications in international congresses. CINNAMON also made it possible to generate i) an information system accessible to the entire scientific community, Cyanorak v2 (www.sb-roscoff.fr/cyanorak/), which gathers a large number of marine picocyanobacteria genomes, ii) a multi-marker reference database to analyze the genetic diversity of these organisms and iii) several communication tools on plankton intended for the general public.

Oceans are particularly affected by the global change, which notably causes an increase in seawater temperature and an expansion of iron (Fe)-poor areas, whilst Fe depletion is already impairing phytoplankton growth in as much as 35 % of the global ocean. This raises the questions of the capacity of local marine phytoplanktonic populations to adapt to these harsh conditions and of the consequences of Fe depletion on the ocean ability to sequester CO2 via the biological carbon pump. In this context, the recent discovery of one clade (CRD1) of the marine cyanobacterium Synechococcus predominating in low-Fe niches, with three genetically distinct populations displaying different temperature ranges, constitutes a unique opportunity to unveil the combined effects of Fe depletion and temperature on phytoplankton at all scales of organization from the gene to the ecosystem.
The CINNAMON project will use a systems biology approach, combining laboratory and field work, to characterize and model the main acclimation (physiological) and adaptation (evolutionary) mechanisms involved in the differential responses of Synechococcus ecotypes to Fe limitation and temperature variations, with the goal to better predict their respective adaptability, and hence future distribution and dynamics in a changing environment. First, we will validate the occurrence of distinct Fe and/or temperature ecotypes within the CRD1 clade, notably by delineating the growth optima and boundary limits for Fe and temperature of representative strains. In parallel, the comparison i) of genomes of marine picocyanobacteria (about 60 Synechococcus genomes, including at least one for each CRD1 genotype and 2 low-Fe Prochlorococcus metagenomes) and ii) of transcriptomes from different CRD1 and control strains generated in response to +Fe/-Fe, should allow us to decipher the genetic basis of their specific adaptability to changes in temperature and Fe availability. These data will also be integrated into co-expression and metabolic networks in order to determine the respective role of metabolic vs. regulatory pathways in the differential behavior of the tested strains when subjected to Fe depletion and high/low temperature. A last approach will consist in using meta-omics data from major global ocean surveys (Tara-Oceans, Tara-Polar Circle, Tara-Pacific and Malaspina expeditions) covering a wide range of oceanic regimes to validate at the population level the observations made on representative strains, but also to identify additional genes and biosynthetic pathways potentially responsible for the capacity of these ecotypes to adapt to cold or warm, low-Fe regions of the world ocean. Altogether, this cross-scales approach from the genes to the global ocean should allow us to delineate a limited set of ecotype- and/or niche-specific genes that are differentially expressed in response to Fe availability. Such genes will constitute privileged targets for further functional analyses, including gene inactivation followed by physiological characterization of mutants, to better understand molecular processes underlying adaptation to low Fe niches.
The CINNAMON project is both ambitious by the extent and variety of analyses that will be made and innovative since results will not be limited to a model Synechococcus strain, but will take into account the ecotypic variability within this major component of the oceanic ecosystem. Results will thus be of both evolutionary and ecological interest as they should allow us to better understand i) how iron availability has driven genetic diversification within picocyanobacteria, but also ii) the consequences of this diversification on the community composition and dynamics of these key organisms, in the context of global change. A major societal goal of the project will be to raise awareness among general public about the impact of global change on marine biodiversity and to provide tools to stakeholders to monitor these effects.