Soil life is far more complex than what we see with our eyes. Beneath every field, forest, and grassland lies a dynamic microbial world that drives nutrient cycling, plant growth, carbon storage, and ecosystem resilience.

In the latest webinar hosted on the Soil Community Platform, experts from leading European institutions explored how we measure, interpret, and monitor soil microorganisms, and why this matters for soil policy and land management across Europe. The Soil Community Platform, developed under the InBestSoil and BIOservicES projects, continues to provide a space for researchers, practitioners, and policymakers to exchange knowledge and align efforts on soil health.

Webinar Highlights

This session focused on microorganisms, from bacteria and fungi to protists and nematodes, and their role in ecosystem functioning, monitoring frameworks, and land management practices.

Intercropping, Soil Microbial Communities, and Ecosystem Cycles

Shamina Imran Pathan (University of Florence, LEGUMINOSE project) opened the session by presenting preliminary results from long-term field trials exploring legume-cereal intercropping systems.

The LEGUMINOSE project aims to move intercropping from niche practice to mainstream agriculture across Europe. Beyond nitrogen fixation, the project investigates how plant diversity influences soil microbial communities and ecosystem processes.

Key takeaways included:

• Management practices had a stronger impact on soil microbial structure than intercropping alone.
• Functional gene analysis revealed that intercropping, particularly under organic management, increased nitrification potential and soil multifunctionality.
• Soil context matters: the effect of intercropping depends heavily on soil properties and management history.

As Shamina Imran Pathan emphasized in the presentation, “the impact is highly context dependent and varies according to the surrounding environment, either the soil properties or the management practices.” 

The results reinforced a central message echoed throughout the webinar: understanding soil health requires going beyond community composition and examining functional potential.

Beyond Taxonomy: Functional Gene Diversity via Metagenomics

Dr. Jessica Cuatero Moñino (WSL, SOB4ES project) presented the potential of shotgun metagenomics for soil monitoring.

Traditional amplicon sequencing provides insights into who is present in soil. Shotgun sequencing, however, allows researchers to explore what those organisms are genetically capable of doing. As she explained, “we are getting all the genes that we have in the soil, all of them, millions of them.” 

Using long-term field trials comparing conventional tillage and no-till systems, she showed:

• Arable soils exhibited higher functional gene diversity than permanent grasslands in the studied system.
• Conventional tillage slightly increased functional gene diversity compared to no-till management.
• Functional pathways related to nutrient cycling and organic matter degradation varied between management systems.

Jessica emphasized that metagenomics offers a broader view of soil functional capacity, but must be combined with physical and chemical indicators for robust soil monitoring.

From Data to Decisions: Microbiome Analysis in Practice

Julien Winkel (Soilytix) shifted the discussion toward applied soil microbiome analysis, demonstrating how digital tools can support researchers and land managers in handling large datasets.

He presented an integrated approach that connects sampling design, laboratory analysis, and data visualization, helping users interpret complex microbial data more efficiently. As he noted, “soil data can be quite extensive… we created a software that can really help you to get answers out of your data.” 

A key highlight of his presentation was the latest advancement in sequencing capabilities, detailed in Soilytix’s recent white paper: “Advancing Fungal Amplicon Sequencing: Transition from ITS1 to Full ITS1–5.8S–ITS2 Profiling Using Extended-Read Illumina Technology.” 

This development enables longer read lengths, up to 900 base pairs, allowing for more accurate fungal identification and improved species-level resolution, which has traditionally been a limitation in amplicon sequencing. By capturing the full ITS region, researchers can better understand fungal diversity and its ecological roles in soil systems.

The message was clear: as sequencing technologies evolve and datasets grow in complexity, combining advanced methodologies with accessible tools will be essential to translate microbial data into meaningful, actionable insights.

Soil Microbial Patterns Across Europe

Maëva Labouyrie (European Commission Joint Research Centre) presented findings from the LUCAS Soil Biodiversity survey, the largest harmonized soil biodiversity dataset at the European scale.

Analyzing bacterial and fungal communities across diverse land uses, her team explored how soil properties, vegetation type, and climate shape microbial distribution.

Key findings included:

• Soil properties primarily drove bacterial richness.
• Fungal communities were more strongly influenced by vegetation cover.
• Highly managed systems often showed higher microbial richness, but also higher proportions of plant pathogens.

A crucial takeaway was that taxonomic diversity alone does not fully reflect ecosystem health. Functional profiles and environmental context must also be considered. As highlighted in the presentation, “if we only looked at community metrics, we would think that a higher diversity means improved ecosystem functioning, but that would be only half the story.” 

Maeva also recommended exploring the Global Soil Biodiversity Atlas to appreciate the “beauty of soil life,” a suggestion that fits well with the atlas’s goal of helping readers understand and visually engage with the incredible biodiversity living beneath our feet.

The discussion also addressed the EU Soil Monitoring Law and the need for harmonized methodologies, including common recommendations for sampling, sequencing depth, and data interpretation across Member States.

Protists, Nematodes, and Soil Food Webs

Stefan Geisen (Wageningen University, BIOservicES) concluded the session by drawing attention to often-overlooked soil organisms: protists and nematodes.

These microbial predators regulate bacterial and fungal communities, influence nutrient release, and shape soil food webs. As he pointed out, “almost 60% of life on Earth is in soil.” 

Highlights included:

• Nematodes are abundant and occupy multiple trophic levels, linking microbes to higher organisms.
• Protists play key roles as microbial grazers and can serve as indicators of soil disturbance.
• Experimental results showed that microbiome predators can significantly influence bacterial community composition and plant biomass.
• Higher diversity of protists and nematodes increased plant growth even without additional nitrogen input.

Explaining their functional importance, he noted that these organisms “feed on the microbiome and release nutrients that plants can take up, and therefore the plant benefits.” 

His presentation underscored the importance of adopting a more holistic view of soil biodiversity, integrating trophic interactions rather than focusing solely on bacteria and fungi.

Post-Webinar Reflections

Several overarching themes emerged from the discussion:

• Functional diversity must complement taxonomic diversity in soil assessment.
• Soil context and management history strongly influence microbial responses.
• Standardization and harmonization are essential for European-level monitoring efforts.
• Soil food webs extend beyond bacteria and fungi, and incorporating protists and nematodes provides a more complete understanding of ecosystem functioning.

As policy frameworks such as the Soil Monitoring Law evolve, scientific collaboration and shared methodologies will be central to ensuring reliable and comparable data across Europe.

Through continued dialogue on the Soil Community Platform, the connection between research, practice, and policy grows stronger, helping build a shared understanding of what healthy soils truly mean in ecological and societal terms. Stay connected with the platform for upcoming webinars, including the next session focusing on policy and governance for soil biodiversity and soil health.