Natural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off\uffe2\uff80\uff90target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co\uffe2\uff80\uff90operation and Development, which is a key international standard\uffe2\uff80\uff90setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5\uffe2\uff80\uff90dichloraniline). We determined the following in three different soils: (i) ammonium (NH4+) and nitrate (NO3\uffe2\uff88\uff92) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q\uffe2\uff80\uff90PCR).
RESULTSAll pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose\uffe2\uff80\uff90dependent effects on NH4+ and NO3\uffe2\uff88\uff92 levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q\uffe2\uff80\uff90PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5\uffe2\uff80\uff90dichloraniline.
CONCLUSIONOur findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well\uffe2\uff80\uff90standardized tools. \uffc2\uffa9 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas.
Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium).
Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam\uffe2\uff80\uff90disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.
The \uffe2\uff80\uff98state of alert\uffe2\uff80\uff99 detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.
", "keywords": ["0301 basic medicine", "Proteome", "Propanols", "Arbuscular mycorrhizal fungi", "arbuscular mycorrhizal fungi", "tomato", "Lignin", "Models", " Biological", "Plant Roots", "defence responses", "Tomato", "Soil", "03 medical and health sciences", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Stress", " Physiological", "microbiota", "Plant Immunity", "Soil Microbiology", "suppressive and conducive soils", "susceptible and resistant genotypes", "2. Zero hunger", "0303 health sciences", "Defence responses", "Microbiota", "15. Life on land", "Lignin biosynthesis", "Gene Ontology", "Susceptible and resistant genotypes", "Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science", "Suppressive and conducive soils", "Transcriptome", "lignin biosynthesis"]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1660820/1/Chialva%20et%20al%20Iris.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014"}, {"href": "https://doi.org/10.1111/nph.15014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.15014", "name": "item", "description": "10.1111/nph.15014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.15014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-09T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2018.12.062", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:53Z", "type": "Journal Article", "created": "2018-12-18", "title": "H2S removal and microbial community composition in an anoxic biotrickling filter under autotrophic and mixotrophic conditions", "description": "Removal of H2S from gas streams using NO3--containing synthetic wastewater was investigated in an anoxic biotrickling filter (BTF) at feed N/S ratios of 1.2-1.7\u2009mol mol-1 with an empty bed residence time of 3.5\u2009min and a hydraulic retention time of 115\u2009min. During 108 days of operation under autotrophic conditions, the BTF showed a maximum elimination capacity (EC) of 19.2\u2009g S m-3\u2009h-1 and H2S removal efficiency (RE) >99%. When the BTF was operated under mixotrophic conditions by adding organic carbon (10.2\u2009g acetate m-3\u2009h-1) to the synthetic wastewater, the H2S EC decreased from 16.4 to 13.1\u2009g S m-3\u2009h-1, while the NO3- EC increased from 9.9 to 11.1\u2009g NO3--N m-3\u2009h-1, respectively. Thiobacillus sp. (98-100% similarity) was the only sulfur-oxidizing nitrate-reducing bacterium detected in the BTF biofilm, while the increased abundance of heterotrophic denitrifiers, i.e. Brevundimonas sp. and Rhodocyclales, increased the N/S ratio during BTF operation. Residence time distribution tests showed that biomass accumulation during BTF operation reduced gas and liquid retention times by 17.1% and 83.5%, respectively.", "keywords": ["570", "Air Pollutants", "Nitrates", "550", "Bacteria", "Microbiota", "116 Chemical sciences", "116", "Waste Disposal", " Fluid", "01 natural sciences", "6. Clean water", "Bioreactors", "Denitrification", "Hydrogen Sulfide", "Filtration", "Water Pollutants", " Chemical", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2018.12.062"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2018.12.062", "name": "item", "description": "10.1016/j.jhazmat.2018.12.062", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2018.12.062"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2020.123208", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:53Z", "type": "Journal Article", "created": "2020-06-17", "title": "Effects of prescription antibiotics on soil- and root-associated microbiomes and resistomes in an agricultural context", "description": "The use of treated wastewater for crop irrigation is rapidly increasing to respond to the ever-growing demands for water and food resources. However, this practice may contribute to the spread of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in agricultural settings. To evaluate this potential risk, we analyzed microbiomes and resistomes of soil and Lactuca sativa L. (lettuce) root samples from pots irrigated with tap water spiked with 0, 20, or 100 \u03bcg L-1 of a mixture of three antibiotics (Trimethoprim, Ofloxacin, Sulfamethoxazole). The presence of antibiotics induced changes in bacterial populations, particularly in soil, as revealed by 16S rDNA sequence analysis. Parallel shotgun sequencing identified a total of 56 different ARGs conferring resistance against 14 antibiotic families. Antibiotic -treated samples showed increased loads of ARGs implicated in mutidrug resistance or in both direct and indirect acquired resistance. These changes correlated with the prevalence of Xantomonadales species in the root microbiomes. We interpret these data as indicating different strategies of soil and root microbiomes to cope with the presence of antibiotics, and as a warning that their presence may increase the loads of ARBs and ARGs in edible plant parts, therefore constituting a potential risk for human consumers.", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Microbiota", "Angiotensin-Converting Enzyme Inhibitors", "Drug Resistance", " Microbial", "6. Clean water", "Anti-Bacterial Agents", "Angiotensin Receptor Antagonists", "Soil", "03 medical and health sciences", "Prescriptions", "Genes", " Bacterial", "Humans", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2020.123208"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2020.123208", "name": "item", "description": "10.1016/j.jhazmat.2020.123208", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2020.123208"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2024.134885", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:54Z", "type": "Journal Article", "created": "2024-06-12", "title": "Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes", "description": "Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.", "keywords": ["Bacteria", "Antibiotic resistance", "Microbiota", "Water Pollution", "Metagenome assembled genomes", "Drug Resistance", " Microbial", "Horizontal gene transfer", "Wastewater", "extracellular DNA; antibiotic resistance; metagenome assembled genomes; transformation; horizontal gene transfer", "Transformation", "Anti-Bacterial Agents", "Lakes", "Extracellular DNA", "Genes", " Bacterial", "Drug Resistance", " Bacterial", "Water Microbiology", "Plasmids"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/1115155/2/Sivalingam%20et%20al%202024.pdf"}, {"href": "https://doi.org/10.1016/j.jhazmat.2024.134885"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2024.134885", "name": "item", "description": "10.1016/j.jhazmat.2024.134885", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2024.134885"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2024.134231", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:54Z", "type": "Journal Article", "created": "2024-04-06", "title": "Soil microbial community fragmentation reveals indirect effects of fungicide exposure mediated by biotic interactions between microorganisms", "description": "Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.", "keywords": ["2. Zero hunger", "570", "Bacteria", "hymexazol", "[SDV]Life Sciences [q-bio]", "Microbiota", "Fungi", "500", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "15. Life on land", "Fungicides", " Industrial", "[SDV] Life Sciences [q-bio]", "nitrogen cycling", "13. Climate action", "network", "ammonia-oxidizing microorganism", "Soil Pollutants", "Microbial Interactions", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "pesticide", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2024.134231"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2024.134231", "name": "item", "description": "10.1016/j.jhazmat.2024.134231", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2024.134231"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-05-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2016.07.135", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:06Z", "type": "Journal Article", "created": "2016-07-27", "title": "Biochar Decreased Microbial Metabolic Quotient And Shifted Community Composition Four Years After A Single Incorporation In A Slightly Acid Rice Paddy From Southwest China", "description": "While numerous studies both in laboratory and field have showed short term impacts of biochar on soil microbial community, there have been comparatively few reports addressing its long term impacts particular in field condition. This study investigated the changes of microbial community activity and composition in a rice paddy four years after a single incorporation of biochar at 20 and 40t/ha. The results indicated that biochar amendment after four years increased soil pH, soil organic C (SOC), total N and C/N ratio and decreased bulk density, particularly for the 40t/ha treatment compared to the control (0t/ha). Though no significant difference was observed in soil basal respiration, biochar amendment increased soil microbial biomass C and resulted in a significantly lower metabolic quotient. Besides, dehydrogenase and \u03b2-glucosidase activities were significantly decreased under biochar amendment relative to the control. The results of Illumina Miseq sequencing showed that biochar increased \u03b1-diversity of bacteria but decreased that of fungi and changed both bacterial and fungal community structures significantly. Biochar did not change the relative abundances of majority of bacteria at phylum level with the exception of a significant reduction of Actinobacteria, but significantly changed most of bacterial groups at genus level, particularly at 40t/ha. In contrast, biochar significantly decreased the relative abundances of Ascomycota and Basidiomycota by 11% and 66% and increased the relative abundances of Zygomycota by 147% at 40t/ha compared to the non-amended soil. Redundancy analysis (RDA) indicated that biochar induced changes in soil chemical properties, such as pH, SOC and C/N, were important factors driving community composition shifts. This study suggested that biochar amendment may increase microbial C use efficiency and reduce some microorganisms that are capable of decomposing more recalcitrant soil C, which may help stabilization of soil organic matter in paddy soil in long term.", "keywords": ["2. Zero hunger", "China", "Microbiota", "Fungi", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "Bacterial Physiological Phenomena", "6. Clean water", "Soil", "Biodegradation", " Environmental", "13. Climate action", "Charcoal", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Seasons", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2016.07.135"}, {"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.2016.07.135", "name": "item", "description": "10.1016/j.scitotenv.2016.07.135", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2016.07.135"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-11-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2024.170290", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:10Z", "type": "Journal Article", "created": "2024-01-19", "title": "Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability", "description": "Survival and growth strategies of Antarctic endolithic microbes residing in Earth's driest and coldest desert remain virtually unknown. From 109 endolithic microbiomes, 4539 metagenome-assembled genomes were generated, 49.3\u00a0% of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability.", "keywords": ["570", "Bacteria", "Microbiota", "Habitability", "500", "Antarctic Regions", "Astronomical Sciences", "15. Life on land", "Extremophiles", "13. Climate action", "Physical Sciences", "Antarctica", "Metagenome", "Metagenomics", "14. Life underwater", "Adaptation", "MAGs", "Settore BIO/19 - MICROBIOLOGIA GENERALE", "Environmental Sciences"]}, "links": [{"href": "https://openpub.fmach.it/bitstream/10449/83880/5/2024%20STE%20Albanese.pdf"}, {"href": "https://doi.org/10.1016/j.scitotenv.2024.170290"}, {"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.2024.170290", "name": "item", "description": "10.1016/j.scitotenv.2024.170290", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.170290"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-03-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2016.05.073", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:06Z", "type": "Journal Article", "created": "2016-06-09", "title": "Associations Between Soil Bacterial Community Structure And Nutrient Cycling Functions In Long-Term Organic Farm Soils Following Cover Crop And Organic Fertilizer Amendment", "description": "Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(\u00ae) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-\u03b2-d-glucosaminidase and \u03b2-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were better explained using both soil physicochemical test values and bacterial community structure data than using soil tests alone. Pursuing a better understanding of bacterial community composition and how it is affected by farming practices is a promising avenue for increasing our ability to predict the impact of management practices on important soil functions.", "keywords": ["Crops", " Agricultural", "2. Zero hunger", "Environmental Engineering", "Farms", "Bacteria", "Microbiota", "Agriculture", "04 agricultural and veterinary sciences", "15. Life on land", "Pollution", "6. Clean water", "RNA", " Bacterial", "Soil", "13. Climate action", "RNA", " Ribosomal", " 16S", "Environmental Chemistry", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Waste Management and Disposal", "Soil Microbiology", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2016.05.073"}, {"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.2016.05.073", "name": "item", "description": "10.1016/j.scitotenv.2016.05.073", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2016.05.073"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-10-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2018.10.268", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:07Z", "type": "Journal Article", "created": "2018-10-22", "title": "Antibiotic resistance genes distribution in microbiomes from the soil-plant-fruit continuum in commercial Lycopersicon esculentum fields under different agricultural practices", "description": "While the presence of antibiotic resistance genes (ARGs) in agricultural soils and products has been firmly established, their distribution among the different plant parts and the contribution of agricultural practices, including irrigation with reclaimed water, have not been adequately addressed yet. To this end, we analyzed the levels of seven ARGs (sul1, blaTEM, blaCTX-M-32, mecA, qnrS1, tetM, blaOXA-58), plus the integrase gene intl1, in soils, roots, leaves, and fruits from two commercial tomato fields irrigated with either unpolluted groundwater or from a channel impacted by treated wastewater, using culture-independent, quantitative real-time PCR methods. ARGs and intl1 sequences were found in leaves and fruits at levels representing from 1 to 10% of those found in roots or soil. The relative abundance of intl1 sequences correlated with tetM, blaTEM, and sul1 levels, suggesting a high horizontal mobility potential for these ARGs. High-throughput 16S rDNA sequencing revealed microbiome differences both between sample types (soil plus roots versus leaves plus fruits) and sampling zones, and a correlation between the prevalence of Pseudomonadaceae and the levels of different ARGs, particularly in fruits and leaves. We concluded that both microbiome composition and ARGs levels in plants parts, including fruits, were likely influenced by agricultural practices.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Antibiotic resistance", "Microbiota", "Microbiomes", "Agriculture", "Drug Resistance", " Microbial", "Horizontal gene transfer", "Irrigation water", "15. Life on land", "6. Clean water", "qPCR", "Soil", "03 medical and health sciences", "Solanum lycopersicum", "Genes", " Bacterial", "Fruit", "Soil Microbiology", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2018.10.268"}, {"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.2018.10.268", "name": "item", "description": "10.1016/j.scitotenv.2018.10.268", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2018.10.268"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2019.04.038", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:07Z", "type": "Journal Article", "created": "2019-04-04", "title": "When the exception becomes the rule: An integrative approach to symbiosis", "description": "Symbiosis, mainly due to the advances in -omics technology and to the microbiome revolution, is being increasingly acknowledged as fundamental to explain any aspect of life existence. Previously considered an exception, a peculiar characteristic of few systems like lichens, corals and mycorrhizas, symbiosis is nowadays recognized as the rule, with the microbiome being part of all living entities and systems. However, our knowledge of the ecological meaning and functioning of many symbiotic systems is still limited. Here, we discuss a new, integrative approach based on current findings that looks at commonalities among symbiotic systems to produce theoretical models and conceptual knowledge that would allow a more efficient exploitation of symbiosis-based biotechnologies. The microbiome recruitment and assemblage processes are indicated as one of the potential targets where a holistic approach could bring advantages. Finally, we reflect on the potential socio-economic and environmental consequences of a symbiotic view of the world, where co-dependence is the matrix of life.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Microbiota", "Animals", "Anthozoa", "Symbiosis"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2019.04.038"}, {"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.2019.04.038", "name": "item", "description": "10.1016/j.scitotenv.2019.04.038", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2019.04.038"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-07-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2022.154405", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:09Z", "type": "Journal Article", "created": "2022-03-08", "title": "Pedogenesis shapes predator-prey relationships within soil microbiomes", "description": "Pedogenesis determines soil physicochemical properties and many biodiversity facets, including belowground microbial bacteria and fungi. At the local scale, top-down predation by microbial protists regulates the soil microbiome, while the microbiome also affects protistan communities. However, it remains unknown how pedogenesis affects protistan communities and the potential protist-microbiome predator-prey relationships. With 435 soil samples representing different stages of pedogenesis ranging in soil age from centuries to millennia, we examined the influence of pedogenesis on the main protistan groups, and the interrelationships between protistan predators and microbial prey biomass. We revealed an enrichment in the diversity of total protists across pedogenesis and increasing richness of phototrophic protists in the medium compared with the early stages of pedogenesis. The richness of predatory protists accumulated throughout pedogenesis, which was more strongly determined by microbial biomass than environmental factors. Predator-prey associations were stronger in the young and the medium soils than in the older soils, likely because prey biomass accumulated in the latter and might be no longer limit predators. Together, our work provides evidence that pedogenesis shapes predatory protists differently than their prey, leading to shifts in predator-prey relationships. This knowledge is critical to better understand how soil food webs develop across soil development which might lead to changes in ecosystem functions.", "keywords": ["Predator-prey relationships", "2. Zero hunger", "Food Chain", "Microbiota", "Microbial biomass", "Eukaryota", "Biodiversity", "04 agricultural and veterinary sciences", "15. Life on land", "Soil", "Soil formation", "13. Climate action", "Predatory Behavior", "XXXXXX - Unknown", "Chronosequences", "Protistan predators", "Animals", "0401 agriculture", " forestry", " and fisheries", "Microbiome"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2022.154405"}, {"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.2022.154405", "name": "item", "description": "10.1016/j.scitotenv.2022.154405", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2022.154405"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2023.165179", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:09Z", "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": "10.1016/j.scitotenv.2023.167674", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:09Z", "type": "Journal Article", "created": "2023-10-07", "title": "Outdoor climate drives diversity patterns of dominant microbial taxa in caves worldwide", "description": "The cave microbiota is assumed to be shaped by indoor microclimate, biotic and abiotic factors, which are largely dependent from outside environmental conditions; however, this knowledge is available at local or regional scales only. To address this knowledge gap, we reanalyzed over 1050 bacterial and fungal communities of caves worldwide, and found that outdoor temperature and rainfall play a critical role in explaining differences in microbial diversity patterns of global caves, selecting specific dominant taxa across gradients of growing aridity conditions with arid climate leading to a reduction in total cave microbial diversity. Moreover, we found that fungal (from 186 to 1908 taxa) and bacterial (from 467 to 1619 taxa) diversity increased under temperate-tropical and temperate-continental climatic regions, respectively, highlighting an opposite preference for the two microbial compartments. We hypothesized that outdoor geographical, climatic variables and lithology are critical epistatic drivers in assembling microbial communities and their dominant taxa, whose ecological responses could be useful to predict the fate of these subterranean environments in the context of climate change. Our work elucidates the intimate connection between caves microbiota and surface ecosystems highlighting the sensitivity of cave microbial communities to climatic changes and environmental degradation. This work also provides a natural benchmark for the biogeographic information for caves globally and for protection strategies aiming at conservation of underground environments.", "keywords": ["Cave ecosystems", "Bacteria", "Geography", "Microbiota", "Microbiomes", "15. Life on land", "Microbial ecology", "Caves", "13. Climate action", "XXXXXX - Unknown", "Climate change", "Environmental drivers", "Top dominant species", "Mycobiome"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2023.167674"}, {"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.2023.167674", "name": "item", "description": "10.1016/j.scitotenv.2023.167674", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2023.167674"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2024.177557", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:10Z", "type": "Journal Article", "created": "2024-11-20", "title": "Dynamic response of soil microbial communities and network to hymexazol exposure", "description": "Fungicides are an essential component of current agricultural practices, but their extensive use has raised concerns about their effects on non-target soil microorganisms, which carry out essential ecosystem functions. However, despite the complexity of microbial communities, many studies investigating their response to fungicides focus only on bacteria or fungi at one point in time. In this study, we used amplicon sequencing to assess the effect of the fungicide hymexazol on the diversity, composition, and co-occurrence network of soil bacteria, fungi, and protists at 7, 21, and 60\u00a0days after application. We found that hymexazol had very little effect on microbial alpha-diversity, but that microbial community composition and OTU differential abundance were altered over the duration of the experiment, even after hymexazol concentrations were undetectable. The co-occurrence patterns within and between microbial kingdoms were affected by hymexazol dose, suggesting that indirect effects may play a role in the microbial community response. Nitrogen cycling was also affected, with a transient hymexazol-associated increase in the abundance of ammonia-oxidizing microorganisms and soil nitrate concentration. These findings highlight that the effects of fungicides on soil microorganisms are dynamic and extensive, spanning several taxonomic kingdoms.", "keywords": ["570", "Bacteria", "Fungicide", "Microbiota", "Fungi", "Protists", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "Nitrification", "630", "Fungicides", " Industrial", "Pesticide", "Soil", "Soil Pollutants", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "Soil Microbiology", "Nitrogen cycling"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2024.177557"}, {"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.2024.177557", "name": "item", "description": "10.1016/j.scitotenv.2024.177557", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.177557"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-12-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2020.107876", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:25Z", "type": "Journal Article", "created": "2020-06-07", "title": "The physical structure of soil: Determinant and consequence of trophic interactions", "description": "Open AccessSoil Biology and Biochemistry, 148", "keywords": ["0301 basic medicine", "2. Zero hunger", "Matric potential", "Soil pores", "Microbiota", "04 agricultural and veterinary sciences", "15. Life on land", "Mesofauna", "03 medical and health sciences", "Soil microhabitat", "Soil food web", "13. Climate action", "Soil pores; Soil microhabitat; Microbiota; Mesofauna; Soil food web; Matric potential", "0401 agriculture", " forestry", " and fisheries"], "contacts": [{"organization": "Erktan, Amandine, Or, Dani, Scheu, Stefan,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2020.107876"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2020.107876", "name": "item", "description": "10.1016/j.soilbio.2020.107876", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2020.107876"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-01T00:00:00Z"}}, {"id": "10.1111/gcb.12418", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:20Z", "type": "Journal Article", "created": "2013-10-12", "title": "Soil Microbial And Nutrient Responses To 7years Of Seasonally Altered Precipitation In A Chihuahuan Desert Grassland", "description": "AbstractSoil microbial communities in Chihuahuan Desert grasslands generally experience highly variable spatiotemporal rainfall patterns. Changes in precipitation regimes can affect belowground ecosystem processes such as decomposition and nutrient cycling by altering soil microbial community structure and function. The objective of this study was to determine if increased seasonal precipitation frequency and magnitude over a 7\uffe2\uff80\uff90year period would generate a persistent shift in microbial community characteristics and soil nutrient availability. We supplemented natural rainfall with large events (one/winter and three/summer) to simulate increased precipitation based on climate model predictions for this region. We observed a 2\uffe2\uff80\uff90year delay in microbial responses to supplemental precipitation treatments. In years 3\uffe2\uff80\uff935, higher microbial biomass, arbuscular mycorrhizae abundance, and soil enzyme C and P acquisition activities were observed in the supplemental water plots even during extended drought periods. In years 5\uffe2\uff80\uff937, available soil P was consistently lower in the watered plots compared to control plots. Shifts in soil P corresponded to higher fungal abundances, microbial C utilization activity, and soilpH. This study demonstrated that 25% shifts in seasonal rainfall can significantly influence soil microbial and nutrient properties, which in turn may have long\uffe2\uff80\uff90term effects on nutrient cycling and plant P uptake in this desert grassland.
", "keywords": ["precipitation manipulation", "Climate Change", "Rain", "extreme climate events", "Soil", "XXXXXX - Unknown", "Big Bend National Park", "Soil Microbiology", "2. Zero hunger", "Ecology", "Bacteria", "Microbiota", "Fungi", "04 agricultural and veterinary sciences", "Biological Sciences", "15. Life on land", "Grassland", "Texas", "6. Clean water", "desert ecosystems", "13. Climate action", "soil microbial communities", "0401 agriculture", " forestry", " and fisheries", "Seasons", "Desert Climate", "Environmental Sciences"]}, "links": [{"href": "https://escholarship.org/content/qt4v79d7f4/qt4v79d7f4.pdf"}, {"href": "https://doi.org/10.1111/gcb.12418"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/gcb.12418", "name": "item", "description": "10.1111/gcb.12418", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.12418"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-04-04T00:00:00Z"}}, {"id": "10.1016/j.watres.2021.116818", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:43Z", "type": "Journal Article", "created": "2021-01-08", "title": "Antibiotic resistance gene load and irrigation intensity determine the impact of wastewater irrigation on antimicrobial resistance in the soil microbiome", "description": "Treated wastewater (TWW) irrigation is a useful counter-measure against the depletion of freshwater (FW) resources. However, TWW contains several contaminants of emerging concern, such as antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). Thus, TWW irrigation might promote the spread of antimicrobial resistance in soil environments. In the present work, we hypothesized that the ARG load and irrigation intensity define the effect of TWW irrigation on ARG spread dynamics in soil. This hypothesis was tested using a multiphase approach: a) comparing soil from a full-scale, commercially operated, TWW irrigated field with non-irrigated soil, b) long-term sampling of the TWW irrigated field over one year with different irrigation intensities and intercepted by irrigation breaks and c) laboratory-scale soil microcosms irrigated with TWW compared to FW. Six ARGs, the integrase gene intI1 and the 16S rRNA were quantified using qPCR. In addition, effects of TWW irrigation on bacterial community composition of microcosm-samples were analysed with 16S rRNA amplicon sequencing. The genes sul1, qnrS, blaOXA-58, tet(M) and intI1 were significantly more abundant in the TWW irrigated field soil, whereas blaCTX--M-32 and blaTEM, the least abundant genes in the TWW irrigation, showed higher abundance in the non-irrigated soil. The relative abundance of sul1, qnrS, blaOXA-58, tet(M) and intI1 correlated with TWW irrigation intensity and decreased during irrigation breaks. Despite the decrease, the levels of these genes remained consistently higher than the non-irrigated soil indicating persistence upon their introduction into the soil. Microcosm experiments verified observations from the field study: TWW irrigation promoted the spread of ARGs and intI1 into soil at far elevated levels compared to FW irrigation. However, the impact of TWW irrigation on 16S rRNA absolute abundance and the soil microbial community composition was negligible. In conclusion, the impact of TWW irrigation depends mainly on the introduced ARG load and the irrigation intensity.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Agricultural Irrigation", "Microbiota", "Angiotensin-Converting Enzyme Inhibitors", "Wastewater", "15. Life on land", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Angiotensin Receptor Antagonists", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "Drug Resistance", " Bacterial", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.watres.2021.116818"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.watres.2021.116818", "name": "item", "description": "10.1016/j.watres.2021.116818", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.watres.2021.116818"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-01T00:00:00Z"}}, {"id": "10.1021/acs.est.0c06687", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:49Z", "type": "Journal Article", "created": "2021-02-10", "title": "Microbial Interactions Drive the Complete Catabolism of the Antibiotic Sulfamethoxazole in Activated Sludge Microbiomes", "description": "Microbial communities are believed to outperform monocultures in the complete catabolism of organic pollutants via reduced metabolic burden and increased robustness to environmental challenges; however, the interaction mechanism in functional microbiomes remains poorly understood. Here, three functionally differentiated activated sludge microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2: complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole (3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX) were enriched. Combining time-series cultivation-independent microbial community analysis, DNA-stable isotope probing, molecular ecological network analysis, and cultivation-dependent function verification, we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were primary degraders for the initial cleavage of the sulfonamide functional group (-C-S-N- bond) and 3A5MI degradation, respectively. Complete catabolism of SMX was achieved by their cross-feeding. The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved in the enhancement of 3A5MI degradation. Moreover, we unraveled the internal labor division patterns and connections among the active members centered on the two primary degraders. Overall, the proposed methodology is promisingly applicable and would help generate mechanistic, predictive, and operational understanding of the collaborative biodegradation of various contaminants. This study provides useful information for synthetic activated sludge microbiomes with optimized environmental functions.", "keywords": ["Sulfamethoxazole", "Physiology", "Science Policy", "analysis", "0211 other engineering and technologies", "02 engineering and technology", "Microbiology", "Environmental Sciences not elsewhere classified", "heterocyclic product 3-", "11. Sustainability", "Activated Sludge Microbiomes Microb.", "Acidovorax", "SMX degradation process", "Molecular Biology", "cultivation-dependent function veri.", "phenyl", "Ecology", "Sewage", "Microbiota", "catabolism", "Nocardioide", "Computational Biology", "Cell Biology", "6. Clean water", "Sphingobium", "Anti-Bacterial Agents", "sludge microbiomes", "Infectious Diseases", "Complete", "Biodegradation", " Environmental", "Microbial Interactions Drive", "degrader", "Microbial Interactions", "labor division patterns", "5MI degradation", "Water Pollutants", " Chemical", "Developmental Biology", "Biological Sciences not elsewhere classified"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.0c06687"}, {"href": "https://doi.org/10.1021/acs.est.0c06687"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.0c06687", "name": "item", "description": "10.1021/acs.est.0c06687", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.0c06687"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-10T00:00:00Z"}}, {"id": "10.1021/acs.est.9b07562", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:50Z", "type": "Journal Article", "created": "2020-02-24", "title": "Silver Nanoparticles Alter Soil Microbial Community Compositions and Metabolite Profiles in Unplanted and Cucumber-Planted Soils", "description": "The rapid development of nanotechnology makes the environmental impact assessment a necessity to ensure the sustainable use of engineered nanomaterials. Here, silver nanoparticles (AgNPs) at 100 mg/kg were added to soils in the absence or presence of cucumber (Cucumis sativa) plants for 60 days. The response of the soil microbial community and associated soil metabolites was investigated by 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics, respectively. The results show that AgNP exposure significantly increased the soil pH in both unplanted and cucumber-planted soils. The soil bacterial community structure was altered upon Ag exposure in both soils. Several functionally significant bacterial groups, which are associated with carbon, nitrogen, and phosphorus cycling, were compromised by AgNPs in both unplanted and cucumber-planted soils. Generally, plants played a limited role in mediating the impact of AgNPs on the bacterial community. Soil metabolomic analysis showed that AgNPs altered the metabolite profile in both unplanted and cucumber-planted soils. The significantly changed metabolites are involved in sugar and amino acid-related metabolic pathways, indicating the perturbation of C and N metabolism, which is consistent with the bacterial community structure results. In addition, several fatty acids were significantly decreased upon exposure to AgNPs in both unplanted and cucumber-planted soils, suggesting the possible oxidative stress imposed on microbial cell membranes. These results provide valuable information for understanding the biological and biochemical impact of AgNP exposure on both plant species and on soil microbial communities; such understanding is needed to understand the risk posed by these materials in the environment.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Silver", "Microbiota", "Metal Nanoparticles", "15. Life on land", "6. Clean water", "Soil", "03 medical and health sciences", "13. Climate action", "RNA", " Ribosomal", " 16S", "Cucumis sativus", "Soil Microbiology"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.9b07562"}, {"href": "https://doi.org/10.1021/acs.est.9b07562"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.9b07562", "name": "item", "description": "10.1021/acs.est.9b07562", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.9b07562"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-24T00:00:00Z"}}, {"id": "10.1038/s41396-018-0335-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:10Z", "type": "Journal Article", "created": "2019-01-03", "title": "Ant colonies promote the diversity of soil microbial communities", "description": "AbstractLittle is known about the role of ant colonies in regulating the distribution and diversity of soil microbial communities across large spatial scales. Here, we conducted a survey across >1000\uffe2\uff80\uff89km in eastern Australia and found that, compared with surrounding bare soils, ant colonies promoted the richness (number of phylotypes) and relative abundance of rare taxa of fungi and bacteria. Ant nests were also an important reservoir for plant pathogens. Our study also provides a portfolio of microbial phylotypes only found in ant nests, and which are associated with high nutrient availability. Together, our work highlights the fact that ant nests are an important refugia for microbial diversity.Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional aqueous system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1\uffe2\uff80\uff89\uffc2\uffb5m-sized metabolite producer, receiver, and competitor cells in different spatial structures. We show that receivers cannot interact with producers located on average 15\uffe2\uff80\uff89\uffc2\uffb5m away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and varied the receiver cells\uffe2\uff80\uff99 product affinity, to show that within producer\uffe2\uff80\uff93receiver aggregates even low-affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces metabolic interaction distances to the low \uffc2\uffb5m-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.The relationship between biodiversity and biomass has been a long standing debate in ecology. Soil biodiversity and biomass are essential drivers of ecosystem functions. However, unlike plant communities, little is known about how the diversity and biomass of soil microbial communities are interlinked across globally distributed biomes, and how variations in this relationship influence ecosystem function. To fill this knowledge gap, we conducted a field survey across global biomes, with contrasting vegetation and climate types. We show that soil carbon (C) content is associated to the microbial diversity\uffe2\uff80\uff93biomass relationship and ratio in soils across global biomes. This ratio provides an integrative index to identify those locations on Earth wherein diversity is much higher compared with biomass and vice versa. The soil microbial diversity-to-biomass ratio peaks in arid environments with low C content, and is very low in C-rich cold environments. Our study further advances that the reductions in soil C content associated with land use intensification and climate change could cause dramatic shifts in the microbial diversity-biomass ratio, with potential consequences for broad soil processes.Soil microbial communities play a pivotal role in regulating ecosystem functioning. But they are increasingly being shaped by human-induced environmental change, including intense \uffe2\uff80\uff9cpulse\uffe2\uff80\uff9d perturbations, such as droughts, which are predicted to increase in frequency and intensity with climate change. While it is known that soil microbial communities are sensitive to such perturbations and that effects can be long-lasting, it remains untested whether there is a threshold in the intensity and frequency of perturbations that can trigger abrupt and persistent transitions in the taxonomic and functional characteristics of soil microbial communities. Here we demonstrate experimentally that intense pulses of drought equivalent to a 30-year drought event (<15% WHC) induce a major shift in the soil microbial community characterised by significantly altered bacterial and fungal community structures of reduced complexity and functionality. Moreover, the characteristics of this transformed microbial community persisted after returning soil to its previous moisture status. As a result, we found that drought had a strong legacy effect on bacterial community function, inducing an enhanced growth rate following subsequent drought. Abrupt transitions are widely documented in aquatic and terrestrial plant communities in response to human-induced perturbations. Our findings demonstrate that such transitions also occur in soil microbial communities in response to high intensity pulse perturbations, with potentially deleterious consequences for soil health.Soil-transmitted helminth infections represent a large burden with over a quarter of the world\uffe2\uff80\uff99s population at risk. Low cure rates are observed with standard of care (albendazole); therefore, a more effective combination therapy (albendazole and ivermectin) is being investigated but showed variable treatment efficacies without evidence of intrinsic parasite resistance. Here, we analyzed the microbiome ofTrichuris trichiuraand hookworm-infected patients and found an association of different enterotypes with treatment efficacy. 80\uffe2\uff80\uff89T. trichiura-infected patients with hookworm co-infections\uffc2\uffa0from Pak-Khan, Laos, received either albendazole (n\uffe2\uff80\uff89=\uffe2\uff80\uff8941) or albendazole and ivermectin combination therapy (n\uffe2\uff80\uff89=\uffe2\uff80\uff8939). Pre-/post-treatment stool samples were collected to monitor treatment efficacy and microbial communities were profiled using 16S rRNA gene sequencing, qPCR, and shotgun sequencing. We identified three bacterial enterotypes and show that pre-treatment enterotype is associated with efficacy of the combination treatment for bothT. trichiura(CRET1\uffe2\uff80\uff89=\uffe2\uff80\uff895.8%; CRET2\uffe2\uff80\uff89=\uffe2\uff80\uff8916.6%; CRET3\uffe2\uff80\uff89=\uffe2\uff80\uff8968.8%) and hookworm (CRET1\uffe2\uff80\uff89=\uffe2\uff80\uff8931.3%; CRET2\uffe2\uff80\uff89=\uffe2\uff80\uff8916.6%; CRET3\uffe2\uff80\uff89=\uffe2\uff80\uff8978.6%). This study shows that pre-treatment enterotype enables predicting treatment outcome of combination therapy forT. trichiuraand hookworm infections.
Trial registration: ClinicalTrials.gov, NCT03527732. Registered 17 May 2018,https://clinicaltrials.gov/ct2/show/NCT03527732.The importance of soil age as an ecosystem driver across biomes remains largely unresolved. By combining a cross-biome global field survey, including data for 32 soil, plant, and microbial properties in 16 soil chronosequences, with a global meta-analysis, we show that soil age is a significant ecosystem driver, but only accounts for a relatively small proportion of the cross-biome variation in multiple ecosystem properties. Parent material, climate, vegetation and topography predict, collectively, 24 times more variation in ecosystem properties than soil age alone. Soil age is an important local-scale ecosystem driver; however, environmental context, rather than soil age, determines the rates and trajectories of ecosystem development in structure and function across biomes. Our work provides insights into the natural history of terrestrial ecosystems. We propose that, regardless of soil age, changes in the environmental context, such as those associated with global climatic and land-use changes, will have important long-term impacts on the structure and function of terrestrial ecosystems across biomes.Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.Vitaceae) with amplicon sequence data structures", "description": "Abstract
Impacts of plant genotype on microbial assemblage in the phyllosphere (above-ground parts of plants, which predominantly consists of the set of photosynthetic leaves) of Vitis vinifera cultivars have been studied previously but the impact of grape species (under the grape family Vitaceae) was never investigated. Considering the fact, that the phyllosphere microbiome may have profound effects on host plant health and its performance traits, studying the impact of grape species in microbial taxa structuring in the phyllosphere could be of crucial importance. We performed 16S and ITS profiling (for bacteria and fungi respectively) to access genus level characterization of the microflora present in the leaf phyllosphere of five species within this plant family, sampled in two successive years from the repository situated in the Mediterranean. We also performed \uffce\uffb1 and \uffce\uffb2-diversity analyses with robust statistical estimates to test the impacts of grape species and growing year, over a two-year period. Our results indicated the presence of complex microbial diversity and assemblages in the phyllosphere with a significant effect of both factors (grape species and growing year), the latter effect is being more pronounced. We also compared separate normalization methods for high-throughput microbiome data-sets followed by differential taxa abundance analyses. The results suggested the predominance of a particular normalization method over others. This also indicated the need for more robust normalization methods to study the differential taxa abundance among groups in microbiome research.
", "keywords": ["580", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Vegetal Biology", "Bacteria", "Microbiota", "Fungi", "microbiome", "15. Life on land", "Article", "Plant Leaves", "03 medical and health sciences", "vitis vinifera", "diversit\u00e9 microbienne", "phyllosphere", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "effet g\u00e9notype", "Vitis", "Biologie v\u00e9g\u00e9tale", "Phylogeny"]}, "links": [{"href": "https://www.nature.com/articles/s41598-019-50839-0.pdf"}, {"href": "https://hal.inrae.fr/hal-02617774/file/2019_Singh_Scientific%20Reports_1.pdf"}, {"href": "https://doi.org/10.1038/s41598-019-50839-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-019-50839-0", "name": "item", "description": "10.1038/s41598-019-50839-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-019-50839-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-04T00:00:00Z"}}, {"id": "10.1038/srep14378", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:19Z", "type": "Journal Article", "created": "2015-09-23", "title": "Effects Of Nitrogen And Phosphorus Additions On Soil Microbial Biomass And Community Structure In Two Reforested Tropical Forests", "description": "AbstractElevated nitrogen (N) deposition may aggravate phosphorus (P) deficiency in forests in the warm humid regions of China. To our knowledge, the interactive effects of long-term N deposition and P availability on soil microorganisms in tropical replanted forests remain unclear. We conducted an N and P manipulation experiment with four treatments: control, N addition (15\uffe2\uff80\uff89g N m\uffe2\uff88\uff922\uffc2\uffb7yr\uffe2\uff88\uff921), P addition (15\uffe2\uff80\uff89g P m\uffe2\uff88\uff922\uffc2\uffb7yr\uffe2\uff88\uff921) and N and P addition (15\uffe2\uff80\uff89+\uffe2\uff80\uff8915\uffe2\uff80\uff89g N and P m\uffe2\uff88\uff922\uffc2\uffb7yr\uffe2\uff88\uff921, respectively) in disturbed (planted pine forest with recent harvests of understory vegetation and litter) and rehabilitated (planted with pine, but mixed with broadleaf returning by natural succession) forests in southern China. Nitrogen addition did not significantly affect soil microbial biomass, but significantly decreased the abundance of gram-negative bacteria PLFAs in both forest types. Microbial biomass increased significantly after P addition in the disturbed forest but not in the rehabilitated forest. No interactions between N and P additions on soil microorganisms were observed in either forest type. Our results suggest that microbial growth in replanted forests of southern China may be limited by P rather than by N and this P limitation may be greater in disturbed forests.
", "keywords": ["China", "Principal Component Analysis", "Nitrates", "Rainforest", "Nitrogen", "Microbiota", "Fatty Acids", "Forestry", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Gram-Positive Bacteria", "Article", "Carbon Cycle", "Phosphates", "Multidisciplinary Sciences", "Soil", "Gram-Negative Bacteria", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Fertilizers", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep14378"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep14378", "name": "item", "description": "10.1038/srep14378", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep14378"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-09-23T00:00:00Z"}}, {"id": "10.1073/pnas.1904326116", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:38Z", "type": "Journal Article", "created": "2019-05-21", "title": "Microbial biospherics: The experimental study of ecosystem function and evolution", "description": "Awareness that our planet is a self-supporting biosphere with sunlight as its major source of energy for life has resulted in a long-term historical fascination with the workings of self-supporting ecological systems. However, the studies of such systems have never entered the canon of ecological or evolutionary tools and instead, have led a fringe existence connected to life support system engineering and space travel. We here introduce a framework for a renaissance in biospherics based on the study of matter-closed, energy-open ecosystems at a microbial level (microbial biospherics). Recent progress in genomics, robotics, and sensor technology makes the study of closed systems now much more tractable than in the past, and we argue that the time has come to emancipate the study of closed systems from this fringe context and bring them into a mainstream approach for studying ecosystem processes. By permitting highly replicated long-term studies, especially on predetermined and simplified systems, microbial biospheres offer the opportunity to test and develop strong hypotheses about ecosystem function and the ecological and evolutionary determinants of long-term system failure or persistence. Unlike many sciences, ecosystem ecology has never fully embraced a reductionist approach and has remained focused on the natural world in all its complexity. We argue that a reductionist approach to ecosystem ecology, using microbial biospheres, based on a combination of theory and the replicated study of much simpler self-enclosed microsystems could pay huge dividends.
", "keywords": ["0301 basic medicine", "0303 health sciences", "Ecology", "Atmosphere", "Earth", " Planet", "Microbiota", "Space Flight", "15. Life on land", "Biological Evolution", "03 medical and health sciences", "Engineering", "13. Climate action", "8. Economic growth", "Sunlight", "Ecological Systems", " Closed", "Ecosystem", "Life Support Systems"]}, "links": [{"href": "https://pnas.org/doi/pdf/10.1073/pnas.1904326116"}, {"href": "https://doi.org/10.1073/pnas.1904326116"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.1904326116", "name": "item", "description": "10.1073/pnas.1904326116", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.1904326116"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-20T00:00:00Z"}}, {"id": "10.1080/1040841x.2022.2132850", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:49Z", "type": "Journal Article", "created": "2022-10-26", "title": "Bioinformatic approaches for studying the microbiome of fermented food", "description": "High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.", "keywords": ["2. Zero hunger", "0301 basic medicine", "metatranscriptomics", "Microbiota", "0206 medical engineering", "high-throughput sequencing", "Computational Biology", "High-Throughput Nucleotide Sequencing", "bioinformatics", "02 engineering and technology", "fermented foods", "03 medical and health sciences", "Metagenome", "Metagenomics", "Fermented Foods"]}, "links": [{"href": "https://www.tandfonline.com/doi/pdf/10.1080/1040841X.2022.2132850"}, {"href": "https://doi.org/10.1080/1040841x.2022.2132850"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Critical%20Reviews%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1080/1040841x.2022.2132850", "name": "item", "description": "10.1080/1040841x.2022.2132850", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1080/1040841x.2022.2132850"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-10-26T00:00:00Z"}}, {"id": "10.1080/15592324.2018.1464855", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:51Z", "type": "Journal Article", "created": "2018-04-27", "title": "Not only priming: Soil microbiota may protect tomato from root pathogens", "description": "An increasing number of studies have investigated soil microbial biodiversity. However, the mechanisms regulating plant responses to soil microbiota are largely unknown. A previous work tested the hypothesis that tomato plants grown on native soils with their complex microbiotas respond differently from tomato growing in a sterile substrate. Two soils, suppressive or conducive to Fusarium oxysporum f. sp. lycopersici (FOL), and two genotypes susceptible and resistant to the same pathogen were considered. The work highlighted that the two tested soil microbiotas, irrespectively of their taxonomic composition, elicit the PAMP-triggered Immunity Pathway, the first level of plant defence, as well as an increased lignin synthesis, leading to an active protection when FOL is present in the soil. Here, we tested the expression of a panel of genes involved in Effector-Triggered Immunity (ETI), demonstrating that soil microbiota, beside genotype, affects plant resistance to FOL also modulating this pathway.", "keywords": ["suppressive and conducive soils", "susceptible and resistant genotypes", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "defence responses; Fusarium oxysporum f. sp. lycopersici; arbuscular mycorrhizal fungi; gene expression; lignin biosynthesis; microbiota; suppressive and conducive soils; susceptible and resistant genotypes; tomato; Plant Science", "arbuscular mycorrhizal fungi", "tomato", "15. Life on land", "defence responses", "03 medical and health sciences", "Fusarium", "Solanum lycopersicum", "microbiota", "gene expression", "Fusarium oxysporum f. sp. lycopersici", "lignin biosynthesis", "Soil Microbiology", "Plant Diseases"]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1677702/2/Chialva_et_al_2018_PostPrint.pdf"}, {"href": "https://www.tandfonline.com/doi/pdf/10.1080/15592324.2018.1464855"}, {"href": "https://doi.org/10.1080/15592324.2018.1464855"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Signaling%20%26amp%3B%20Behavior", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1080/15592324.2018.1464855", "name": "item", "description": "10.1080/15592324.2018.1464855", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1080/15592324.2018.1464855"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-27T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microbiota&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microbiota&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microbiota&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microbiota&offset=50", "hreflang": "en-US"}], "numberMatched": 154, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-04-16T06:41:14.725329Z"}