Exploring the evolution of wild microbes using a molecular genomic approach

Project Information

WildE

Grant agreement ID: 895338

DOI

10.3030/895338

Project closed

EC signature date 20 April 2020

Start date 1 September 2021

End date 21 March 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 172 932,48

EU contribution

€ 172 932,48

Coordinated by

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

Periodic Reporting for period 1 - WildE (Exploring the evolution of wild microbes using a molecular genomic approach)

Reporting period: 2021-09-01 to 2023-08-31

Summary of the context and overall objectives of the project

Marine microbes are the foundation of all life in the oceans, yet our understanding of how they are reacting to global change is limited. These microbes typically exist in large populations and reproduce quickly, which might enable them to rapidly adapt to environmental stressors compared to larger organisms. However, there is limited genetic evidence of contemporary evolution in wild marine microbes.

Understanding how marine microbes evolve is crucial for society because they are essential to ocean life. We do not currently know how these microbes will adapt to future global changes and what the potential consequences will be for ocean ecosystems and the food chain. Changes in microbial traits, such as growth rates, cell size, chlorophyll content, and photosynthesis, could lead to shifts in bloom events, primary production, and species composition. This, in turn, could affect the biogeochemical cycles that sustain life in the ocean.

The overall objectives are to:
- Improve understanding of how marine microbes are evolving in response to global change.
- Establish long-term studies (time series) to track changes in ocean microbes.

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

To achieve the goals of the WildE project, the research fellow designed a long-term mesocosm experiment to monitor changes in microbial populations. Temporal mesocosm experiments can take laboratory experiments a step closer to the complexity of the natural world, providing important insights into how whole communities might evolve and interact under future global change scenarios. This 14-month experiment used natural assemblages of microbes from a freshwater lake to replicate future global warming scenarios. Environmental DNA (eDNA) was sampled every two weeks and environmental RNA (eRNA) was collected during the last three weeks of the experiment. Both eDNA and eRNA were sequenced to track microbial evolution over time.

Additionally, the project utilised the Blanes Bay Microbial Observatory (BBMO) time series data, covering 2009-2020, to measure the rate of evolution in wild microbes. Metagenome assembled genomes (MAGs) were created from this data, and the most abundant MAGs were analysed. This analysis is ongoing, with a manuscript in preparation to quantify how environmental drivers influence microbial community assemblages.

The project also produced an invited opinion article in "Trends in Microbiology," highlighting the importance of understanding microbial evolution in response to global changes. Novel DNA and RNA data banks have been created and will be made publicly available, enabling further research and collaboration. The fellow has contributed to six co-author papers, one textbook chapter, and additional manuscripts in preparation, significantly advancing the understanding of microbial evolution.

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)

The mesocosm experiment represents a significant advancement by using natural assemblages instead of single isolates, providing a more accurate reflection of how wild populations respond to environmental changes. This approach allows for the disentanglement of specific temperature effects from other environmental drivers.

The project has generated two novel time-series datasets: a 12-year monthly sampling from the Mediterranean and a 14-month bi-weekly sampling from a mesocosm. These datasets contribute to a deeper understanding of microbial evolution in response to environmental drivers. Given the crucial roles of marine microbes in global carbon and nitrogen fixation, this research helps predict how future global changes might impact ecological services.

The sequence data will be accessible for future research, fostering collaborations and advancements in the field. The socio-economic impacts include better-informed policies for ecosystem management and climate change mitigation, benefiting both scientists and policymakers.

Illustration of the current state of knowledge and future goals in microbial evolution research.