1. Application of self-organizing maps to explore the interactions of microorganisms with soil properties in fruit crops under different management and pedo-climatic conditionsFrancesca Antonucci, Simona Violino, Loredana Canfora, Malgorzata Tartanus, Ewa M. Furmanczyk, Sara Turci, Maria Grazia Tommasini, Nika Cvelbar Weber, Jaka Razinger, Morgane Ourry, Samuel Bickel, Thomas A. J. Passey, Anne Bohr, Heinrich Maisel, Massimo Pugliese, Francesco Vitali, Stefano Mocali, Federico Pallottino, Simone Figorilli, Corrado Costa, Eligio Malusà, 2025, izvirni znanstveni članek Povzetek: Self-organizing maps (SOMs) are a class of neural network algorithms able to visually describe a high-dimensional dataset onto a two-dimensional grid. SOMs were explored to classify soils based on an array of physical, chemical, and biological parameters. Methods: The SOM analysis was performed considering soil physical, chemical, and microbial data gathered from an array of apple orchards and strawberry plantations managed by organic or conventional methods and located in different European climatic zones. Results: The SOM analysis considering the “climatic zone” categorical variables was able to discriminate the samples from the three zones for both crops. The zones were associated with different soil textures and chemical characteristics, and for both crops, the Continental zone was associated with microbial parameters—including biodiversity indices derived from the NGS data analysis. However, the SOM analysis based on the “management method” categorical variables was not able to discriminate the soils between organic and integrated management. Conclusions: This study allowed for the Soil Syst. 2025, 9, 10 https://doi.org/10.3390/soilsystems9010010 Soil Syst. 2025, 9, 10 2 of 14 discrimination of soils of medium- and long-term fruit crops based on their pedo-climatic characteristics and associating these characteristics to some indicators of the soil biome, pointing to the possibility of better understanding the interactions among diverse variables, which could support unraveling the intricate web of relationships that define soil quality.
Ključne besede: apple, neural networks, soil microbiome diversity, strawberry
Objavljeno v DiRROS: 03.02.2025; Ogledov: 684; Prenosov: 386
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2. The effect of forest gaps on the diversity and composition of bacterial communities in mixed-type forest soils across the Carpathian mountainsNejc Suban, Olivera Maksimović, Nataša Šibanc, Tijana Martinović, Eva Dařenová, Matjaž Čater, Tine Grebenc, 2024, izvirni znanstveni članek Povzetek: Mixed forests of European beech (Fagus sylvatica L.) and silver fir (Abies alba Mill.) play a vital ecological role in Central and South-Eastern Europe. This study investigates the diversity and composition of soil bacterial communities in these forests, focusing on rhizosphere and bulk soils under varying canopy structures. Soil samples were collected from eight sites along the Carpathian Mountains, including managed forests and the remnants of old growth. Metabarcoding of bacterial communities revealed that alpha diversity (species richness, Shannon index, and evenness) was significantly affected by sampling location but not by forest canopy structure or soil type (rhizosphere and bulk soil). The lowest bacterial diversity was found in the old-growth forest of the Beskidy region, while the highest was recorded in managed forest in Vrancea. Beta diversity analyses showed minimal variation between rhizosphere and bulk soil bacterial communities, with geographic distance being the strongest predictor of community composition. Actinobacteriota and Proteobacteria were the dominant phyla across all sites, with higher relative abundance of Actinobacteriota in all rhizosphere samples compared to bulk soil. Complex combinations of various environmental conditions at each sampling location, including soil parameters (mainly pH and C:N ratio), the age of forest gaps, the type and intensity of disturbances, and species composition of above-ground vegetation, can strongly affect soil bacterial communities. A closer examination of additional environmental variables would be necessary to better explain the observed differences in the diversity and composition of bacterial communities.
Ključne besede: forest gaps, forest management, soil microbiome, soil, rhizosphere, Carpathians, temperate forest
Objavljeno v DiRROS: 30.12.2024; Ogledov: 2029; Prenosov: 863
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3. Soil microbiome along the carpathian mountainsNejc Suban, Olivera Maksimović, Nataša Šibanc, Tijana Martinović, Eva Dařenová, Matjaž Čater, Tine Grebenc, 2024, objavljeni povzetek znanstvenega prispevka na konferenci Ključne besede: soil microbiome, next-generation sequencing, climate change, forest soil, fungi, bacteria
Objavljeno v DiRROS: 02.09.2024; Ogledov: 1035; Prenosov: 330
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4. Unearthing the soil-borne microbiome of land plantsRaúl Ochoa-Hueso, David J. Eldridge, Miguel Berdugo, Pankaj Trivedi, Blessing Sokoya, Concha Cano-Díaz, Sebastian Abades, Fernando D. Alfaro, Adebola R. Bamigboye, Felipe Bastida, Tine Grebenc, Tina Unuk Nahberger, 2024, izvirni znanstveni članek Povzetek: Plant–soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.
Ključne besede: belowground networks, environmental thresholds, moss microbiome, plant microbiome, plant–soil interactions
Objavljeno v DiRROS: 31.05.2024; Ogledov: 1092; Prenosov: 591
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