Molecular divergence in a marine animal-microbial symbiosis since the closure of the Isthmus of Panamá

Project Information

PANSYMBIOSIS

Grant agreement ID: 101025649

DOI

10.3030/101025649

Project closed

EC signature date 23 February 2021

Start date 1 March 2021

End date 28 February 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 174 806,40

EU contribution

€ 174 806,40

Coordinated by

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Germany

Periodic Reporting for period 1 - PANSYMBIOSIS (Molecular divergence in a marine animal-microbial symbiosis since the closure of the Isthmus of Panamá)

Reporting period: 2021-03-01 to 2023-02-28

Summary of the context and overall objectives of the project

As oceans change due to human activities, understanding marine adaptation is crucial. Studying past geological events like the formation of the Isthmus of Panamá, which divided marine life into the Pacific Ocean and the Caribbean Sea, provides valuable insights. This separation led to different habitats, making the Isthmus ideal for exploring speciation, diversification, and adaptation through convergent evolution.

Microorganisms (archaea, bacteria, viruses, fungi) significantly impact host health and fitness, influencing responses to environmental changes. This project examined the convergent evolution of closely related hosts and their associated bacteria on both sides of the Isthmus. We focused on lucinid clams, which rely on bacterial symbionts in their gills for nutrition, comparing these symbionts at the genomic and transcriptomic levels across the Isthmus.

Documenting Bacterial Symbiont Adaptation:

● Estimating the molecular evolution and divergence in host-associated bacterial genomes.
● Inferring signals of positive selection and increased recombination rates in orthologous genes.
● Performing a comparative genomic analysis with other closely related lucinid symbionts in the same habitat.

Genotype to Phenotype Focus:

● Comparing gene expression among symbiont populations in geminate host species pairs divided by the Isthmus of Panama.
● Revealing whether genes identified as evolutionarily relevant are also expressed and identifying consistently differentially expressed genes across the Isthmus.

Investigating Co-speciation and Diversification:

● Comparing molecular divergence rates between symbiont genomes, host mitochondrial genomes, and exome-wide host genomes.
● Applying a recently developed pipeline to infer non-model host population genetic structure and differentiation by integrating metagenomic and metatranscriptomic data.
● By focusing on bivalve species pairs that survived on both sides of the Isthmus, we aimed to understand how their associated bacterial symbionts enabled them to adapt to this massive environmental change. Although both Caribbean and Tropical Eastern Pacific (TEP) bivalves host Candidatus Thiodiazotropha symbionts, only those on the Caribbean side are capable of nitrogen fixation. This capability does not align with symbiont evolutionary history, indicating convergent evolution due to similar environmental pressures.

Exploring the genetic history of lucinid symbionts globally revealed that the ancestor of Ca. Thiodiazotropha lacked nitrogen fixation genes. Populations in nutrient-poor habitats acquired this capability multiple times through horizontal gene transfer (HGT). Our research underscores the role of HGT in bacterial adaptation and highlights the impact of nitrogen availability on symbiont ecological diversification. It demonstrates how bacterial symbionts can aid marine organisms in adapting to environmental change.

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

We did extensive fieldwork, collecting lucinid clams and their bacterial symbionts in Panamá and Costa Rica. Besides collecting fresh clams, we also collaborated with the Natural History Museums in London, Vienna, and Florida to get material from lucinid clams from around the world. Then, we extracted the total DNA of lucinid gills and sequenced it. We assembled bacterial genomes and did a comparative genomic analysis. Based on the sequenced genomes we also built a phylogenetic tree and reconstructed the phylogenetic relationships among the clam symbionts. We tested whether any genes in the clam symbionts are under positive selection and/or only found in a specific environment. Since we found that all the genes involved in nitrogen fixation are unique to lucinid clam symbionts in the Caribbean Sea, we did a comparative analysis with lucinid clam symbionts from around the world. We found that all symbionts living in oligotrophic environments possess these genes. With the help of a reconciliation analysis, we found out that the most recent common ancestor of these clam symbionts lacked these genes and picked them up through horizontal gene transfer from a closely related bacterial species living in the same sand sediment.

Our study suggests that horizontal gene transfer of these nitrogen fixation genes has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.
Hence, with regard to our objectives, we successfully estimated the molecular evolution and divergence in host-associated bacterial genomes, inferred signals of positive selection and increased recombination rates in orthologous symbiont genes, and we performed a comparative genomic analysis with other closely related lucinid symbionts across the world in similar habitats.

This work has been published in an open access peer-reviewed journal PLoS Genetics earlier this year:
Isidora Morel-Letelier, Benedict Yuen, A. Carlotta Kück, Yolanda E. Camacho-García, Jillian M. Petersen, Minor Lara, Matthieu Leray, Jonathan A. Eisen, Jay T. Osvatic, Olivier Gros, and Laetitia G. E. Wilkins (2024): Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts. PLOS Genetics. Published: May 31, 2024

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)

This project advances the state of the art in several key areas:

Symbiont Genomics and Evolution: By analyzing the genomic and transcriptomic responses of bacterial symbionts, we are uncovering the molecular mechanisms underlying symbiont adaptation to new environments. This includes identifying genes under positive selection and understanding the role of recombination in genetic diversity.

Convergent Evolution: Our focus on convergent evolution in lucinid clams and their symbionts provides new insights into how similar environmental pressures can lead to similar adaptations in different populations. This adds to the understanding of evolutionary processes in marine ecosystems.

Horizontal Gene Transfer (HGT): The discovery that nitrogen fixation genes were acquired multiple times through HGT highlights the importance of gene transfer in bacterial adaptation. This finding has broader implications for understanding microbial evolution and ecology and the roles of bacteria in the evolution of animal microbial symbioses.

Marine Conservation: Understanding how marine organisms adapt to changing environments can inform conservation strategies, helping to preserve biodiversity and ecosystem services essential for human well-being.

Climate Change Adaptation: The project contributes to the broader understanding of how marine ecosystems respond to climate change, which is crucial for developing mitigation and adaptation strategies.

Closure of the Isthmus of Panama.

Moving from correlation to causation in the Pansymbiosis project. The three main research axes.