{"type": "FeatureCollection", "features": [{"id": "10.3390/genes15010107", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:24Z", "type": "Journal Article", "created": "2024-01-16", "title": "Structural and Functional Shifts in the Microbial Community of a Heavy Metal-Contaminated Soil Exposed to Short-Term Changes in Air Temperature, Soil Moisture and UV Radiation", "description": "

The interplay between metal contamination and climate change may exacerbate the negative impact on the soil microbiome and, consequently, on soil health and ecosystem services. We assessed the response of the microbial community of a heavy metal-contaminated soil when exposed to short-term (48 h) variations in air temperature, soil humidity or ultraviolet (UV) radiation in the absence and presence of Enchytraeus crypticus (soil invertebrate). Each of the climate scenarios simulated significantly altered at least one of the microbial parameters measured. Irrespective of the presence or absence of invertebrates, the effects were particularly marked upon exposure to increased air temperature and alterations in soil moisture levels (drought and flood scenarios). The observed effects can be partly explained by significant alterations in soil properties such as pH, dissolved organic carbon, and water-extractable heavy metals, which were observed for all scenarios in comparison to standard conditions. The occurrence of invertebrates mitigated some of the impacts observed on the soil microbial community, particularly in bacterial abundance, richness, diversity, and metabolic activity. Our findings emphasize the importance of considering the interplay between climate change, anthropogenic pressures, and soil biotic components to assess the impact of climate change on terrestrial ecosystems and to develop and implement effective management strategies.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Soil invertebrates", "Soil microbiome", "Soil drought", "Ultraviolet Rays", "Soil pollution", "Microbiota", "Temperature", "Enchytraeus crypticus", "15. Life on land", "01 natural sciences", "Article", "6. Clean water", "Soil", "03 medical and health sciences", "13. Climate action", "UVR exposure", "Metals", " Heavy", "Climate change", "Soil flood", "Metagenomics", "Increased temperature", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.3390/genes15010107"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes15010107", "name": "item", "description": "10.3390/genes15010107", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes15010107"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-16T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2023.165179", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:18:18Z", "type": "Journal Article", "created": "2023-06-28", "title": "Intensive vegetable production under plastic mulch: A field study on soil plastic and pesticide residues and their effects on the soil microbiome", "description": "Intensive agriculture relies on external inputs to reach high productivity and profitability. Plastic mulch, mainly in the form of Low-Density Polyethylene (LDPE), is widely used in agriculture to decrease evaporation, increase soil temperature and prevent weeds. The incomplete removal of LDPE mulch after use causes plastic contamination in agricultural soils. In conventional agriculture, the use of pesticides also leaves residues accumulating in soils. Thus, the objective of this study was to measure plastic and pesticide residues in agricultural soils and their effects on the soil microbiome. For this, we sampled soil (0-10\u00a0cm and 10-30\u00a0cm) from 18 parcels from 6 vegetable farms in SE Spain. The farms were under either organic or conventional management, where plastic mulch had been used for >25\u00a0years. We measured the macro- and micro-light density plastic debris contents, the pesticide residue levels, and a range of physiochemical properties. We also carried out DNA sequencing on the soil fungal and bacterial communities. Plastic debris (>100\u00a0\u03bcm) was found in all samples with an average number of 2\u00a0\u00d7\u00a0103\u00a0particles\u00a0kg-1 and area of 60\u00a0cm2\u00a0kg-1. We found 4-10 different pesticide residues in all conventional soils, for an average of 140\u00a0\u03bcg\u00a0kg-1. Overall, pesticide content was \u223c100 times lower in organic farms. The soil microbiomes were farm-specific and related to different soil physicochemical parameters and contaminants. Regarding contaminants, bacterial communities responded to the total pesticide residues, the fungicide Azoxystrobin and the insecticide Chlorantraniliprole as well as the plastic area. The fungicide Boscalid was the only contaminant to influence the fungal community. The wide spread of plastic and pesticide residues in agricultural soil and their effects on soil microbial communities may impact crop production and other environmental services. More studies are required to evaluate the total costs of intensive agriculture.", "keywords": ["2. Zero hunger", "Plastic mulch", "Soil microbiome", "Microbiota", "Microplastic", "Pesticide Residues", "Pesticides residues", "Agriculture", "12. Garantizar modalidades de consumo y producci\u00f3n sostenibles", "15. Life on land", "Fungicides", " Industrial", "Edafolog\u00eda y Qu\u00edmica Agr\u00edcola", "Soil", "Intensive vegetable production", "13. Climate action", "Agriculture contamination", "Polyethylene", "Vegetables", "31 Ciencias Agrarias::3101 Agroqu\u00edmica", "Pesticides"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2023.165179"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2023.165179", "name": "item", "description": "10.1016/j.scitotenv.2023.165179", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2023.165179"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10.5281/zenodo.8333110", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:27:05Z", "type": "Dataset", "title": "Growth Chamber mesocosm experiment to assess the effects of the OSS decoupled from the presence of G. senegalensis (PRJNA930014)", "description": "The Sahel region of West Africa is a vulnerable eco-region where a growing population and climate-change induced drought threaten food security. The subsistence farmers here grow pearl millet (Pennisetum glaucum) without fertilizers or irrigation. Local and biologically-based means of maintaining yields are needed, and an agroforestry system in Senegal - the Optimized Shrub-intercropping System (OSS) - provides a solution. In the OSS, the shrub Gueira senegalensis performs hydraulic lift, distributing deep subsurface water to neighboring millet plants. The shrub also supports a distinct microbial community and significantly improves carbon storage and nutrient dynamics. Here, we aimed to test whether shrub-impacted soils differed in microbiome and millet outcomes under simulated early-season drought in a growth chamber. Shrub impact was separated into residual impacts on microbiome and soil, versus ongoing shrub-derived organic matter (OM) input. decoupled from the effects of the growing shrub. Methods: We characterized the microbiota through dry-down and rewetting periods, with particular attention to lineages with known plant growth promoting (PGP) properties, via amplicon sequencing of the 16S rRNA gene V3-V4 region and the ITS2, . Results: Both bacterial and fungal communities were significantly altered by imposed drought, OM amendment, and original soil type (+/-OSS). The largest significant bacterial community impact under dry down occurred for +shrub/-OM treatments, and under rewetting for -OM treatment regardless of +/- OSS. Known bacterial PGP lineages were only enriched under drought in +OSS/-OM treatments. The fungal community behaved differently with a significant dry-down impact only in +OSS/+OM treatments, while rewetting enriched for fungal pathogens but only in -OSS/+OM soils. Decoupled from ongoing shrub growth, both residual shrub impacts and shrub OM inputs altered microbiota and increased millet biomass under drought. These results are part of a growing body of work aimed at understanding microbiome roles in increasing ecological resilience and combating food insecurity. Metagenomic and amplicon sequencing data are publicly available via NCBI PRJNA930014. Here we present all associated soil chemical, enzyme, and plant physical and chemical data", "keywords": ["2. Zero hunger", "sustainable agriculture", "Soil microbiome", "13. Climate action", "sahel", "15. Life on land", "pearl millet", "6. Clean water", "growth chamber"], "contacts": [{"organization": "Mason, Laura, Charles, Christine, Rich, Virginia, Dick, Richard,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.8333110"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.8333110", "name": "item", "description": "10.5281/zenodo.8333110", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.8333110"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-09-11T00:00:00Z"}}, {"id": "10.1038/s41558-023-01868-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:23Z", "type": "Journal Article", "created": "2023-12-04", "title": "The soil microbiome governs the response of microbial respiration to warming across the globe", "description": "Open AccessThe sensitivity of soil microbial respiration to warming (Q10) remains a major source of uncertainty surrounding the projections of soil carbon emissions to the atmosphere as the factors driving Q10 patterns across ecosystems have been assessed in isolation from each other. Here we report the results of a warming experiment using soils from 332 sites across all continents and major biomes to simultaneously evaluate the main drivers of global Q10 patterns. Compared with biochemical recalcitrance, mineral protection, substrate quantity and environmental factors, the soil microbiome (that is, microbial biomass and bacterial taxa) explained the largest portion of variation in Q10 values. Our work provides solid evidence that soil microbiomes largely govern the responses of soil heterotrophic respiration to warming and thus need to be explicitly accounted for when assessing land carbon\u2013climate feedbacks.", "keywords": ["2. Zero hunger", "Soil microbiome", "Microbial respiration", "13. Climate action", "XXXXXX - Unknown", "Warming", "15. Life on land", "12. Responsible consumption"]}, "links": [{"href": "https://doi.org/10.1038/s41558-023-01868-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Climate%20Change", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41558-023-01868-1", "name": "item", "description": "10.1038/s41558-023-01868-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41558-023-01868-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "10.1093/ismeco/ycae116", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:08Z", "type": "Journal Article", "created": "2024-10-08", "title": "Land use effects on soil microbiome composition and traits with consequences for soil carbon cycling", "description": "Abstract

The soil microbiome determines the fate of plant-fixed carbon. The shifts in soil properties caused by land use change leads to modifications in microbiome function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated using metaproteomics, metabarcoding, and a 13C-labeled litter decomposition experiment across two temperate sites with differing soil pH each with a paired land use intensity contrast. 13C incorporation into microbial biomass increased with land use intensification in low-pH soil but decreased in high-pH soil, with potential impact on carbon use efficiency in opposing directions. Reduction in biosynthesis traits was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. We observed divergent pH-controlled pathways of SOC cycling. In low-pH soil, land use intensification alleviates microbial abiotic stress resulting in increased biomass production but promotes decomposition and SOC loss. In contrast, in high-pH soil, land use intensification increases microbial physiological constraints and decreases biomass production, leading to reduced necromass build-up and SOC stabilization. We demonstrate how microbial biomass production and respiration dynamics and therefore carbon use efficiency can be decoupled from SOC highlighting the need for its careful consideration in managing SOC storage for soil health and climate change mitigation.

We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community\u2019s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 \u00b0C + 50% water holding capacity (WHC)); increased air temperature (15\u201325 \u00b0C or 20\u201330 \u00b0C + 50% WHC); flood (20 \u00b0C + 75% WHC); drought (20 \u00b0C + 25% WHC); and ultraviolet radiation (UV) (20 \u00b0C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community\u2019s physiological profile and the bacterial community\u2019s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20\u201330 \u00b0C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome\u2013invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.

", "keywords": ["0301 basic medicine", "Soil invertebrates", "Ultraviolet Rays", "drought", "microbial activity", "DNA", " Ribosomal", "Flood", "Article", "Quantitative PCR", "Soil", "03 medical and health sciences", "soil microbiome", "2. Zero hunger", "metagenomics", "increased temperature; drought; flood; UV exposure; microbial activity; bacterial diversity; metagenomics; quantitative PCR; soil microbiome; soil invertebrates", "Soil microbiome", "0303 health sciences", "Drought", "Bacteria", "Microbiota", "bacterial diversity", "Temperature", "Water", "flood", "15. Life on land", "soil invertebrates", "6. Clean water", "UV exposure", "Microbial activity", "Bacterial diversity", "13. Climate action", "quantitative PCR", "Metagenomics", "Increased temperature", "increased temperature"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/13/5/850/pdf"}, {"href": "https://doi.org/10.3390/genes13050850"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes13050850", "name": "item", "description": "10.3390/genes13050850", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes13050850"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-10T00:00:00Z"}}, {"id": "10.3390/su17031093", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:39Z", "type": "Journal Article", "created": "2025-01-29", "title": "Microbial Bioindicators for Monitoring the Impact of Emerging Contaminants on Soil Health in the European Framework", "description": "

Antibiotic resistance (AR) is recognized by the World Health Organization as a major threat to human health, and recent studies highlight the role of microplastics (MPs) in its spread. MPs in the environment may act as vectors for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Bacterial communities on the plastisphere, the surface of MPs, are influenced by plastic properties, allowing ARB to colonize and form biofilms. These biofilms facilitate the transfer of ARGs within microbial communities. This study analyzed data from the LUCAS soil dataset (885 soil samples across EU countries) using the Emu tool to characterize microbial communities at the genus/species level. Functional annotation via PICRUSt2, supported by a custom tool for Emu output formatting, revealed significant correlations between the genera Solirubrobacter, Bradyrhizobium, Nocardioides, and Bacillus with pathways linked to microplastic degradation and antibiotic resistance. These genera were consistently present in various soil types (woodland, grassland, and cropland), suggesting their potential as bioindicators of soil health in relation to MP pollution. The findings underscore MPs as hotspots for ARB and ARGs, offering new insights into the identification of bioindicators for monitoring soil health and the ecological impacts related to MP contamination.

", "keywords": ["microplastics; antibiotic resistance genes; soil microbiome; LUCAS soil"], "contacts": [{"organization": "Andrea Visca, Luciana Di Gregorio, Manuela Costanzo, Elisa Clagnan, Lorenzo Nolfi, Roberta Bernini, Alberto Orgiazzi, Arwyn Jones, Francesco Vitali, Stefano Mocali, Annamaria Bevivino,", "roles": ["creator"]}]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/1142151/2/sustainability-17-01093.pdf"}, {"href": "https://www.mdpi.com/2071-1050/17/3/1093/pdf"}, {"href": "https://doi.org/10.3390/su17031093"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sustainability", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/su17031093", "name": "item", "description": "10.3390/su17031093", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/su17031093"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-01-29T00:00:00Z"}}, {"id": "10.3389/fmicb.2021.676251", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:12Z", "type": "Journal Article", "created": "2021-06-07", "title": "Dynamics of Soil Bacterial and Fungal Communities During the Secondary Succession Following Swidden Agriculture IN Lowland Forests", "description": "

Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe\uffe2\uff80\uff93plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant\uffe2\uff80\uff93growth\uffe2\uff80\uff93promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

", "keywords": ["0301 basic medicine", "570", "plant\u2013growth\u2013promotion (PGP)", "metagenomically-assembled-genomes (MAGs)", "Article", "03 medical and health sciences", "carbon dioxide fixation", "Ammonia", "metagenomic binning", "Germany", "soil microbiome", "Proteobacteria", "Humans", "biocontrol", "secondary metabolite synthesis", "suppressive soil", "Phylogeny", "Soil Microbiology", "soil microbiome; suppressive soil; biocontrol; plant\u2013growth\u2013promotion (PGP); metagenomic binning; metagenomically-assembled-genomes (MAGs); secondary metabolite synthesis; carbon dioxide fixation; carbohydrate-active enzymes; differentially abundant features (DAFs)", "2. Zero hunger", "Bacteria", "Bacteroidetes", "Agriculture", "differentially abundant features (DAFs)", "15. Life on land", "Archaea", "Actinobacteria", "carbohydrate-active enzymes", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://doi.org/10.3390/genes10060424"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10060424", "name": "item", "description": "10.3390/genes10060424", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10060424"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-03T00:00:00Z"}}, {"id": "10.3390/soilsystems9010010", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:37Z", "type": "Journal Article", "created": "2025-01-27", "title": "Application of Self-Organizing Maps to Explore the Interactions of Microorganisms with Soil Properties in Fruit Crops Under Different Management and Pedo-Climatic Conditions", "description": "

Background: 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 \u201cclimatic zone\u201d 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\u2014including biodiversity indices derived from the NGS data analysis. However, the SOM analysis based on the \u201cmanagement method\u201d categorical variables was not able to discriminate the soils between organic and integrated management. Conclusions: This study allowed for the 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.

", "keywords": ["Physical geography", "Chemistry", "soil microbiome diversity", "apple", "strawberry", "neural networks", "QD1-999", "GB3-5030"]}, "links": [{"href": "https://www.mdpi.com/2571-8789/9/1/10/pdf"}, {"href": "https://doi.org/10.3390/soilsystems9010010"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Systems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/soilsystems9010010", "name": "item", "description": "10.3390/soilsystems9010010", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/soilsystems9010010"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-01-26T00:00:00Z"}}, {"id": "10.5061/dryad.cc2fqz6d9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:24:05Z", "type": "Dataset", "created": "2023-12-20", "title": "Data from: Do Tasmanian devil declines impact ecosystem function?", "description": "unspecifiedTasmanian eucalypt forests are among the most carbon-dense in the world, but projected changes in climate could destabilize this critical carbon sink. While the impact of abiotic factors on forest ecosystem carbon dynamics have received considerable attention, biotic factors, such as the input of animal scat, are less understood. Tasmanian devils (Sarcophilus harrisii)\u2014an osteophageous scavenger that can ingest and solubilize nutrients locked in bone material\u2014may subsidize plant and microbial productivity by concentrating bioavailable nutrients (e.g., nitrogen and phosphorus) in scat latrines. Dramatic declines in devil population densities are driven by the spread of a transmissible cancer and may have underappreciated consequences for soil organic carbon (SOC) storage and forest productivity by altering nutrient cycling. Here, we fuse experimental data and modeling to quantify and predict future changes to forest productivity and SOC under various climate and scat-quality futures. We find that devil scat significantly increases concentrations of nitrogen, ammonium, phosphorus, and phosphate in the soil, and shifts soil microbial communities towards those dominated by r-selected (e.g., fast-growing) phyla. Further, under simulated increases in temperature and precipitation, devil scat inputs are projected to increase above- and belowground net primary productivity and microbial biomass carbon through 2100. In contrast, when devil scat is replaced by lower-quality scat (e.g., from non-osteophageous scavengers and herbivores), forest carbon pools either increase more slowly or decline. Together, our results suggest biotic factors will interact with climate change to drive current and future carbon pool dynamics in Tasmanian forests.", "keywords": ["forest productivity", "Tasmanian devils", "soil microbiome", "Climate change", "nutrient cycling", "FOS: Earth and related environmental sciences", "scat inputs", "Soil carbon"], "contacts": [{"organization": "Stephenson, Torrey", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.cc2fqz6d9"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.cc2fqz6d9", "name": "item", "description": "10.5061/dryad.cc2fqz6d9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.cc2fqz6d9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-07-09T00:00:00Z"}}, {"id": "10.5061/dryad.gxd2547hz", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:24:07Z", "type": "Dataset", "title": "Data from: Chemical structure predicts the effect of plant-derived low-molecular weight compounds on soil microbiome structure and pathogen suppression", "description": "1. Plant-derived low molecular weight compounds play a crucial role in shaping soil microbiome functionality. While various compounds have been demonstrated to affect soil microbes, most data are case-specific and do not provide generalizable predictions on their effects. Here we show that the chemical structural affiliation of low molecular weight compounds typically secreted by plant roots \u2013 sugars, amino acids, organic acids and phenolic acids \u2013 can predictably affect microbiome diversity, composition and functioning in terms of plant disease suppression. 2. We amended soil with single or mixtures of representative compounds, mimicking carbon deposition by plants. We then assessed how different classes of compounds, or their combinations, affected microbiome composition and the protection of tomato plants from the soil-borne Ralstonia solanacearum bacterial pathogen. 3. We found that chemical class predicted well the changes in microbiome composition and diversity. Organic and amino acids generally decreased the microbiome diversity compared to sugars and phenolic acids. These changes were also linked to disease incidence, with amino acids and nitrogen-containing compound mixtures inducing more severe disease symptoms connected with a reduction in bacterial community diversity. 4. Together, our results demonstrate that low molecular weight compounds can predictably steer rhizosphere microbiome functioning providing guidelines to engineer microbiomes based on root exudation patterns by specific plant cultivars or crop regimes.", "keywords": ["2. Zero hunger", "Chemical structure", "13. Climate action", "Plant-derived low molecular weight compounds", "soil suppressiveness", "soil microbiome", "15. Life on land"], "contacts": [{"organization": "Gu, Yian, Wang, Xiaofang, Yang, Tianjie, Friman, Ville Petri, Geisen, Stefan, Wei, Zhong, Xu, Yangchun, Jousset, Alexandre, Shen, Qirong,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.gxd2547hz"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.gxd2547hz", "name": "item", "description": "10.5061/dryad.gxd2547hz", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.gxd2547hz"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "10317/18590", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:28:23Z", "type": "Journal Article", "created": "2023-06-27", "title": "Intensive vegetable production under plastic mulch: A field study on soil plastic and pesticide residues and their effects on the soil microbiome", "description": "Intensive agriculture relies on external inputs to reach high productivity and profitability. Plastic mulch, mainly in the form of Low-Density Polyethylene (LDPE), is widely used in agriculture to decrease evaporation, increase soil temperature and prevent weeds. The incomplete removal of LDPE mulch after use causes plastic contamination in agricultural soils. In conventional agriculture, the use of pesticides also leaves residues accumulating in soils. Thus, the objective of this study was to measure plastic and pesticide residues in agricultural soils and their effects on the soil microbiome. For this, we sampled soil (0-10\u00a0cm and 10-30\u00a0cm) from 18 parcels from 6 vegetable farms in SE Spain. The farms were under either organic or conventional management, where plastic mulch had been used for >25\u00a0years. We measured the macro- and micro-light density plastic debris contents, the pesticide residue levels, and a range of physiochemical properties. We also carried out DNA sequencing on the soil fungal and bacterial communities. Plastic debris (>100\u00a0\u03bcm) was found in all samples with an average number of 2\u00a0\u00d7\u00a0103\u00a0particles\u00a0kg-1 and area of 60\u00a0cm2\u00a0kg-1. We found 4-10 different pesticide residues in all conventional soils, for an average of 140\u00a0\u03bcg\u00a0kg-1. Overall, pesticide content was \u223c100 times lower in organic farms. The soil microbiomes were farm-specific and related to different soil physicochemical parameters and contaminants. Regarding contaminants, bacterial communities responded to the total pesticide residues, the fungicide Azoxystrobin and the insecticide Chlorantraniliprole as well as the plastic area. The fungicide Boscalid was the only contaminant to influence the fungal community. The wide spread of plastic and pesticide residues in agricultural soil and their effects on soil microbial communities may impact crop production and other environmental services. More studies are required to evaluate the total costs of intensive agriculture.", "keywords": ["2. Zero hunger", "Plastic mulch", "Soil microbiome", "Microbiota", "Microplastic", "Pesticide Residues", "Pesticides residues", "Agriculture", "12. Garantizar modalidades de consumo y producci\u00f3n sostenibles", "15. Life on land", "Fungicides", " Industrial", "Edafolog\u00eda y Qu\u00edmica Agr\u00edcola", "Soil", "Intensive vegetable production", "13. Climate action", "Agriculture contamination", "Polyethylene", "Vegetables", "31 Ciencias Agrarias::3101 Agroqu\u00edmica", "Pesticides"]}, "links": [{"href": "https://doi.org/10317/18590"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10317/18590", "name": "item", "description": "10317/18590", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10317/18590"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10400.14/37827", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:28:24Z", "type": "Journal Article", "created": "2022-05-10", "title": "Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation", "description": "

We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community\u2019s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 \u00b0C + 50% water holding capacity (WHC)); increased air temperature (15\u201325 \u00b0C or 20\u201330 \u00b0C + 50% WHC); flood (20 \u00b0C + 75% WHC); drought (20 \u00b0C + 25% WHC); and ultraviolet radiation (UV) (20 \u00b0C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community\u2019s physiological profile and the bacterial community\u2019s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20\u201330 \u00b0C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome\u2013invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.

", "keywords": ["0301 basic medicine", "Soil invertebrates", "Ultraviolet Rays", "drought", "microbial activity", "DNA", " Ribosomal", "Flood", "Article", "Quantitative PCR", "Soil", "03 medical and health sciences", "soil microbiome", "2. Zero hunger", "metagenomics", "increased temperature; drought; flood; UV exposure; microbial activity; bacterial diversity; metagenomics; quantitative PCR; soil microbiome; soil invertebrates", "Soil microbiome", "0303 health sciences", "Drought", "Bacteria", "Microbiota", "bacterial diversity", "Temperature", "Water", "flood", "15. Life on land", "soil invertebrates", "6. Clean water", "UV exposure", "Microbial activity", "Bacterial diversity", "13. Climate action", "quantitative PCR", "Metagenomics", "Increased temperature", "increased temperature"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/13/5/850/pdf"}, {"href": "https://doi.org/10400.14/37827"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10400.14/37827", "name": "item", "description": "10400.14/37827", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10400.14/37827"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-10T00:00:00Z"}}, {"id": "10400.14/44005", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:28:24Z", "type": "Journal Article", "created": "2024-01-16", "title": "Structural and Functional Shifts in the Microbial Community of a Heavy Metal-Contaminated Soil Exposed to Short-Term Changes in Air Temperature, Soil Moisture and UV Radiation", "description": "

The interplay between metal contamination and climate change may exacerbate the negative impact on the soil microbiome and, consequently, on soil health and ecosystem services. We assessed the response of the microbial community of a heavy metal-contaminated soil when exposed to short-term (48 h) variations in air temperature, soil humidity or ultraviolet (UV) radiation in the absence and presence of Enchytraeus crypticus (soil invertebrate). Each of the climate scenarios simulated significantly altered at least one of the microbial parameters measured. Irrespective of the presence or absence of invertebrates, the effects were particularly marked upon exposure to increased air temperature and alterations in soil moisture levels (drought and flood scenarios). The observed effects can be partly explained by significant alterations in soil properties such as pH, dissolved organic carbon, and water-extractable heavy metals, which were observed for all scenarios in comparison to standard conditions. The occurrence of invertebrates mitigated some of the impacts observed on the soil microbial community, particularly in bacterial abundance, richness, diversity, and metabolic activity. Our findings emphasize the importance of considering the interplay between climate change, anthropogenic pressures, and soil biotic components to assess the impact of climate change on terrestrial ecosystems and to develop and implement effective management strategies.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "Soil invertebrates", "Soil microbiome", "Soil drought", "Ultraviolet Rays", "Soil pollution", "Microbiota", "Temperature", "Enchytraeus crypticus", "15. Life on land", "01 natural sciences", "Article", "6. Clean water", "Soil", "03 medical and health sciences", "13. Climate action", "UVR exposure", "Metals", " Heavy", "Climate change", "Soil flood", "Metagenomics", "Increased temperature", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10400.14/44005"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10400.14/44005", "name": "item", "description": "10400.14/44005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10400.14/44005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-16T00:00:00Z"}}, {"id": "1959.7/uws:74648", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:29:05Z", "type": "Journal Article", "created": "2023-12-04", "title": "The soil microbiome governs the response of microbial respiration to warming across the globe", "description": "Open AccessThe sensitivity of soil microbial respiration to warming (Q10) remains a major source of uncertainty surrounding the projections of soil carbon emissions to the atmosphere as the factors driving Q10 patterns across ecosystems have been assessed in isolation from each other. Here we report the results of a warming experiment using soils from 332 sites across all continents and major biomes to simultaneously evaluate the main drivers of global Q10 patterns. Compared with biochemical recalcitrance, mineral protection, substrate quantity and environmental factors, the soil microbiome (that is, microbial biomass and bacterial taxa) explained the largest portion of variation in Q10 values. Our work provides solid evidence that soil microbiomes largely govern the responses of soil heterotrophic respiration to warming and thus need to be explicitly accounted for when assessing land carbon\u2013climate feedbacks.", "keywords": ["2. Zero hunger", "Soil microbiome", "Microbial respiration", "13. Climate action", "XXXXXX - Unknown", "Warming", "15. Life on land", "12. Responsible consumption"]}, "links": [{"href": "https://doi.org/1959.7/uws:74648"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Climate%20Change", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1959.7/uws:74648", "name": "item", "description": "1959.7/uws:74648", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1959.7/uws:74648"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "2164/24787", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:29:32Z", "type": "Journal Article", "created": "2024-10-08", "title": "Land use effects on soil microbiome composition and traits with consequences for soil carbon cycling", "description": "Abstract

The soil microbiome determines the fate of plant-fixed carbon. The shifts in soil properties caused by land use change leads to modifications in microbiome function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated using metaproteomics, metabarcoding, and a 13C-labeled litter decomposition experiment across two temperate sites with differing soil pH each with a paired land use intensity contrast. 13C incorporation into microbial biomass increased with land use intensification in low-pH soil but decreased in high-pH soil, with potential impact on carbon use efficiency in opposing directions. Reduction in biosynthesis traits was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. We observed divergent pH-controlled pathways of SOC cycling. In low-pH soil, land use intensification alleviates microbial abiotic stress resulting in increased biomass production but promotes decomposition and SOC loss. In contrast, in high-pH soil, land use intensification increases microbial physiological constraints and decreases biomass production, leading to reduced necromass build-up and SOC stabilization. We demonstrate how microbial biomass production and respiration dynamics and therefore carbon use efficiency can be decoupled from SOC highlighting the need for its careful consideration in managing SOC storage for soil health and climate change mitigation.

Antibiotic resistance (AR) is recognized by the World Health Organization as a major threat to human health, and recent studies highlight the role of microplastics (MPs) in its spread. MPs in the environment may act as vectors for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Bacterial communities on the plastisphere, the surface of MPs, are influenced by plastic properties, allowing ARB to colonize and form biofilms. These biofilms facilitate the transfer of ARGs within microbial communities. This study analyzed data from the LUCAS soil dataset (885 soil samples across EU countries) using the Emu tool to characterize microbial communities at the genus/species level. Functional annotation via PICRUSt2, supported by a custom tool for Emu output formatting, revealed significant correlations between the genera Solirubrobacter, Bradyrhizobium, Nocardioides, and Bacillus with pathways linked to microplastic degradation and antibiotic resistance. These genera were consistently present in various soil types (woodland, grassland, and cropland), suggesting their potential as bioindicators of soil health in relation to MP pollution. The findings underscore MPs as hotspots for ARB and ARGs, offering new insights into the identification of bioindicators for monitoring soil health and the ecological impacts related to MP contamination.

", "keywords": ["microplastics; antibiotic resistance genes; soil microbiome; LUCAS soil"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/1142151/2/sustainability-17-01093.pdf"}, {"href": "https://www.mdpi.com/2071-1050/17/3/1093/pdf"}, {"href": "https://doi.org/2434/1142151"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sustainability", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2434/1142151", "name": "item", "description": "2434/1142151", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2434/1142151"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-01-29T00:00:00Z"}}, {"id": "2946862318", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:29:54Z", "type": "Journal Article", "created": "2019-06-03", "title": "Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes", "description": "

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe\u2013plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant\u2013growth\u2013promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

", "keywords": ["0301 basic medicine", "570", "plant\u2013growth\u2013promotion (PGP)", "metagenomically-assembled-genomes (MAGs)", "Article", "03 medical and health sciences", "carbon dioxide fixation", "Ammonia", "metagenomic binning", "Germany", "soil microbiome", "Proteobacteria", "Humans", "biocontrol", "secondary metabolite synthesis", "suppressive soil", "Phylogeny", "Soil Microbiology", "soil microbiome; suppressive soil; biocontrol; plant\u2013growth\u2013promotion (PGP); metagenomic binning; metagenomically-assembled-genomes (MAGs); secondary metabolite synthesis; carbon dioxide fixation; carbohydrate-active enzymes; differentially abundant features (DAFs)", "2. Zero hunger", "Bacteria", "Bacteroidetes", "Agriculture", "differentially abundant features (DAFs)", "15. Life on land", "Archaea", "Actinobacteria", "13. Climate action", "carbohydrate-active enzymes", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://doi.org/2946862318"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2946862318", "name": "item", "description": "2946862318", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2946862318"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-03T00:00:00Z"}}, {"id": "3171272055", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:30:19Z", "type": "Journal Article", "created": "2021-06-07", "title": "Dynamics of Soil Bacterial and Fungal Communities During the Secondary Succession Following Swidden Agriculture IN Lowland Forests", "description": "

Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe\u2013plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant\u2013growth\u2013promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

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