An Odyssey without borders: soil microbiota as drivers of plant species coexistence along successional gradients

Project Information

BelowGround

Grant agreement ID: 101110604

DOI

10.3030/101110604

Project closed

EC signature date 17 March 2023

Start date 1 June 2023

End date 30 June 2026

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 203 464,32

Coordinated by

KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW
Netherlands

Periodic Reporting for period 1 - BelowGround (An Odyssey without borders: soil microbiota as drivers of plant species coexistence along successional gradients)

Reporting period: 2023-06-01 to 2026-06-30

Summary of the context and overall objectives of the project

Biodiversity is declining at an unprecedented rate worldwide, threatening ecosystem stability and resilience. Supporting the EU Biodiversity Strategy for 2030 requires effective approaches to conserve and restore species-rich ecosystems. Because plants form the foundation of terrestrial food webs and support overall ecosystem functioning, understanding the processes that maintain plant diversity is essential for successful biodiversity restoration. A major challenge is that the mechanisms allowing multiple plant species to coexist remain incompletely understood. Increasing evidence shows that soil microorganisms play a key role in shaping plant communities. These organisms include pathogens, which can reduce plant performance, and mutualistic symbionts, which provide benefits such as improved nutrient uptake. Both groups can influence whether plant species become dominant or whether diverse plant communities are maintained.

However, two competing hypotheses currently exist regarding how soil microorganisms promote plant coexistence. One proposes that soil-borne pathogens accumulate around abundant plant species and prevent them from dominating, thereby promoting diversity. The other suggests that beneficial soil symbionts can also promote coexistence by modifying competitive interactions among neighbouring plants. The contrasting predictions of these hypotheses limit our ability to predict how belowground biodiversity influences aboveground plant diversity and hinder the development of evidence-based restoration strategies. Plant community succession provides an ideal framework for addressing this challenge. Early successional communities are often characterized by stronger pathogen effects, whereas mutualistic interactions become increasingly important in later stages. Despite this shift, late-successional communities frequently maintain high levels of plant diversity, suggesting that both types of soil organisms may contribute to coexistence.

The overall objective of this project is to develop a unified framework explaining how soil pathogens and mutualistic microorganisms jointly influence plant species coexistence. Specifically, the project investigates which microbes accumulate around plants as they become more abundant, how host-specific these microbes are, and how they affect competition among plant species. By improving understanding of the microbial mechanisms that support plant diversity, the project will provide knowledge that can contribute to more effective biodiversity conservation and ecosystem restoration across Europe.

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

The project successfully established a field experiment along a chronosequence of agricultural land abandonment in the Veluwe region of the Netherlands. This study system enables the investigation of how plant, microbial, and soil communities develop during ecological succession following the cessation of agricultural practices. During implementation, the originally planned plant density treatment was adapted to a nitrogen addition treatment. This adjustment strengthened the project's ability to investigate the role of nitrogen availability, an important environmental challenge in many European ecosystems, in shaping interactions between soil pathogens and beneficial symbiotic microorganisms.

Comprehensive field sampling was completed across all study sites. Data were collected on aboveground plant community composition, soil abiotic characteristics, and belowground microbial communities using high-throughput DNA sequencing approaches targeting bacteria, fungi, and other soil microorganisms. In addition, soil nematode communities, which include important plant antagonists, were quantified using AI-assisted microscopy and characterized through DNA sequencing. To directly connect belowground biodiversity with plant community dynamics, the project also applied an innovative DNA-based approach to identify plant roots recovered from soil samples. This enabled the assessment of belowground plant species composition and abundance, providing a detailed link between plant communities and their associated soil organisms.

A major achievement of the project is the completion of all planned fieldwork, laboratory analyses, and bioinformatic processing. The resulting dataset integrates aboveground and belowground biodiversity across multiple trophic groups and stages of ecological succession. Initial analyses reveal how plant, microbial, and nematode communities change following land abandonment, providing new insights into the processes that drive biodiversity development during ecosystem recovery. The first scientific manuscript is currently being prepared and focuses on how gains and losses of aboveground and belowground biodiversity occur during succession. Further analyses will examine associations between plant species and soil microbial communities using network-based approaches, which will contribute to the completion of the project's objectives and the development of a unified framework linking soil microorganisms to plant species coexistence.

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)

Initial analyses show that ecological succession following agricultural abandonment is characterised by gradual but highly selective changes in belowground communities. Across multiple groups of organisms, including plants, fungi, prokaryotes, nematodes and mycorrhizal fungi, only a small proportion of taxa consistently established over time. Most taxa were either transient or occurred only at individual sites, highlighting both strong local variation and the importance of identifying general patterns in ecosystem recovery.
For soil fungi and prokaryotes, a limited number of taxa established persistently during succession, typically appearing around 10 years after agricultural abandonment and reaching relatively high abundances once established. Many other taxa appeared only temporarily, indicating that community assembly is a dynamic process in which only a subset of organisms successfully become long-term components of recovering ecosystems.

The project also found that plant species richness increased during the first two decades after agricultural abandonment, while soil fungal richness initially declined before stabilising. At the same time, new plant and fungal taxa colonised recovering grasslands, demonstrating ongoing biodiversity recovery. However, these newly arriving species generally remained less abundant than species already present in agricultural fields. This suggests that agricultural legacies can persist for several decades after land-use change, potentially influencing the pace and trajectory of biodiversity restoration.

These early findings provide new evidence that aboveground and belowground communities may recover at different rates and through different mechanisms. Understanding which soil organisms establish successfully during succession and how they influence plant community development is essential for developing a unified framework linking soil biodiversity to plant coexistence.
In the longer term, the project will generate knowledge that can support ecosystem restoration and biodiversity conservation efforts across Europe. By identifying the microbial interactions that promote the establishment and persistence of diverse plant communities, the results may help improve restoration strategies aimed at achieving the objectives of the European Union Biodiversity Strategy for 2030.