Microbial services addressing climate change risks for biodiversity and for agricultural and forestry ecosystems: enabling curiosity-driven research and advancing frontier knowledge

Project Information

MICROBES-4-CLIMATE

Grant agreement ID: 101131818

DOI

10.3030/101131818

EC signature date 24 November 2023

Start date 1 February 2024

End date 31 January 2029

Funded under

• Research infrastructures

Total cost

€ 14 494 818,44

EU contribution

€ 14 494 818,43

Coordinated by

MICROBIAL RESOURCE RESEARCH INFRASTRUCTURE - EUROPEAN RESEARCH INFRASTRUCTURE CONSORTIUM
Portugal

Periodic Reporting for period 1 - MICROBES-4-CLIMATE (Microbial services addressing climate change risks for biodiversity and for agricultural and forestry ecosystems: enabling curiosity-driven research and advancing frontier knowledge)

Reporting period: 2024-02-01 to 2025-07-31

Summary of the context and overall objectives of the project

Terrestrial biodiversity and ecosystems are increasingly threatened by global changes, with agricultural and forestry ecosystems facing some of the most severe environmental and socio-economic challenges confronting our planet and humanity. Climate change is widely recognized as a major global change, significantly impacting biodiversity and ecosystem services. Consequently, addressing climate change and its effects on terrestrial ecosystems must go hand in hand.

Microbes play a crucial role as the life support system of the biosphere, yet they are often overlooked in discussions about climate change. Our understanding of how climate change affects microbiomes, including their assembly and functions, remains limited. The impact of climate change on the complex interactions between microbes, plants, and soil—and the subsequent effects on plant performance and productivity—are not well understood. Furthermore, there is a need to explore how microbiomes can mitigate stress conditions caused by climate change and their role in overall ecosystem functioning.

The MICROBES-4-CLIMATE project aims to address these gaps by providing a broad community of users and researchers, regardless of their location, with efficient access to a network of world-class research infrastructures. This network offers integrated, advanced services, as well as training and scientific or technical support. At the heart of the project is an excellence-driven Transnational Access program, which will facilitate curiosity-driven research on terrestrial biodiversity and ecosystems. This research will focus on the still poorly understood interactions between microbiomes, plants, and soil, and their roles in climate change responses, resilience, and mitigation.

By advancing frontier knowledge and enabling applied research, the project will contribute to harnessing plant-microbiome interactions to enhance plant and crop climate resilience. This, in turn, will support the development of precision, sustainable, and resilient agricultural practices.

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

In the first reporting period, MICROBES-4-CLIMATE established the scientific and technical foundations for its objectives. The Catalogue of Services was launched with more than 100 offers, accompanied by two cross-RI workflows integrated into the Collaborative Working Environment. The first Transnational Access (TNA) call attracted 26 proposals from 20 countries, validating the technical set-up for user access. On the scientific side, the consortium developed the SINCERE-DATA pipeline for single-cell microbial genomics and initiated optimisation of wet-lab protocols. Large-scale sampling campaigns in France, Greece, and Italy generated extensive collections of microbial isolates, laying the groundwork for synthetic microbial communities (SynComs). In parallel, the first version of the project ontology and a FAIR-compliant Dataverse were deployed, harmonising data across infrastructures. Finally, preliminary ethical recommendations were produced, ensuring that future applications of SynComs and microbial resources are developed under robust ethical and regulatory guidance.

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)

MICROBES-4-CLIMATE delivered results that extend beyond current scientific and technical practices during RP1. The SINCERE-DATA pipeline provides a novel solution for single-cell microbial genomics, reducing contamination and enabling more accurate genome reconstruction. In parallel, the project has established harmonised protocols for sampling and isolating plant and soil microbiomes, paving the way for the design of synthetic microbial communities (SynComs) to enhance crop resilience under drought stress. The development of an integrated ontology, Dataverse instance, and the Collaborative Working Environment goes beyond fragmented infrastructures by creating a FAIR-compliant digital backbone that aligns with EOSC. Preliminary ethical recommendations further advance the state of the art by addressing regulatory and bioethical gaps specific to microbiome applications. To ensure uptake, further demonstration of SynComs under field conditions, sustained investment in digital infrastructures, and the development of EU-level regulatory standards will be essential.