Microbial biodiversity of soils in Europe, analyzes and perspectives

microbial biodiversity

‘Patterns in soil microbial diversity across Europe’ (Labouyrie et al., 2023) – the study published in Nature Communications by researchers from the Joint Research Center (JRC), University of Zurich and Tartu, Agroscope – offers a valuable analysis on the microbial biodiversity of soils in Europe. (1)

The processing of biological and microbiological data collected in the #LUCAS project (JRC et al., 2016) made it possible to observe the interactions between the different types of vegetal soil cover, anthropic disturbances and the climate with the soil characteristics, as well as the microbial communities and the functions associated with them.

EU vegetation cover
Figure 1. a. Distribution of sampling points colored by vegetation cover type in biogeographical regions. The number of sites is indicated in parentheses. b Vegetation cover types ordered along a gradient of increasing land use disturbance. (1)

1) Soil, the vital role of microorganisms

Microorganisms present in soils play a vital role in the decomposition of organic matter, the regulation of carbon reserves and nutrient cycling, as well as facilitating the absorption of nutrients by plants. (2) Anthropic disturbances in land use, climate, specific soil properties (eg pH, nitrogen availability) and plant biodiversity in turn have a crucial role in modeling microbial associations (3,4) .

The whole of these factors can therefore cause significant changes in the soil microbiome. (5) And changes in the composition and functions of microbial communities can influence the ecosystem services provided by soil. It is therefore fundamental to understand the impacts of anthropogenic and environmental factors on biodiversity and underground microbial functions, even on a large scale. (6)

2) The LUCAS project

LUCAS (Land Use and Coverage Area frame Survey) is a research project conducted in 28 Member States of the European Union, with the aim of collecting detailed data on the composition of soils and their vegetation cover in the Old Continent. (7) This project – in addition to analyzing the physical and chemical properties of soils (ie pH, nutrients) – identifies and catalogs the microorganisms present there, through advanced DNA ‘metabarcoding’ techniques. (8) Data standardization is indeed essential to have an overall vision, evaluating and comparing national and regional soil inventories.

LUCAS project workflow
Figure 2. LUCAS Soil workflow from sampling to database generation (8)

3) Impact of vegetation cover and climate

Vegetable cover has a significant role in bacterial and fungal community structure. The analysis involved 79.593 bacterial units and 25.962 fungal units. (1) Croplands and meadows with high clay content and pH host more chemoheterotrophic bacteria, forests with a high C/N (carbon/nitrogen) ratio and low bulk density have more ectomycorrhizal fungi, coniferous forests more N-bacteria fixators. Interactions between soil properties, vegetation cover, and climate explain differences in microbial diversity between sites. The analysis also reveals how the interaction between soil pH and temperature seasonality influences the diversity and proportion of fungal plant pathogens. (9)

4) Effects of anthropogenic disturbances in land use on microbial communities

The soil microbiome it is influenced by land disturbances, with an increase in microbial richness and diversity in the most disturbed areas (i.e. cultivated lands) compared to less disturbed forests. The greater microbial diversity – both taxonomic and functional – is not, however, an a priori positive signal.

The areas highly disturbed can in fact host greater quantities of potentially unwanted microorganisms. Thus, potential fungal pathogens are widespread in the most managed areas, nitrogen-fixing bacteria in extensively managed forests and meadows. (1) The various types of vegetation cover in turn lead to significant variations in the main microbial groups.

5) Limits and prospects

Researchers – despite having considered significant variables – they detected an unexplained variance that could perhaps be explained by the effect of other forces, such as wilting point and micronutrients not investigated by the model.

Lack of detailed data on plant cover, the limited functional annotation of microbes, especially bacteria – and the agronomic practices adopted (organic, conventional), adds the writer (9) – constitute potentially significant limitations. Further future research should consider microscopic-scale variability and improve the taxonomic and functional characterization of microbial communities.

Experimental approaches such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics could refine the functional annotation. A cause-and-effect analysis could correlate the presence of plant pathogens with plant growth. Applying these approaches to LUCAS Soil could open up new perspectives, but current limitations indicate the need for further targeted research to fully understand large-scale microbial ecology.(10)

6) EU policies

The European Commission, as we have seen, adopted the ‘EU Soil Strategy for 2021’ in 2030. (11) The objectives indicated in the ‘Farm to Fork’ and ‘Biodiversity 2030’ strategies, moreover, had already been disavowed in the report ‘EU agricultural outlook for markets, income and environment, 2020-2030’ (European Commission, JRC, 2021 See notes 12,13).

The European Parliament moreover, it is now watering down the draft regulations NRL (Nature Restoration Law) and SUR (Sustainable Use and Reduction of pesticides. See notes 14,15). Ambitions on a proposed ‘Soil Health Law’ project – which had been scheduled for 2023 (16) – have in turn foundered in a reductive ‘Soil Monitoring Law’ project (16,17).

7) Provisional conclusions

The study under consideration highlights the importance of considering both the taxonomic and functional diversity of microbial communities to understand the impacts of land use intensification, agronomic practices and environmental factors on soil biodiversity.

The approach based on the interactions between environmental factors, it offers new monitoring perspectives but must be accompanied by policies suitable for the restoration of European soils, whose current levels of degradation expose populations to non-negligible food security risks.

Gabriele Sapienza and Dario Dongo


(1) Labouyrie, M., Ballabio, C., Romero, F. et al. Patterns in soil microbial diversity across Europe. Nat Commun 14, 3311 (2023). https://doi.org/10.1038/s41467-023-37937-4

(2) European Commission, Joint Research Centre, Johnson, N., Scheu, S., Ramirez, K. et al., Global soil biodiversity atlas, Johnson, N., Scheu, S., Ramirez, K., Lemanceau, P., Eggleton, P., Jones, A., Moreira, F., Barrios, E., De Deyn, G., Briones, M., Kaneko, N., Kandeler, E., Wall, D., Six , J., Fierer, N., Jeffery, S., Lavelle, P., Putten, W., Singh, B., Miko, L., Hedlund, K., Orgiazzi, A., Chotte, J., Bardgett , R., Behan-Pelletier, V., Fraser, T., Montanarella, L., Publications Office, 2016, https://data.europa.eu/doi/10.2788/2613

(3) Donato Ferrucci, Dario Dongo. Nutrition of soils and crops, the integrated action plan in the EU. GIFT (Great Italian Food Trade). 17.7.22

(4) Dario Dongo, Giulia Torre. Microorganisms and microalgae in agriculture, sustainable innovation. GIFT (Great Italian Food Trade). 22.6.20

(5) Gabriele Sapienza. Biopreparations based on microorganisms, regulation and benefits. GIFT (Great Italian Food Trade). 4.10.23

(6) Guido Cortese, Dario Dongo. Microbiome and glyphosate, new studies. GIFT (Great Italian Food Trade). 27.4.19

(7) Orgiazzi, A., Panagos, P., Fernandez Ugalde, O., Wojda, P., Labouyrie, M., Ballabio, C., Franco, A., Pistocchi, A., Montanarella, L. and Jones , A., LUCAS Soil Biodiversity and LUCAS Soil Pesticides, new tools for research and policy development, EUROPEAN JOURNAL OF SOIL SCIENCE, ISSN 1351-0754, 73 (5), 2022, p. e13299, JRC125332. https://doi.org/10.1111/ejss.13299

(8) LUCAS: Land Use and Coverage Area frame Survey, https://esdac.jrc.ec.europa.eu/projects/lucas

(9) Dario Dongo, Andrea Adelmo Della Penna. Organic food and the immune system, scientific evidence. GIFT (Great Italian Food Trade). 11.4.20

(10) Labouyrie, M., Ballabio, C., Romero, F. et al. Publisher Correction: Patterns in soil microbial diversity across Europe. Nat Commun 14, 4298 (2023). https://doi.org/10.1038/s41467-023-39596-x

(11) Dario Dongo. Soil protection, 2030 strategy. ABC. GIFT (Great Italian Food Trade). 6.12.21

(12) Dario Dongo, Giulia Torre. Special – EU 2030 Biodiversity Strategy, the plan announced in Brussels. GIFT (Great Italian Food Trade). 31.5.20

(13) Dario Dongo, Giulia Orsi. Agriculture in EU-27, scenario report 2020-2030. GIFT (Great Italian Food Trade). 12.1.21

(14) Dario Dongo. Nature Restoration Law, reduction of pesticides. MEPs at the service of agro-industrial lobbies. GIFT (Great Italian Food Trade). 17.10.23

(15) Dario Dongo. Reduction of pesticides in the EU, ahead with mockery. GIFT (Great Italian Food Trade). 25.10.23

(16) Koeninger, J., Panagos, P., Jones, A., Briones, M. and Orgiazzi, A., In defense of soil biodiversity: Towards an inclusive protection in the European Union, BIOLOGICAL CONSERVATION, ISSN 0006-3207 , 268, 2022, p. 109475, JRC125863. https://dx.doi.org/10.1016/j.biocon.2022.109475

(17) Proposal for a Directive of the European Parliament and of the European Parliament and of the Council on Soil Monitoring and Resilience (Soil Monitoring Law) https://tinyurl.com/4yua4tdf

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Graduated in Agronomy, with experience in sustainable agriculture and permaculture, laboratory and ecological monitoring.

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Dario Dongo, lawyer and journalist, PhD in international food law, founder of WIISE (FARE - GIFT - Food Times) and Égalité.


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