Agricultural soils in intensive farming sustain high crop production yields but endanger other regulating ecosystem services. Strengthening the simultaneous delivery of multiple soil functions is therefore essential to achieve high crop yields while lowering the environmental impact. We investigated how this so-called soil multifunctionality is related to management intensity in conventional and organic arable farming, and to specific practices regarding e.g. crop rotation, fertilization or tillage. We furthermore explored whether soil organic carbon and soil microbiotic parameters could explain relationships between agricultural management and soil functioning.

We collected 57 soil samples in Dutch arable fields and interviewed farmers about their farm management. Soil multifunctionality was measured by aggregating 9 indicators of different functions such as nutrient cycling, soil structure, and disease suppression. We characterized the species composition and abundance of the soil microbial community with 15 parameters, and soil carbon quantity and quality with 16 parameters.

We show that increasing management intensity is associated with declining soil multifunctionality across all fields, whereas multifunctionality was not related with organic vs. conventional farming. Greater soil multifunctionality was also associated with less frequent inversion tillage and higher frequency of grass-legume cover cropping. Bacterial biomass and total soil organic carbon content, respectively, were the strongest biotic and abiotic predictors of soil multifunctionality. No other biotic parameters were related to soil multifunctionality, whereas the majority of soil carbon parameters were significantly related. Our results suggest that reducing management intensity will enhance soil multifunctionality in both conventional and organic farming systems, so that in highly intensive and productive agricultural systems, the paradigm of sustainable intensification should be replaced by “productive de-intensification.”

How to cite: Koorneef, G., van Rijssel, S., Veen, C., Pulleman, M., de Goede, R., Comans, R., van der Putten, W., and Mason-Jones, K.: Exploring potential success factors for soil multifunctionality: effects of agricultural management, soil life and soil carbon, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-1059, https://doi.org/10.5194/egusphere-egu25-1059, 2025.

Bridging Morphological and Molecular Approaches in Soil Fauna Diversity Assessments at European level

Köninger, J., Potapov, A., Ross, G., Tsiafouli, M., Seeber, J., Beule, L., Hedlund, K., Frouz, J., Blasbichler, H., Orgiazzi, A., Briones, M.J. I.

Recent advances in molecular approaches to identify multiple species from a mixed sample, have expanded our availability to perform large-scale analyses of soil biodiversity. However, methodological challenges remain, particularly when trying to reconcile molecular results with those derived from traditional morphological-based identifications. For example, previous studies have recorded unexpected higher diversities in the more intensively managed agricultural lands compared to woodlands and grasslands, which contrasts with earlier morphological analyses and highlights the need for methodological cross-validation.

Here, we address these challenges by comparing soil fauna diversity data derived from several international large-scale surveys. For example, the SOB4ES EU-funded project encompassing diverse European land uses and the Biodiversa+ project (accronym) focussing on woodlands both collected morphological as well as molecular data. Additionally, we compared the DNA metabarcoding results from LUCAS (2018 survey) with morphological data derived from the EcoFINDERS and SOILSERVICE projects. Our analyses reveal the existence of a significant variability in diversity metrics between ecosystem types, emphasizing the importance of contextualizing molecular results through complementary morphological analyses. Furthermore, our results also highlight the need to refine molecular methods (e.g. primer choice and removal of relict DNA) to ensure the robustness of the data interpretations for their potential use in policy-making and biodiversity indicator development.

How to cite: Köninger, J.: Bridging Morphological and Molecular Approaches in Soil Fauna Diversity Assessments at European level, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-4295, https://doi.org/10.5194/egusphere-egu25-4295, 2025.

Mycorrhizal symbiosis of plants is widely distributed worldwide, and most of the forests form either ectomycorrhizal (ECM) or arbuscular mycorrhizal (AM) fungal associations [1]. Therefore, mycelium of mycorrhizal fungi is being discussed as one of the important functional components of soil microbiome, and also as a feeding resource for soil biota. Nematodes are one of the key consumers of both roots and mycorrhizal fungi [2, 3]. In soil horizons deeper than 20-30 cm or subsoils [4], the mycelium of mycorrhizal fungi can be an even more important driver and source of nutrients compared to topsoil, due to the lack of plant-derived resources [5, 6]; but our knowledge on its functional role in subsoil is extremely scarce. Therefore, the high reliance of subsoil-living nematodes on the mycorrhizal fungi as a feeding substrate was hypothesized.

The research was carried out based on ten-years-old MyDiv tree diversity experiment, Bad Lauchstädt, Germany. The soil at the site is classified as Haplic Chernozem. The experiment manipulates tree species richness and mycorrhizal types; the detailed site description is given in Ferlian et al., 2018 [7]. We exclusively focused on plots exclusively represented by either ectomycorrhizal (ECM, four plots) or arbuscular mycorrhizal (AM, four plots) tree stands. Soil cores, 5 cm in diameter were sampled up to the depth of 1 meter using motorized soil auger. Soil profile was studied divided by genetic horizons: Ap1 (~0-10 cm), Ap2 (~10-35 cm), Ah (~40-60 cm) and C (~60-100 cm). Nematodes were extracted within a week of sampling using a modified Baermann method. Soil parameters (water content, % and bulk density, g*cm^-3) were estimated in parallel. Nematodes were counted and biomass estimated using an inverse microscope (Leica DM) under ×400 magnification, and then 100 specimens per sample were identified to genus level. Feeding types of nematodes were assigned to genera following Yeates et al. (1993) [8].

Our data show that the nematode community of only top soil horizon Ap1 (~0-10 cm) differ (MANOVA, F = 2.525; p = 0.0332) between ECM and AM dominated ecosystems. Both biomass and density of nematodes significantly decreased with depth, being the most pronounced for bacterivores in ECM systems (Least-squared Means test, t-ratio ≤ -5.293; p < 0.0001). The shown effects are likely related to the legacy of post-agricultural soil and high buffer capacity of Chernozem soils. The importance of further subsoil studies in mature forest stands, as well as the research on the nematode communities of post-agricultural reforestation successions is proposed.

References:

• Soudzilovskaia NA, et al. (2019). Nat Commun 10:5077. https://doi.org/10.1038/s41467-019-13019-2

• Kudrin AA, et al. (2021). Soil Biol Biochem 155:108184. https://doi.org/10.1016/j.soilbio.2021.108184

• Li Y, et al. (2009). Soil Biol Biochem 41:877–882. https://doi.org/10.1016/j.soilbio.2008.07.031

• Frelih-Larsen A, et al. (2018). Sustainability 10:3006. https://doi.org/10.3390/su10093006

• Callesen I, et al. (2016). For Ecol Manag 359. https://doi.org/10.1016/j.foreco.2015.08.019

• Dietzel R, et al. (2017). Soil 3:139–152. https://doi.org/10.5194/soil-3-139-2017

• Ferlian O, et al. (2018). Ecosphere 9:e02226. https://doi.org/10.1002/ecs2.2226

• Yeates GW, et al. (1993). J Nematol 25(3):315-331.

How to cite: Zuev, A., Peter, S., Eisenhauer, N., Ferlian, O., Hohberg, K., and Potapov, A.: Nematodes in deep soil profiles under young mycorrhizal forest stands, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-8542, https://doi.org/10.5194/egusphere-egu25-8542, 2025.

Soil microbial biodiversity studies commonly rely on molecular datasets from microbial communities extracted from their natural contexts. While immensely important for many research questions, this can lead to artefacts such as falsely interpreting interactions where organisms were strongly spatially separated in the soil habitat, and difficulties in differentiating active from passive or dormant organisms.

We developed a way to overcome some of the problems of the extraction steps: Microfluidic soil chips, transparent micromodels of the soil pore space, can be incubated in, or inoculated with, soil, from which the microorganisms move into, grow into, or are transported into it by water streaming. This allows for direct microscopic examination of bacteria, fungi, and protist communities under closer-to natural conditions. AI-aided image analysis helps to quantify population sizes and gives information on the community’s morphodiversity: Changes in cellular size and shapes, and the spatial distribution of the cells including group formation up to simple biofilms. Direct observations can be made on the growth and interactions of the organisms, with each other and with their immediate environment.

We found differences in microbial communities over large geographical patterns (Arctic via temperate to tropical soil bacteria) in bacterial cell sizes and their microspatial distribution. Morphodiversity of the bacterial community were also found to change across microscale soil pore space characteristics, where cells were larger in more connected microhabitats compared to less connected and more tortuous ones. Comparing the molecular microbial biodiversity in chips to the microbial biodiversity of the adjacent soil via metabarcoding, we found in chips an amplicon sequence variant richness of around 30% of the adjacent soil, indicating a reduced but still relevantly diverse microbial community. Also, fungal and protist communities can be studied in soil chips, especially valuable for research questions of interactions such as interactions with the pore space, predation, behavior, and direct reactions to experimental factors such as a pollutant.

We argue that soil chips are an intriguing complement to molecular techniques to study soil microbial diversity, and will help us to better understand soil microbial activity and interactions with each other and their environment.

How to cite: Hammer, E., Pinholt, F., Klinghammer, F., Karlsson, E., Sopasakis, A., Ohlsson, P., Lake, F., Maillard, F., and Zou, H.: Studying soil microbial diversity and their ecological interactions via Soil Chips, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-9034, https://doi.org/10.5194/egusphere-egu25-9034, 2025.

Microorganisms in agricultural soils play a key role in nutrient recycling and nutrient availability for plants. The diversity and abundance of these microorganisms and the subsequent microbiological processes can however be influenced by different factors. This includes among others the crop type grown on the field, the farmers’ agricultural field management and various soil parameters as these farming processes may highly affect the soil microbiological diversity and abundance. Some farming practices aiming at increasing crop yield such as ploughing or nitrogen fertilization might actually endanger soil processes provided by microorganisms supporting crop yield. It is therefore important to better understand the complexity of soil microbial abundance and diversity – including bacterial, fungal and protist – in relation to agricultural soil management.

The objective of this study is to determine the structure of the microbiota (including bacteria, fungi and protists) in agricultural soils in Skåne, Sweden, across different farming conditions and soil characteristics.

To achieve this, soil samples were collected from agricultural fields with the primary focus on two crops:  small grain cereals (annual) and ley (perennial). Samples were collected from a total of 25 farms including conventional farms and organic farms, varying in time since transition, to account for potential differences in farming practices. The soil samples were incubated using soil chips to observe the abundance of the various types of microorganisms. We also compared microbial morphodiversity with molecular biodiversity measurements. In addition, the soil characteristics such as pH, organic matter and electrical conductivity were determined for correlation analysis with microbiological presence/abundance.

The abundance of microbiological groups examined via microscopic analysis in soil chips proved to be highly variable within crop types and agricultural field management (conventional/organic). However, time since transition to organic farming practices might influence the abundance for the microbiological groups with an increase in abundance for older organic farms. In addition, the analysis of soil parameters such as pH, soil organic matter and electrical conductivity also showed to be highly variable within crop types and agricultural field management.

This study shows that abundances of microbiological groups in various types of agricultural soils might be highly variable, in which the years of organic farming, but not the categorical farming practices tend to affect microbiological group abundance.

How to cite: Lake, F. B., Carrié, R., Bacon, C. D., Ekroos, J., and Hammer, E. C.: Soil microbiome diversity under annual and perennial crops in conventional and organic agriculture. , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-11990, https://doi.org/10.5194/egusphere-egu25-11990, 2025.

Soil biota can sustain a wide range of functions and as such are intrinsically connected to soil health, which is defined as the capacity of a soil to function within ecosystem and land-use boundaries. Land use, soil management and land degradation can affect soil biodiversity and ultimately soil health. Soil fauna is an integral part of soil biodiversity connected at various levels of the food web with other important soil organisms such as bacteria and fungi. Nematodes are ubiquitous organisms sensitive to disturbances, and can be divided into functional groups based on feeding preferences and life-history strategies. Mites and collembola are two groups of microarthropods that are sensitive to land use change and soil management. These different groups of organisms can be used as indicators of soil biodiversity and health and can be measured with both morphological and molecular methods. Molecular methods offer great advantages compared to morphological methods, such as increase throughput and decrease costs and expertise needed for analysis, however only few studies have compared the information coming from both analyses. The objective of this study is to compare results of nematodes and microarthopods characterization obtained from morphological and eDNA methods in the framework of the European project SOILGUARD. To achieve this, nematodes, acari and collembola community characteristics have been assessed in seven European NUTS regions with different land use (forest, grassland and arable land), management (clearcutting vs continuous cover, grass monoculture vs grass-clover mix, organic vs conventional agriculture), pedo-climatic (texture, climate) characteristics, and land degradation gradient (organic matter levels). Soi fauna communities have been analysed with traditional morphological characterisation after extraction from soil and molecular methods with direct eDNA extraction from soil. Fauna-based soil health indices based on their abundance were calculated with information coming from both assessment methods. Results show disagreement between the two methods. More details about the outcome of this comparison will be presented and discussed during the conference.

How to cite: Bongiorno, G., Sanchez-Cuetos, P., Llado’, S., Soliveres, S., and De Goede, R. G. M.: Effects of land use and agricultural management along soil degradation gradients on soil fauna in European sites (SOILGUARD) – a comparison between morphological and molecular data, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-15401, https://doi.org/10.5194/egusphere-egu25-15401, 2025.

Soil ecosystems harbor a vast diversity of organisms—ranging from microbes (bacteria, fungi, archaea) to meso- and macrofauna (e.g., protists, nematodes, mites, insects)—that collectively drive soil functions such as nutrient cycling, organic matter decomposition, and plant productivity. These processes depend on intricate interactions within the soil food web. Despite the acknowledged importance of meso- and macrofauna in maintaining soil health and mediating biogeochemical cycles, effective chemical proxies for these organisms remain constrained to specific groups, limiting their use in comprehensive soil biodiversity assessments.

To address this gap, we applied a lipidomic approach to more than 80 single species spanning 26 phyla of soil biota, including Euryarchaeota (archaea), Proteobacteria and Actinobacteriota (bacteria), Ascomycota and Mucoromycota (fungi), Chlorophyta (algae), Arthropoda, Nematoda and Mollusca (meso- and macrofauna), and Tracheophyta (higher plants). Through high-resolution mass spectrometry and molecular networking, we identified more than 700 novel molecular lipid families within 12,000 lipid compounds, many lipid families being unique to specific phyla. These findings establish a robust framework for developing phylum-specific biomarkers and deepen our understanding of the soil food web. By focusing the current study on pure species, and by quantifying their content in the specific organisms, we enable biomass quantification across the whole soil food web and improve taxonomic resolution with phylum-specific chemical proxies, revealing distinct lipid signatures—such as ceramides in arthropods and cardiolipins in bacteria—that illustrate the metabolic specializations and ecological adaptations of these organisms.

This integrative approach underscores lipidomics as a powerful tool for linking molecular-level data with taxonomy and allowing biomass quantitation across complete food webs. As global environmental pressures intensify, our findings pave the way for biomarker-driven strategies to monitor, conserve, and elucidate soil biodiversity, ultimately supporting the essential services that soil ecosystems provide.

How to cite: Samrat, R. and Wanek, W.: Revealing Phylum-Specific Signatures in Intact Lipids: A Novel Biomarker Approach in Soil Biodiversity Research, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-17948, https://doi.org/10.5194/egusphere-egu25-17948, 2025.

Environmental DNA (eDNA) analysis can facilitate biodiversity monitoring within a bulk sample, especially valuable to evaluate soil ecosystems. eDNA can persist in soil as living cells, dead cells, and extracellular DNA either as free or adsorbed to particles in the soil. Each of these ‘states’ of eDNA can have differing persistence times from a few days to hundreds of years. Better understanding to target and isolate particular states of eDNA is imperative to derive valuable information, for instance, recent occupancy indicated by freshly released eDNA or eDNA within living cells.

This presentation will present cases showing the variability of eDNA persistence in different states with a focus on the adsorbed state. I will then discuss the adsorption mechanism of eDNA and introduce novel methods of isolating the states of eDNA from a single sample for independent analysis. Lastly, I will show data from a landscape level study with water samples collected from 221 sites from 58 streams in eight Swiss watersheds. All the samples were state sorted and analyzed with board range metabarcoding assays for identifying metazoan diversity. The results show that each state consists of unique diversity information and state sorting methodologies should be considered when processing bulk soil samples for eDNA analysis. While this presentation will have some studies using water samples, they elucidate the behavior of eDNA bound to soil and sediment particles as well.

How to cite: Kirtane, A.: Consideration of eDNA states to analyze bulk soil samples via metabarcoding, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-18094, https://doi.org/10.5194/egusphere-egu25-18094, 2025.

Soil health is defined as the capacity of soil to function as a vital living system within ecosystem and land-use boundaries to sustain biological productivity, maintain environmental quality, and promote plant, animal, and human health. The decline of soil health due to human impacts is an urgent ecological issue.

This study explores the diversity patterns and within-field variability of soil macrofauna communities across different land management systems in Portugal, employing a robust, multi-faceted approach. Two case studies were conducted to evaluate diversity patterns in forests (oak- and pine-dominated) and olive groves (intensive and extensive systems). Sampling was carried out in April and May 2024, utilizing a systematic grid design that incorporated two spatial methodologies: a k-means-based grid and random point allocation, resulting in 36–39 sampling points per system. To enhance comparability, an additional sampling point was included following the LUCAS methodology.

Macrofauna were identified morphologically at the order level, and abundance data were systematically recorded. For each land-use type, a subset of samples was analysed to quantify the biomass of individual taxonomic orders, providing deeper insights into the relevance of biomass as an ecological parameter. Species richness was assessed using incidence frequency data and compared across the various management systems, with a focus on Hill numbers. 

Diversity estimates for the agricultural sites indicate that extensive agricultural systems support higher potential species diversity as sampling efforts increase, while intensive agricultural systems generally sustain a lower and less diverse macrofauna community. Similarly, forested site estimates reveal that oak-dominated habitats harbour significantly greater species diversity compared to pine-dominated habitats. The metabarcoding approach corroborated these patterns, providing complementary insights, and the correlation between high-throughput sequencing (HTS) reads and biomass is critically analysed.

This methodological framework underscores the profound impact of land-use practices on soil macrofauna diversity, highlighting their essential role in sustaining soil health and broader ecosystem functionality. By integrating soil macrofauna diversity into soil health assessments, this study addresses a significant knowledge gap and offers practical guidance for developing improved soil management strategies that support sustainable land-use practices.

How to cite: Steiner, E., Campello, C., Reis, F., Fraga Dornellas, L., Leitão, R., Simões, S., Sousa, J. P., and Cunha, L.: Soil Health Through the Lens of Macrofauna Diversity: Insights from Forests and Olive Groves, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-19428, https://doi.org/10.5194/egusphere-egu25-19428, 2025.