Exploring the mechanisms underlying the evolution of plastids through the study of an unusual nitrogen-fixing symbiosis

Project Information

UCYN2PLAST

Grant agreement ID: 749380

DOI

10.3030/749380

Project closed

EC signature date 10 March 2017

Start date 1 January 2018

End date 1 November 2021

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 246 668,40

EU contribution

€ 246 668,40

Coordinated by

SORBONNE UNIVERSITE
France

Periodic Reporting for period 2 - UCYN2PLAST (Exploring the mechanisms underlying the evolution of plastids through the study of an unusual nitrogen-fixing symbiosis)

Reporting period: 2020-01-01 to 2020-12-31

Summary of the context and overall objectives of the project

The proposed research in the UCYN2PLAST project was conceived to understand the evolution of intracellular plastids and niche adaptation processes of unicellular eukaryotes in nitrogen-limited environments such as the open ocean.

Primary cyanobacterial-like plastids have experienced modifications in their genomes during the evolution towards a plastid lifestyle, but the underlying processes remain difficult to address because they occur over geological time scales. Thus, the study of present-day symbiotic associations between unicellular eukaryotes and prokaryotes might be an alternative way to understand how symbioses are established.

A particular case of such symbiosis involves species closely related to the single-celled marine alga Braarudosphaera bigelowii (Prymnesiophyceae) and unicellular nitrogen-fixing cyanobacteria. This cyanobacterial symbiont, Candidatus Atelocyanobacterium thalassa (UCYN-A), is a widely distributed member of the marine plankton and a key player in the nitrogen cycle

The parallelism between the endosymbiosis that originated the plastids in eukaryotes and the UCYN-A symbiosis makes this symbiosis a unique model to gain insight into the evolution of plastids, and further poses the question of whether we are currently witnessing an evolutionary process that will eventually lead to the establishment of a nitrogen fixing plastid.

In this context, the UCYN2PLAST project was designed to explore the ecology and evolution of the UCYN-A nitrogen-fixing symbiosis as a way to better understand the mechanisms underlying plastid formation.

Therefore, the overall objectives of the UCYN2PLAST project are:

Objective #1 (outgoing phase): To identify and characterize new UCYN-A association trough microscopic and molecular techniques to gain insight into the evolution of the symbioses across lineages.

Objective #2 (outgoing phase): To experimentally disentangle the temporal interplay between partners along a day-night cycle at three levels: whole-genome expression, nutrient assimilation, and metabolic exchange.

Objective #3 (return phase): To explore the large-scale biogeography patterns in the distribution of these types of symbiotic associations across the global ocean and their underlying drivers.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

First, we have generated new genomic information on a new UCYN-A sublineage via single-cell sorting and genomics, which allowed us to designed DNA probes targeting the ribosomal genes. These probes allowed to detect and distinguish new sublineages of the UCYN-A symbiosis in open ocean samples from the North Pacific Ocean and in coastal seawater samples collected nearby the Scripps Oceanographic Institution in San Diego (California, USA). In addition, through the analysis of metagenomic samples, we were able of reconstructing the partial genome of a third species of the UCYN-A group, and we used this information to explore the evolutionary relationship between this third species, called UCYN-A3, and the two previously identified species, i.e. UCYN-A1 and UCYN-A2. These findings were published in the format of a scientific article in the peer-review journal Environmental Microbiology (Cornejo-Castillo et al. 2019, Environmental Microbiology).

Second, we have discovered novel cellular mechanisms that directly affect the metabolic coupling between symbiotic partners and revealed the effect of environmental factors in the communication between symbiotic partners in the UCYN-A symbiosis. The analysis of all the publicly available cyanobacterial genomes led to uncover the distribution pattern of a genetic pathway involved in the protection from oxygen of the key enzyme for nitrogen fixation, which is an extremely oxygen-sensitive enzyme. Also, we designed an experimental setup to ascertain the role of light in the exchange of nutrients between symbiotic partners in the UCYN-A symbiosis. Our results demonstrated that the light period is critical for maintenance of regular patterns of gene expression, N2 fixation and symbiont replication and cell division. Our findings suggest a crucial role for the algal host of UCYN-A as a producer of fixed carbon, rather than light itself, in the regulation and implementation of the aforementioned cellular processes in UCYN-A. These findings were published in the prestigious peer-reviewed journal PNAS (Cornejo-Castillo & Zehr 2019. PNAS) and in Frontiers in Microbiology (Landa, Turk-Kubo, Cornejo-Castillo et al. 2021. Frontiers in Microbiology). Moreover, these results have also been presented in international scientific meetings and in social media.

Finally, we have described the distribution of symbiotic nitrogen-fixing microorganisms at the global ocean scale using high-throughput DNA and RNA sequencing data collected during the TARA Oceans expedition (https://fondationtaraocean.org/en/expedition/tara-oceans/). Besides, we explored two important aspects of nitrogen-fixing microorganisms, which are their nitrogen-fixation activity and their contribution to the sequestration of CO2 into the deep ocean. This part of the project concerning objective #3 has originated three scientific articles, one published in The ISME Journal (Cornejo-Castillo & Zehr 2021. The ISME Journal), one in Nature Communications (Pierella Karlusich et al. 2021. Nature Communications) and the third one has been posted in an open access repository BioRxiv (https://tinyurl.com/37mewjxf).

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

All objectives and milestones of the UCYN2PLAST project have been successfully achieved, which has helped to opening new scientific questions and research avenues. We brought the knowledge of marine microbial symbiosis into a higher level of understanding and, proof of that is the high number of articles produced by this project. Overall, the UCYN2PLAST project has generated very relevant scientific publications and, more importantly, it has served as a source of inspiration for other researchers of the world.
This project has contributed to a better understanding of the ecology and evolution of nitrogen-fixing symbionts with their hosts in marine systems. We generated new molecular tools to detect and visualize new symbiotic associations in the open ocean and these tools, are currently being applied by other research groups in the world. Among all our findings, one of the most exciting ones was the discovery of a universal mechanism that might facilitate aerobic nitrogen fixation in the ocean, which deserves more experimental work and will bring new knowledge to the field of marine nitrogen fixation. Finally, and contrary to what it was expected, we showed that small symbiotic nitrogen-fixers, such as UCYN-A, in the sequestration of carbon into the deep ocean as they sink more efficiently than larger colonial nitrogen-fixing cyanobacteria like Trichodesmium. These results are key to update ocean biogeochemical models and will help us to have a better understanding of the carbon and nitrogen cycle in the ocean.

Schematic representation of the evolution and metabolic coupling of the UCYN-A symbiosis