The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H 2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.
IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota , and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment\uffe2\uff80\uff94including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.
", "keywords": ["570", "Bacteria", "Fungi", "Antarctic Regions", "Chloroflexi", "15. Life on land", "Survival strategies", "Cold Temperature", "Extremophiles", "13. Climate action", "Antarctica", "Endolithic communities", "Metagenomics", "14. Life underwater", "Sugars", "Settore BIO/19 - MICROBIOLOGIA GENERALE"]}, "links": [{"href": "https://doi.org/10.1128/aem.02264-23"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.02264-23", "name": "item", "description": "10.1128/aem.02264-23", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02264-23"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-19T00:00:00Z"}}, {"id": "1871.1/c35ee736-19df-4416-b656-7db73f2fbc01", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:24:29Z", "type": "Journal Article", "created": "2025-04-02", "title": "Effects of biodegradable microplastics on soil microbial communities and activities: Insight from an ecological mesocosm experiment", "description": "Microplastics (MP) are being released into the environment at an increasing rate, causing extensive pollution in soils and affecting biota and processes. Although the use of biodegradable plastic has increased, its effects on the soil microbial community are not yet well understood. A controlled mesocosm experiment was conducted to investigate the response of soil microbial communities to increasing amounts of starch-polybutylene adipate terephthalate MPs (PBAT-BD-MPs) added to the soil. The experiment included microbes, earthworms, springtails, and plants. The PBAT-BD-MPs were added to the soil column at doses ranging from 0 to 0.8\u00a0% w/w of soil dry mass, and the columns were incubated for 11\u00a0weeks under controlled climatic conditions. Bacterial and fungal amplicon sequencing was used to investigate the dose-dependent response of the soil microbial communities' alpha and beta diversity. The alpha diversity indices of the bacterial and fungal communities increased with increasing PBAT-BD-MP concentration. Bacterial richness was highest at the highest MP concentration (0.8\u00a0%). A similar trend was observed in the fungal community, with a significant increase in fungal richness as PBAT-BD-MP concentration increased. The alpha diversity of both bacterial and fungal communities significantly increased in MP treatments compared to the control treatment. At the highest MP concentration (0.8\u00a0%), the abundance of the bacterial phylum Planctomycetes showed a significant increase, while Firmicutes showed a significant decrease. The abundance of the fungal phyla Ascomycota and Mortierellomycota also significantly increased at the highest PBAT-BD-MP concentration compared to the control group. Alongside changes in the soil microbial community, we observed a rise in soil respiration as the concentration of PBAT-BD-MPs increased. Our three-month mesocosm study demonstrates that the introduction of biodegradable microplastics into the natural standard soil environment in realistic concentrations (0-0.025-0.05-0.2-0.8\u00a0%) and particle size distribution alters the soil bacterial and fungal community.", "keywords": ["Polybutylene adipate terephthalate PBAT", "Biodegradation", " Environmental", "CLIMECS", "Bacteria", "Microplastics", "Microbiota", "Fungi", "Soil Pollutants", "Animals", "Soil respiration", "Biodegradable Plastics", "Oligochaeta", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/1871.1/c35ee736-19df-4416-b656-7db73f2fbc01"}, {"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": "1871.1/c35ee736-19df-4416-b656-7db73f2fbc01", "name": "item", "description": "1871.1/c35ee736-19df-4416-b656-7db73f2fbc01", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1871.1/c35ee736-19df-4416-b656-7db73f2fbc01"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-05-01T00:00:00Z"}}, {"id": "10449/84316", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:24:06Z", "type": "Journal Article", "created": "2024-02-19", "title": "Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert", "description": "ABSTRACTThe ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H 2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.
IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota , and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment\uffe2\uff80\uff94including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.
", "keywords": ["570", "Bacteria", "Fungi", "Antarctic Regions", "Chloroflexi", "15. Life on land", "Survival strategies", "Cold Temperature", "Extremophiles", "13. Climate action", "Antarctica", "Endolithic communities", "Metagenomics", "14. Life underwater", "Sugars", "Settore BIO/19 - MICROBIOLOGIA GENERALE"]}, "links": [{"href": "https://doi.org/10449/84316"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10449/84316", "name": "item", "description": "10449/84316", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10449/84316"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-19T00:00:00Z"}}, {"id": "10.1016/j.envres.2019.108608", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:16:02Z", "type": "Journal Article", "created": "2019-07-26", "title": "Antibiotic resistance gene distribution in agricultural fields and crops. A soil-to-food analysis", "description": "Despite the social concern about the generalization of antibiotic resistance hotspots worldwide, very little is known about the contribution of different potential sources to the global risk. Here we present a quantitative analysis of the distribution of Antibiotic Resistance Genes (ARGs) in soil, rhizospheric soil, roots, leaves and beans in tomato, lettuce and broad beans crops (165 samples in total), grown in nine commercial plots distributed in four geographical zones in the vicinity of Barcelona (North East Spain). We also analyzed five soil samples from a nearby forest, with no record of agricultural activities. DNA samples were analyzed for their content in the ARGs sul1, tetM, qnrS1, blaCTX-M-32, blaOXA-58, mecA, and blaTEM, plus the integron intI1, using qPCR methods. In addition, soil microbiomes from the different plots were analyzed by amplicon-targeted 16S rRNA gene sequencing. Our data show a decreasing gradient of ARG loads from soil to fruits and beans, the latter showing only from 0.1 to 0.01% of the abundance values in soil. The type of crop was the main determinant for both ARG distribution and microbiome composition among the different plots, with minor contributions of geographic location and irrigation water source. We propose that soil amendment and/or fertilization, more than irrigation water, are the main drivers of ARG loads on the edible parts of the crop, and that they should therefore be specifically controlled.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Microbiomes", "Agriculture", "Drug Resistance", " Microbial", "Irrigation water", "15. Life on land", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "qPCR", "Soil", "03 medical and health sciences", "Antibiotic resistance genes", "Genes", " Bacterial", "Spain", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Endophytes", "Food Analysis", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envres.2019.108608"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envres.2019.108608", "name": "item", "description": "10.1016/j.envres.2019.108608", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envres.2019.108608"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-01T00:00:00Z"}}, {"id": "10.1111/1462-2920.13954", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:18:22Z", "type": "Journal Article", "created": "2022-10-18", "title": "Application of stable-isotope labelling techniques for the detection of active diazotrophs", "description": "SummaryInvestigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N\uffe2\uff80\uff90based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to 15N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting 15N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.
", "keywords": ["Spectrum Analysis", " Raman", "BIOLOGICAL SOIL CRUSTS", "106005 Bioinformatik", "106023 Molekularbiologie", "Nitrogen Fixation", "REVEALS", "FLUORESCENCE", "Research Articles", "Soil Microbiology", "106022 Mikrobiologie", "SPECTROSCOPY", "Bacteria", "Nitrogen Isotopes", "106003 Biodiversity research", "106023 Molecular biology", "GENETIC-REGULATION", "Archaea", "6. Clean water", "SURFACE-ENHANCED RAMAN", "COMMUNITY", "106003 Biodiversit\u00e4tsforschung", "13. Climate action", "Isotope Labeling", "106022 Microbiology", "NITROGEN-FIXATION", "106005 Bioinformatics", "RIBOSOMAL-RNA", "N-2 FIXATION"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13954"}, {"href": "https://doi.org/10.1111/1462-2920.13954"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.13954", "name": "item", "description": "10.1111/1462-2920.13954", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13954"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-12-15T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2023.161600", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:16:40Z", "type": "Journal Article", "created": "2023-01-18", "title": "Risk reductions during pyrene biotransformation and mobilization in a model plant-bacteria-biochar system", "description": "The productive application of motile microorganisms for degrading hydrophobic contaminants in soil is one of the most promising processes in modern remediation due to its sustainability and low cost. However, the incomplete biodegradation of the contaminants and the formation of the intermediary metabolites in the process may increase the toxicity in soil during bioremediation, and motile inoculants may mobilize the pollutants through biosorption. Therefore, controlling these factors should be a fundamental part of soil remediation approaches. The aim of this study was to evaluate the sources of risk associated with the cometabolism-based transformation of 14C-labeled pyrene by inoculated Pseudomonas putida G7 and identify ways to minimize risk. Our model scenario examined the increase in bioaccessibility to a distant source of contamination facilitated by sunflower (Helianthus annuus L.) roots. A biochar trap for mobilized pollutant metabolites and bacteria has also been employed. The experimental design consisted of pots filled with a layer of sand with 14C-labeled pyrene (88 mg kg-1) as a contamination focus located several centimeters from the inoculation point. Half of the pots included a biochar layer at the bottom. The pots were incubated in a greenhouse with sunflower plants and P. putida G7 bacteria. Pots with sunflower plants showed a higher biodegradation of pyrene, its mobilization as metabolites through the percolate and the roots, and bacterial mobilization toward the source of contamination, also resulting in increased pyrene transformation. In addition, the biochar layer efficiently reduced the concentrations of pyrene metabolites collected in the leachates. Therefore, the combination of plants, motile bacteria and biochar safely reduced the risk caused by the biological transformation of pyrene.", "keywords": ["Risk", "2. Zero hunger", "570", "Pyrenes", "Bacteria", "04 agricultural and veterinary sciences", "Plants", "01 natural sciences", "Polycyclic aromatic hydrocarbons", "6. Clean water", "Sunflower", "Soil", "Biodegradation", " Environmental", "13. Climate action", "Biodegradation", "Soil Pollutants", "0401 agriculture", " forestry", " and fisheries", "Polycyclic Aromatic Hydrocarbons", "Bioremediation", "Biotransformation", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2023.161600"}, {"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.2023.161600", "name": "item", "description": "10.1016/j.scitotenv.2023.161600", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2023.161600"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2024.172175", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:16:41Z", "type": "Journal Article", "created": "2024-04-02", "title": "Exploring the potential of earthworm gut bacteria for plastic degradation", "description": "The use of plastic mulch films in agriculture leads to the inevitable accumulation of plastic debris in soils. Here, we explored the potential of earthworm gut-inhabiting bacterial strains (Mycobacterium vanbaalenii (MV), Rhodococcus jostii (RJ), Streptomyces fulvissimus (SF), Bacillus simplex (BS), and Sporosarcina globispora (SG) to degrade plastic films (\u2300\u00a0=\u00a015\u00a0mm) made from commonly used polymers: low-density polyethylene film (LDPE-f), polylactic acid (PLA-f), polybutylene adipate terephthalate film (PBAT-f), and a commercial biodegradable mulch film, Bionov-B\u00ae (composed of Mater-Bi, a feedstock with PBAT, PLA and other chemical compounds). A 180-day experiment was conducted at room temperature (x\u0304 =19.4\u00a0\u00b0C) for different strain-plastic combinations under a low carbon media (0.1\u00d7 tryptic soy broth). Results showed that the tested strain-plastic combinations did not facilitate the degradation of LDPE-f (treated with RJ and SF), PBAT-f (treated with BS and SG), and Bionov-B (treated with BS, MV, and SG). However, incubating PLA-f with SF triggered a reduction in the molecular weights and an increase in crystallinity. Therefore, we used PLA-f as model plastic to study the influence of temperature ('room temperature' & '30\u00a0\u00b0C'), carbon source ('carbon-free' & 'low carbon supply'), and strain interactions ('single strains' & 'strain mixtures') on PLA degradation. SF and SF\u00a0+\u00a0RJ treatments significantly fostered PLA degradation under 30\u00a0\u00b0C in a low-carbon media. PLA-f did not show any degradation in carbon-free media treatments. The competition between different strains in the same system likely hindered the performance of PLA-degrading strains. A positive correlation between the final pH of culture media and PLA-f weight loss was observed, which might reflect the pH-dependent hydrolysis mechanism of PLA. Our results situate SF and its co-culture with RJ strains as possible accelerators of PLA degradation in temperatures below PLA glass transition temperature (Tg). Further studies are needed to test the bioremediation feasibility in soils.", "keywords": ["0301 basic medicine", "Bacteria", "ddc:550", "Polyesters", "01 natural sciences", "6. Clean water", "Gastrointestinal Microbiome", "03 medical and health sciences", "Biodegradation", " Environmental", "Life Science", "Animals", "Soil Pollutants", "Oligochaeta", "Plastics", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2024.172175"}, {"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.2024.172175", "name": "item", "description": "10.1016/j.scitotenv.2024.172175", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.172175"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-06-01T00:00:00Z"}}, {"id": "10.1016/j.eti.2023.103229", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:16:03Z", "type": "Journal Article", "created": "2023-06-02", "title": "Modeling biochar-soil depth dependency on fecal coliform straining under subsurface drip irrigation", "description": "Funding Information: This work was supported by Shahrekord University, Iran. N. Sepehrnia is funded by a Marie Sk\u0142odowska-Curie Individual Fellowship, United Kingdom under the grant agreement No. 101026287. We acknowledge University of Aberdeen, UK for supporting this project. ; Peer reviewed", "keywords": ["GE", "Soil Science", "610", "Plant Science", "04 agricultural and veterinary sciences", "01 natural sciences", "6. Clean water", "510", "Biochar", "Maximum allowable depletion", "0401 agriculture", " forestry", " and fisheries", "Mathematical modeling", "Irrigation strategy", "HYDRUS", "Soil bacteria contamination", "GE Environmental Sciences", "General Environmental Science", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.eti.2023.103229"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Technology%20%26amp%3B%20Innovation", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.eti.2023.103229", "name": "item", "description": "10.1016/j.eti.2023.103229", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.eti.2023.103229"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-08-01T00:00:00Z"}}, {"id": "10.1016/j.nbt.2023.12.003", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:16:30Z", "type": "Journal Article", "created": "2023-12-19", "title": "Phytostabilization of metal(loid)s by ten emergent macrophytes following a 90-day exposure to industrially contaminated groundwater", "description": "Better understanding of macrophyte tolerance under long exposure times in real environmental matrices is crucial for phytoremediation and phytoattenuation strategies for aquatic systems. The metal(loid) attenuation ability of 10 emergent macrophyte species (Carex riparia, Cyperus longus, Cyperus rotundus, Iris pseudacorus, Juncus effusus, Lythrum salicaria, Menta aquatica, Phragmites australis, Scirpus holoschoenus, and Typha angustifolia) was investigated using real groundwater from an industrial site, over a 90-day exposure period. A 'phytobial' treatment was included, with 3 plant growth-promoting rhizobacterial strains. Plants exposed to the polluted water generally showed similar or reduced aerial biomass compared to the controls, except for C. riparia. This species, along with M. aquatica, exhibited improved biomass after bioaugmentation. Phytoremediation mechanisms accounted for more than 60% of As, Cd, Cu, Ni, and Pb removal, whilst abiotic mechanisms contributed to \u223c80% removal of Fe and Zn. Concentrations of metal(loid)s in the roots were generally between 10-100 times higher than in the aerial parts. The macrophytes in this work can be considered 'underground attenuators', more appropriate for rhizostabilization strategies, especially L. salicaria, M. aquatica, S. holoschoenus, and T. angustifolia. For I. pseudacorus, C. longus, and C. riparia; harvesting the aerial parts could be a complementary phytoextraction approach to further remove Pb and Zn. Of all the plants, S. holoschoenus showed the best balance between biomass production and uptake of multiple metal(loid)s. Results also suggest that multiple phytostrategies may be possible for the same plant depending on the final remedial aim. Phytobial approaches need to be further assessed for each macrophyte species.", "keywords": ["Rhizostabilization", "Metalloid", "Biotecnolog\u00eda", "Biolog\u00eda molecular", "Emergent macrophyte", "Metal", "Molecular biology", "Plants", "15. Life on land", "Poaceae", "6. Clean water", "Biodegradation", " Environmental", "Lead", "13. Climate action", "Metals", " Heavy", "Plant growth promoting bacteria", "Biomass", "Groundwater", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.nbt.2023.12.003"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.nbt.2023.12.003", "name": "item", "description": "10.1016/j.nbt.2023.12.003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.nbt.2023.12.003"}, {"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": "10.1111/1462-2920.13842", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:18:22Z", "type": "Journal Article", "created": "2017-06-27", "title": "Identification and characterisation of isoprene-degrading bacteria in an estuarine environment", "description": "SummaryApproximately one\uffe2\uff80\uff90third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA\uffe2\uff80\uff90Stable Isotope Probing (DNA\uffe2\uff80\uff90SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia. Representative isolates, capable of growth on isoprene as sole carbon and energy source, were obtained from marine and estuarine locations, and isoprene\uffe2\uff80\uff90degrading strains of Gordonia and Mycobacterium were characterised physiologically and their genomes were sequenced. Genes predicted to be required for isoprene metabolism, including four\uffe2\uff80\uff90component isoprene monooxygenases (IsoMO), were identified and compared with previously characterised examples. Transcriptional and activity assays of strains growing on isoprene or alternative carbon sources showed that growth on isoprene is an inducible trait requiring a specific IsoMO. This study is the first to identify active isoprene degraders in estuarine and marine environments using DNA\uffe2\uff80\uff90SIP and to characterise marine isoprene\uffe2\uff80\uff90degrading bacteria at the physiological and molecular level.
", "keywords": ["0301 basic medicine", "570", "Volatile Organic Compounds", "0303 health sciences", "550", "Base Sequence", "610", "QR Microbiology", "Sequence Analysis", " DNA", "Environment", "6. Clean water", "Mixed Function Oxygenases", "Mycobacterium", "03 medical and health sciences", "Hemiterpenes", "13. Climate action", "Pentanes", "Butadienes", "Rhodococcus", "14. Life underwater", "Gordonia Bacterium", "Research Articles", "Genome", " Bacterial", "GE Environmental Sciences"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/63998/4/Published_manuscript.pdf"}, {"href": "http://onlinelibrary.wiley.com/wol1/doi/10.1111/1462-2920.13842/fullpdf"}, {"href": "https://doi.org/10.1111/1462-2920.13842"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.13842", "name": "item", "description": "10.1111/1462-2920.13842", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13842"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-21T00:00:00Z"}}, {"id": "0e018dea-ab53-461f-b454-2eaaca8c765c", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[6.67, 47.98], [6.67, 51.27], [10.81, 51.27], [10.81, 47.98], [6.67, 47.98]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "winter wheat"}, {"id": "spring barley"}, {"id": "organic fertilizers"}, {"id": "ammonium"}, {"id": "nitrates"}, {"id": "protein quality"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata; Wheat"}, {"id": "barley"}, {"id": "organic agriculture"}, {"id": "Rhizosphere soil"}, {"id": "bulk soil"}, {"id": "microbial biomass"}, {"id": "microrespiration"}, {"id": "meta-barcode sequencing of bacterial community"}, {"id": "quantification of bacterial inoculant"}, {"id": "gluten"}, {"id": "HMW"}, {"id": "hordein"}, {"id": "ProteinZ"}, {"id": "bread quality"}, {"id": "grain storage protein"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the Rhizo4Bio - bread and beer's research activities.\" Although every care has been taken in preparing and testing the data, the Rhizo4Bio - bread and beer and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the Rhizo4Bio - bread and beer and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The Rhizo4Bio - bread and beer and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2024-08-22", "type": "Dataset", "created": "2024-07-18", "language": "eng", "title": "Production of wheat and barley under reduced input in organic farming - Soil parameters for season I and II", "description": "During the last decades, organic farming has undergone a notable expansion as a common agricultural practice throughout the world. This, together with an increasing demand for fertilizer and pesticide reduction has led to consider different and new approaches. We investigate the effect of Hartmannibacter diazotrophicus strain E19, a plant growth promoting rhizobacterium, in order to enhance the production of wheat and barley under low energy input. For that, we analyze the effect of three factors: organic fertilizer (with and without, only wheat), row distance (15 cm and 50 cm), and bacterial inoculation (E19 and control) at two different organic experimental field stations (Gladbacherhof and Kleinhohenheim). The dataset provides information about different parameter determined from rhizosphere soil and root samples collected at two different developmental stages (flowering and milk/fully ripe), as well as, the grain yield, straw yield, 1000 kernel mass, and seed quality during the seasons 2020-2021 and 2021-2022. The following soil parameter were evaluated: ammonium, nitrate, carbon-nitrogen ratio, microbial biomass, the respiration activity using different carbon sources (glucose, galactose, N-acetylglucosamine, arginine). These data sets are currently under evaluation and complemented with the quantification from root samples through quantitative PCR (qPCR) of strain E19 and the metabarcoding sequencing of the bacterial communities based on 16S rRNA genes obtained from rhizosphere soil samples during the two seasons. Soil parameter data\n\nRelated datasets are listed in the metadata element 'Related Identifier'.\nDataset version 1.0", "formats": [{"name": "CSV"}], "keywords": ["Soil", "winter wheat", "spring barley", "organic fertilizers", "ammonium", "nitrates", "protein quality", "opendata; Wheat", "barley", "organic agriculture", "Rhizosphere soil", "bulk soil", "microbial biomass", "microrespiration", "meta-barcode sequencing of bacterial community", "quantification of bacterial inoculant", "gluten", "HMW", "hordein", "ProteinZ", "bread quality", "grain storage protein", "Boden"], "contacts": [{"name": "Santiago Quiroga", "organization": "Justus-Liebig University Giessen", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "Santiago.Quiroga@umwelt.uni-giessen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0009-0001-1392-8241", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Sylvia Schnell", "organization": "Justus-Liebig University Giessen", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "sylvia.schnell@umwelt.uni-giessen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-3903-6089", "name_url": "", "description": "orcid", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "ZALF", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Stefan Ratering", "organization": "Justus-Liebig University Giessen", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "Stefan.Ratering@umwelt.uni-giessen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0001-7572-6306", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Azin Rekowski", "organization": "University of Hohenheim", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "azin.ghabelrahmat@uni-hohenheim.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-0179-663X", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Christian Z\u00f6rb", "organization": "University of Hohenheim", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "Christian.zoerb@uni-hohenheim.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-0000-5138", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Sylvia Schnell", "organization": "Justus-Liebig University Giessen", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "sylvia.schnell@umwelt.uni-giessen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-3903-6089", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"organization": "University of Hohenheim;Justus-Liebig University Giessen", "roles": ["contributor"]}], "title_alternate": "LTE: Part 1/5, table: Soil parameters for season I and II"}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=0e018dea-ab53-461f-b454-2eaaca8c7gmd:65c", "rel": "download"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/0e018dea-ab53-461f-b454-2eaaca8c765c", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "0e018dea-ab53-461f-b454-2eaaca8c765c", "name": "item", "description": "0e018dea-ab53-461f-b454-2eaaca8c765c", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/0e018dea-ab53-461f-b454-2eaaca8c765c"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-22T00:00:00Z"}}, {"id": "10.1002/advs.201901408", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:15Z", "type": "Journal Article", "created": "2019-09-19", "title": "Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms", "description": "AbstractBiofouling proceeds in successive steps where the primary colonizers affect the phylogenetic and functional structure of a future microbial consortium. Using microbiologically influenced corrosion (MIC) as a study case, a novel approach for material surface protection is described, which does not prevent biofouling, but rather shapes the process of natural biofilm development to exclude MIC\uffe2\uff80\uff90related microorganisms. This approach interferes with the early steps of natural biofilm formation affecting how the community is finally developed. It is based on a multilayer artificial biofilm, composed of electrostatically modified bacterial cells, producing antimicrobial compounds, extracellular antimicrobial polyelectrolyte matrix, and a water\uffe2\uff80\uff90proof rubber elastomer barrier. The artificial biofilm is constructed layer\uffe2\uff80\uff90by\uffe2\uff80\uff90layer (LBL) by manipulating the electrostatic interactions between microbial cells and material surfaces. Field testing on standard steel coupons exposed in the sea for more than 30 days followed by laboratory analyses using molecular\uffe2\uff80\uff90biology tools demonstrate that the preapplied artificial biofilm affects the phylogenetic structure of the developing natural biofilm, reducing phylogenetic diversity and excluding MIC\uffe2\uff80\uff90related bacteria. This sustainable solution for material protection showcases the usefulness of artificially guiding microbial evolutionary processes via the electrostatic modification and controlled delivery of bacterial cells and extracellular matrix to the exposed material surfaces.Selectively fluorinated compounds are found frequently in pharmaceutical and agrochemical products where currently 25\uffe2\uff80\uff9330\uffe2\uff80\uff89% of optimised compounds emerge from development containing at least one fluorine atom. There are many methods for the site\uffe2\uff80\uff90specific introduction of fluorine, but all are chemical and they often use environmentally challenging reagents. Biochemical processes for C\uffe2\uff88\uff92F bond formation are attractive, but they are extremely rare. In this work, the fluorinase enzyme, originally identified from the actinomycete bacterium Streptomyces cattleya, is engineered into Escherichia coli in such a manner that the organism is able to produce 5\uffe2\uff80\uffb2\uffe2\uff80\uff90fluorodeoxyadenosine (5\uffe2\uff80\uffb2\uffe2\uff80\uff90FDA) from S\uffe2\uff80\uff90adenosyl\uffe2\uff80\uff90l\uffe2\uff80\uff90methionine (SAM) and fluoride in live E.\uffe2\uff80\uff85coli cells. Success required the introduction of a SAM transporter and deletion of the endogenous fluoride efflux capacity in order to generate an E.\uffe2\uff80\uff85coli host that has the potential for future engineering of more elaborate fluorometabolites.
", "keywords": ["SAM transporters", "0301 basic medicine", "570", "S-Adenosylmethionine", "0303 health sciences", "Deoxyadenosines", "Halogenation", "DAS", "Fluorine", "Halogenations", "540", "QD Chemistry", "Streptomyces", "3. Good health", "03 medical and health sciences", "Bacterial Proteins", "Isomerism", "Escherichia coli", "QD", "Fluoride channels", "Genetic Engineering", "Oxidoreductases", "Fluorinases"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/cbic.202000051"}, {"href": "https://doi.org/10.1002/cbic.202000051"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/ChemBioChem", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/cbic.202000051", "name": "item", "description": "10.1002/cbic.202000051", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/cbic.202000051"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-03T00:00:00Z"}}, {"id": "10.1002/ecy.1513", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:18Z", "type": "Journal Article", "created": "2016-07-02", "title": "Land Use Intensification In The Humid Tropics Increased Both Alpha And Beta Diversity Of Soil Bacteria", "description": "AbstractAnthropogenic pressures on tropical forests are rapidly intensifying, but our understanding of their implications for biological diversity is still very limited, especially with regard to soil biota, and in particular soil bacterial communities. Here we evaluated bacterial community composition and diversity across a gradient of land use intensity in the eastern Amazon from undisturbed primary forest, through primary forests varyingly disturbed by fire, regenerating secondary forest, pasture, and mechanized agriculture. Soil bacteria were assessed by paired\uffe2\uff80\uff90end Illumina sequencing of 16S rRNA gene fragments (V4 region). The resulting sequences were clustered into operational taxonomic units (OTU) at a 97% similarity threshold. Land use intensification increased the observed bacterial diversity (both OTU richness and community heterogeneity across space) and this effect was strongly associated with changes in soil pH. Moreover, land use intensification and subsequent changes in soil fertility, especially pH, altered the bacterial community composition, with pastures and areas of mechanized agriculture displaying the most contrasting communities in relation to undisturbed primary forest. Together, these results indicate that tropical forest conversion impacts soil bacteria not through loss of diversity, as previously thought, but mainly by imposing marked shifts on bacterial community composition, with unknown yet potentially important implications for ecological functions and services performed by these communities.
", "keywords": ["Rios de composi\u00e7\u00e3o de comunidade bacteriana", "2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "550", "Bacteria", "Biodiversidade subterr\u00e2nea", "Agriculture", "Biodiversity", "Forests", "15. Life on land", "Below\u2010ground biodiversity", "High\u2010throughput sequencing", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Sequenciamento de alto rendimento", "Rivers of bacterial community composition", "Soil Microbiology"]}, "links": [{"href": "https://eprints.lancs.ac.uk/id/eprint/82660/1/de_Carvalho_et_al_2016_raw_pdf.pdf"}, {"href": "https://doi.org/10.1002/ecy.1513"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ecy.1513", "name": "item", "description": "10.1002/ecy.1513", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecy.1513"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-09-09T00:00:00Z"}}, {"id": "10.1007/s00442-007-0836-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:42Z", "type": "Journal Article", "created": "2007-08-27", "title": "Microbial Responses To Nitrogen Addition In Three Contrasting Grassland Ecosystems", "description": "The effects of global N enrichment on soil processes in grassland ecosystems have received relatively little study. We assessed microbial community response to experimental increases in N availability by measuring extracellular enzyme activity (EEA) in soils from three grasslands with contrasting edaphic and climatic characteristics: a semiarid grassland at the Sevilleta National Wildlife Refuge, New Mexico, USA (SEV), and mesic grasslands at Konza Prairie, Kansas, USA (KNZ) and Ukulinga Research Farm, KwaZulu-Natal, South Africa (SAF). We hypothesized that, with N enrichment, soil microbial communities would increase C and P acquisition activity, decrease N acquisition activity, and reduce oxidative enzyme production (leading to recalcitrant soil organic matter [SOM] accumulation), and that the magnitude of response would decrease with soil age (due to higher stabilization of enzyme pools and P limitation of response). Cellulolytic activities followed the pattern predicted, increasing 35-52% in the youngest soil (SEV), 10-14% in the intermediate soil (KNZ) and remaining constant in the oldest soil (SAF). The magnitude of phosphatase response did not vary among sites. N acquisition activity response was driven by the enzyme closest to its pH optimum in each soil: i.e., leucine aminopeptidase in alkaline soil, beta-N-acetylglucosaminidase in acidic soil. Oxidative enzyme activity varied widely across ecosystems, but did not decrease with N amendment at any site. Likewise, SOM and %C pools did not respond to N enrichment. Between-site variation in both soil properties and EEA exceeded any treatment response, and a large portion of EEA variability (leucine aminopeptidase and oxidative enzymes), 68% as shown by principal components analysis, was strongly related to soil pH (r = 0.91, P < 0.001). In these grassland ecosystems, soil microbial responses appear constrained by a molecular-scale (pH) edaphic factor, making potential breakdown rates of SOM resistant to N enrichment.", "keywords": ["2. Zero hunger", "0106 biological sciences", "Analysis of Variance", "Bacteria", "Nitrogen", "New Mexico", "04 agricultural and veterinary sciences", "Kansas", "15. Life on land", "Poaceae", "01 natural sciences", "Carbon", "Enzymes", "Soil", "South Africa", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00442-007-0836-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-007-0836-6", "name": "item", "description": "10.1007/s00442-007-0836-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-007-0836-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-08-28T00:00:00Z"}}, {"id": "10.1002/ecy.2137", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:18Z", "type": "Journal Article", "created": "2018-01-10", "title": "Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere", "description": "AbstractThe ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co\uffe2\uff80\uff90occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co\uffe2\uff80\uff90occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.
", "keywords": ["0301 basic medicine", "Terrestrial Ecosystems", "archaea", "Evolution", "Eukaryotes", "Antarctic Regions", "1105 Ecology", "Biodiversity; Terrestrial Ecosystems; Archaea; Bacteria; Eukaryotes; Australia; Antarctica.", "Terrestrial ecosystems", "Soil", "03 medical and health sciences", "eukaryotes", "Behavior and Systematics", "XXXXXX - Unknown", "14. Life underwater", "bacteria", "Phylogeny", "Soil Microbiology", "biodiversity", "2. Zero hunger", "0303 health sciences", "Bacteria", "Australia", "terrestrial ecosystems", "Biodiversity", "15. Life on land", "archaebacteria", "Archaea", "soil ecology", "13. Climate action", "eukaryotic cells", "Antarctica"]}, "links": [{"href": "https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2137"}, {"href": "https://doi.org/10.1002/ecy.2137"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ecy.2137", "name": "item", "description": "10.1002/ecy.2137", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecy.2137"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-12T00:00:00Z"}}, {"id": "10.1002/jsfa.11205", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:21Z", "type": "Journal Article", "created": "2021-03-12", "title": "A novel ammoniation treatment of barley as a strategy to optimize rumen pH, feed degradability and microbial protein synthesis", "description": "AbstractBACKGROUNDMeeting the energy and nitrogen (N) requirements of high\uffe2\uff80\uff90performing ruminants at the same time as avoiding digestive disturbances (i.e. rumen acidosis) is a key priority in ruminant nutrition. The present study evaluated the effect of a cereal ammoniation treatment, in which barley grains are combined with urea and enzymes that catalyze the conversion of urea to ammonia to optimize rumen function. Twelve rumen cannulated sheep were randomly divided into two groups and fed a diet containing 60% of ammoniated barley (AMM) or untreated barley supplemented with urea (CTL) to investigate the impact on rumen fermentation and feed utilization.
RESULTSAMM had higher total N content and effective rumen degradable N than untreated barely. AMM sheep had a consistently higher rumen pH throughout the day (6.31 versus 6.03) and tended to have a lower post\uffe2\uff80\uff90prandial ammonia peak and higher acetate molar proportion (+5.1%) than CTL sheep. The rumen environment in AMM sheep favored the colonization and utilization of agro\uffe2\uff80\uff90industrial by\uffe2\uff80\uff90products (i.e. orange pulp) by the rumen microbes leading to a higher feed degradability. AMM sheep also had higher total tract apparent N digestibility (+21.7%) and urinary excretion of purine derivatives (+34%), suggesting a higher N uptake and microbial protein synthesis than CTL sheep.
CONCLUSIONThe inclusion of AMM in the diet of ruminants represents a valid strategy for maintaining rumen pH within a physiological range and improving N utilization by the rumen microbes, which could have positive effects on the health and productivity of animals in intensive production systems. These findings warrant further studies under conventional farm conditions. \uffc2\uffa9 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
", "keywords": ["2. Zero hunger", "Rumen", "Sheep", "Bacteria", "Food Handling", "0402 animal and dairy science", "Hordeum", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Animal Feed", "Diet", "Gastrointestinal Microbiome", "Bacterial Proteins", "Ammonia", "Barley", "Rumen fermentation", "Animals", "Urea", "Ammoniation", "Digestion", "Feed utilization", "Research Articles"]}, "links": [{"href": "https://eprints.gla.ac.uk/235892/1/235892.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/jsfa.11205"}, {"href": "https://doi.org/10.1002/jsfa.11205"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.11205", "name": "item", "description": "10.1002/jsfa.11205", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.11205"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-24T00:00:00Z"}}, {"id": "10.1002/jsfa.4533", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:21Z", "type": "Journal Article", "created": "2011-07-27", "title": "Influence Of Fertilisation Regimes On A Nosz-Containing Denitrifying Community In A Rice Paddy Soil", "description": "AbstractBACKGROUND: Denitrification is a microbial process that has received considerable attention during the past decade since it can result in losses of added nitrogen fertilisers from agricultural soils. Paddy soil has been known to have strong denitrifying activity, but the denitrifying microorganisms responsible for fertilisers in paddy soil are not well known. The objective of this study was to explore the impacts of 17\uffe2\uff80\uff90year application of inorganic and organic fertiliser (rice straw) on the abundance and composition of a nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Soil samples were collected from CK plots (no fertiliser), N (nitrogen fertiliser), NPK (nitrogen, phosphorus and potassium fertilisers) and NPK + OM (NPK plus organic matter). The nitrous oxide reductase gene (nosZ) community composition was analysed using terminal restriction fragment length polymorphism, and the abundance was determined by quantitative PCR.
RESULTS: Both the largest abundance of nosZ\uffe2\uff80\uff90denitrifier and the highest potential denitrifying activity (PDA) occurred in the NPK + OM treatment with about four times higher than that in the CK and two times higher than that in the N and NPK treatments (no significant difference). Denitrifying community composition differed significantly among fertilisation treatments except for the comparison between CK and N treatments. Of the measured abiotic factors, total organic carbon was significantly correlated with the observed differences in community composition and abundance (P < 0.01 by Monte Carlo permutation).
CONCLUSION: This study shows that the addition of different fertilisers affects the size and composition of the nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Copyright \uffc2\uffa9 2011 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Nitrogen", "0402 animal and dairy science", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Carbon", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "Denitrification", "0405 other agricultural sciences", "Fertilizers", "Oxidoreductases", "Monte Carlo Method", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.4533"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.4533", "name": "item", "description": "10.1002/jsfa.4533", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.4533"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-27T00:00:00Z"}}, {"id": "10.1002/jsfa.6206", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:21Z", "type": "Journal Article", "created": "2013-05-01", "title": "Effect Of Organic, Conventional And Mixed Cultivation Practices On Soil Microbial Community Structure And Nematode Abundance In A Cultivated Onion Crop", "description": "AbstractBACKGROUNDResponses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long\uffe2\uff80\uff90term field experiment which divides conventional and organic agriculture into component pest\uffe2\uff80\uff90control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles, microbial and nematode counts, and denaturing gradient gel electrophoresis (DGGE) to characterise soil microbial communities in plots used for onion (Allium cepa L.) cultivation.
RESULTSMicrobial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest\uffe2\uff80\uff90control treatment plots.
CONCLUSIONOrganic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. \uffc2\uffa9 2013 Society of Chemical Industry
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Microbial diversity", "Nematoda", "Soil", "03 medical and health sciences", "Onions", "Animals", "DNA", " Fungal", "Ecosystem", "Soil Microbiology", "2. Zero hunger", "Organic Agriculture", "0303 health sciences", "Bacteria", "Denaturing Gradient Gel Electrophoresis", "0402 animal and dairy science", "Fungi", "Denaturing gradient gel electrophoresis", "Agriculture", "Biolog Eco-plates", "04 agricultural and veterinary sciences", "15. Life on land", "Community level physiological profile", "Organic agriculture", "0405 other agricultural sciences"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.6206"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.6206", "name": "item", "description": "10.1002/jsfa.6206", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.6206"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-06-07T00:00:00Z"}}, {"id": "10.1002/ldr.3453", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:22Z", "type": "Journal Article", "created": "2019-10-15", "title": "Increases in aridity lead to drastic shifts in the assembly of dryland complex microbial networks", "description": "AbstractWe have little information on how and why soil microbial community assembly will respond to predicted increases in aridity by the end of this century. Here, we used correlation networks and structural equation modeling to assess the changes in the abundance of the ecological clusters including potential winner and loser microbial taxa associated with predicted increases in aridity. To do this, we conducted a field survey in an environmental gradient from eastern Australia and obtained information on bacterial and fungal community composition for 120 soil samples and multiple abiotic and biotic factors. Overall, our structural equation model explained 83% of the variance in the two mesic modules. Increases in aridity led to marked shifts in the abundance of the two major microbial modules found in our network, which accounted for >99% of all phylotypes. In particular, the relative abundance of one of these modules, the Mesic Module #1, which was positively related to multiple soil properties and plant productivity, declined strongly with aridity. Conversely, the relative abundance of a second dominant module (Xeric Module #2) was positively correlated with increases in aridity. Our study provides evidence that network analysis is a useful tool to identify microbial taxa that are either winners or losers under increasing aridity and therefore potentially under changing climates. Our work further suggests that climate change, and associated land degradation, could potentially lead to extensive microbial phylotypes exchange and local extinctions, as demonstrated by the reductions of up to 97% in the relative abundance of microbial taxa within Mesic Module #1.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.Antibiotics are some of the most widely used drugs. Their release in the environment is of great concern since their consumption is a major factor for antibiotic resistance, one of the most important threats to human health. Their occurrence and fate in agricultural systems have been extensively investigated in recent years. Yet whilst their biotic and abiotic degradation pathways have been thoroughly researched, their biotransformation pathways in plants are less understood, such as in case of trimethoprim. Although trimethoprim has been reported in the environment, its fate in higher plants still remains unknown. A bench-scale experiment was performed and 30 trimethoprim metabolites were identified in lettuce (Lactuca sativa L.), of which 5 belong to phase I and 25 to phase II. Data mining yielded a list of 1018 ions as possible metabolite candidates, which was filtered to a final list of 87 candidates. Molecular structures were assigned for 19 compounds, including 14 TMP metabolites reported for the first time. Alongside well-known biotransformation pathways in plants, additional novel pathways were suggested, namely, conjugation with sesquiterpene lactones, and abscisic acid as a part of phase II of plant metabolism. The results obtained offer insight into the variety of phase II conjugates and may serve as a guideline for studying the metabolization of other chemicals that share a similar molecular structure or functional groups with trimethoprim. Finally, the toxicity and potential contribution of the identified metabolites to the selective pressure on antibiotic resistance genes and bacterial communities via residual antimicrobial activity were evaluated.
", "keywords": ["2. Zero hunger", "High-resolution mass spectrometry", "Phytochemicals", "0211 other engineering and technologies", "02 engineering and technology", "01 natural sciences", "Trimethoprim", "Anti-Bacterial Agents", "3. Good health", "Conjugates", "Antibiotics", "Non-target screening", "Humans", "Plant metabolites", "Biotransformation", "Research Paper", "Lactuca", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Tadi\u0107, \u0110or\u0111e, Gramblicka, Michal, Mistrik, Robert, Bayona, Josep Maria,", "roles": ["creator"]}]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00216-022-03943-6.pdf"}, {"href": "https://doi.org/10.1007/s00216-022-03943-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Analytical%20and%20Bioanalytical%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00216-022-03943-6", "name": "item", "description": "10.1007/s00216-022-03943-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00216-022-03943-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-09T00:00:00Z"}}, {"id": "10.1007/bf01770034", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:32Z", "type": "Journal Article", "created": "2005-07-07", "title": "Effects Of Artificial Acid Rain On Microbial Activity And Biomass", "description": "The emission of air pollutants which form acid components in rain and snow represents a threat to natural ecosystems. Increased leaching of nutrients from soils (ABRAHAMSEN et al. 1976b), decreased pHvalues in lakes and changes in fish populations (SCHOFIELD 1976) have been suggested as some of the consequences of the increased acidity of rain. Scandinavian coniferous forests are very stable ecosystems, and dramatic short-term effects due to acid rain are hardly to be expected. To simulate long-term effects, artificially acidified rain may be used. We report here decreased microbial activity and biomass in a Norwegian forest soil treated with artificially acidified rain. (Less)", "keywords": ["Bacteria", "Ecology", "Norway", "Rain", "Fungi", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "01 natural sciences", "13. Climate action", "Fermentation", "0401 agriculture", " forestry", " and fisheries", "Acids", "Weather", "Soil Microbiology", "0105 earth and related environmental sciences"], "contacts": [{"organization": "B. Lundgren, Bengt S\u00f6derstr\u00f6m, Erland B\u00e5\u00e5th,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/bf01770034"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bulletin%20of%20Environmental%20Contamination%20and%20Toxicology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/bf01770034", "name": "item", "description": "10.1007/bf01770034", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/bf01770034"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1979-12-01T00:00:00Z"}}, {"id": "10.1007/s00018-021-04080-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:33Z", "type": "Journal Article", "created": "2022-01-19", "title": "Outlook on next\u2010generation probiotics from the human gut", "description": "Probiotics currently available on the market generally belong to a narrow range of microbial species. However, recent studies about the importance of the gut microbial commensals on human health highlighted that the gut microbiome is an unexplored reservoir of potentially beneficial microbes. For this reason, academic and industrial research is focused on identifying and testing novel microbial strains of gut origin for the development of next-generation probiotics. Although several of these are promising for the prevention and treatment of many chronic diseases, studies on human subjects are still scarce and approval from regulatory agencies is, therefore, rare. In addition, some issues need to be overcome before implementing their wide application on the market, such as the best methods for cultivation and storage of these oxygen-sensitive taxa. This review summarizes the most recent evidence related to NGPs and provides an outlook to the main issues that still limit their wide employment.", "keywords": ["0301 basic medicine", "Gut microbiome", "Clostridiales", "0303 health sciences", "Bacteria", "Faecalibacterium prausnitzii", "Probiotics", "Next-generation probiotics", "Prevotella", "Akkermansia", "Bacterial Physiological Phenomena", "Gastrointestinal Microbiome", "3. Good health", "03 medical and health sciences", "Akkermansia muciniphila; Faecalibacterium prausnitzii; Gut microbiome; Live biotherapeutics; Next-generation probiotics; Prevotella copri", "Live biotherapeutics", "Dysbiosis", "Humans", "Prevotella copri", "Akkermansia muciniphila"], "contacts": [{"organization": "De Filippis F., Esposito A., Ercolini D.,", "roles": ["creator"]}]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/868940/2/CMLS%2c2022_NGP.pdf"}, {"href": "https://link.springer.com/content/pdf/10.1007/s00018-021-04080-6.pdf"}, {"href": "https://doi.org/10.1007/s00018-021-04080-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Cellular%20and%20Molecular%20Life%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00018-021-04080-6", "name": "item", "description": "10.1007/s00018-021-04080-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00018-021-04080-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-19T00:00:00Z"}}, {"id": "10.1007/s00128-007-9045-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2007-04-04", "title": "Zinc And Copper Toxicity To Soil Bacteria And Fungi From Zinc Polluted And Unpolluted Soils: A Comparative Study With Different Types Of Biolog Plates", "keywords": ["Microbiological Techniques", "Zinc", "Bacteria", "Fungi", "Soil Pollutants", "0401 agriculture", " forestry", " and fisheries", "Poland", "04 agricultural and veterinary sciences", "01 natural sciences", "Copper", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1007/s00128-007-9045-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bulletin%20of%20Environmental%20Contamination%20and%20Toxicology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00128-007-9045-6", "name": "item", "description": "10.1007/s00128-007-9045-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00128-007-9045-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-04-05T00:00:00Z"}}, {"id": "10.1007/s00128-012-0523-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2012-01-25", "title": "Effect Of Long-Term Zinc Pollution On Soil Microbial Community Resistance To Repeated Contamination", "description": "The aim of the study was to compare the effects of stress (contamination trials) on the microorganisms in zinc-polluted soil (5,018\u00a0mg Zn\u00a0kg(-1) soil dry weight) and unpolluted soil (141\u00a0mg Zn kg(-1) soil\u00a0dw), measured as soil respiration rate. In the laboratory, soils were subjected to copper contamination (0, 500, 1,500 and 4,500\u00a0mg\u00a0kg(-1) soil\u00a0dw), and then a bactericide (oxytetracycline) combined with a fungicide (captan) along with glucose (10\u00a0mg\u00a0g(-1) soil\u00a0dw each) were added. There was a highly significant effect of soil type, copper treatment and oxytetracycline/captan treatment. The initial respiration rate of chronically zinc-polluted soil was higher than that of unpolluted soil, but in the copper treatment it showed a greater decline. Microorganisms in copper-treated soil were more susceptible to oxytetracycline/captan contamination. After the successive soil contamination trials the decline of soil respiration was greater in zinc-polluted soil than in unpolluted soil.", "keywords": ["Health", " Toxicology and Mutagenesis", "trace metals", "Oxytetracycline", "Toxicology", "01 natural sciences", "Article", "Captan", "Soil", "Stress", " Physiological", "Soil Pollutants", "Soil Microbiology", "combined stressors", "0105 earth and related environmental sciences", "soil pollution", "Drug Resistance", " Microbial", "04 agricultural and veterinary sciences", "Pollution", "Adaptation", " Physiological", "soil respiration rate", "6. Clean water", "Anti-Bacterial Agents", "Fungicides", " Industrial", "Zinc", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Copper"], "contacts": [{"organization": "Klimek, Beata", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s00128-012-0523-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bulletin%20of%20Environmental%20Contamination%20and%20Toxicology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00128-012-0523-0", "name": "item", "description": "10.1007/s00128-012-0523-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00128-012-0523-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-01-26T00:00:00Z"}}, {"id": "10.1007/s00216-019-01895-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2019-06-10", "title": "Simultaneous determination of multiclass antibiotics and their metabolites in four types of field-grown vegetables", "description": "The developed method was evaluated for the determination of 10 antibiotics belonging to four chemical classes (fluoroquinolones, sulfonamides, lincosamides, and metoxybenzylpyrimidines) and six of their metabolites in four vegetable matrices (lettuce, tomato, cauliflower, and broad beans). The reported method detection limits were sufficiently low (0.1-5.8\u00a0ng/g dry weight) to detect target compounds in vegetables under real agricultural practices. Absolute and relative recovery values ranged from 40 to 118% and from 70 to 118%, respectively, for all targeted compounds at the spike level of 100\u00a0ng/g dry weight. Regarding method precision, the highest relative standard deviation (RSD) was obtained for enrofloxacin in lettuce (20%), while for the rest of the compounds in all matrices, the RSD values were below 20% for the same spike level. Matrix effects, due to electrospray ionization, ranged from -\u200926 to 29% for 85% of all estimated values. In a field study, four of the 10 targeted antibiotics were detected in tested vegetables. For the first time, antibiotic metabolites were quantified in vegetables grown under real field conditions. More specifically, decarboxyl ofloxacin and TMP304 were detected in tomato fruits (1.5\u00a0ng/g dry weight) and lettuce leaves (21.0-23.1\u00a0ng/g dry weight), respectively. It is important to remark that the concentration of TMP304 was five times higher than that from the parental compound, emphasizing the importance of metabolite analysis in monitoring studies. Therefore, the method provided a robust, reliable, and simple-to-use tool that could prove useful for routine multiclass analysis of antibiotics and their metabolites in vegetable samples. Graphical abstract.", "keywords": ["Crops", " Agricultural", "2. Zero hunger", "Spectrometry", " Mass", " Electrospray Ionization", "Agricultural Irrigation", "Solid Phase Extraction", "Reproducibility of Results", "LC-ESI-MS/MS", "01 natural sciences", "Anti-Bacterial Agents", "0104 chemical sciences", "3. Good health", "Antibiotics", "Limit of Detection", "Ultrasound-assisted extraction", "Vegetables", "Metabolites", "Chromatography", " Liquid", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Tadi\u0107, \u0110or\u0111e, Matamoros, V\u00edctor, Bayona, Josep M.,", "roles": ["creator"]}]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s00216-019-01895-y.pdf"}, {"href": "https://doi.org/10.1007/s00216-019-01895-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Analytical%20and%20Bioanalytical%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00216-019-01895-y", "name": "item", "description": "10.1007/s00216-019-01895-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00216-019-01895-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-10T00:00:00Z"}}, {"id": "10.1007/s00253-020-10982-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:35Z", "type": "Journal Article", "created": "2020-11-11", "title": "Living with sulfonamides: a diverse range of mechanisms observed in bacteria", "description": "Sulfonamides are the oldest class of synthetic antibiotics still in use in clinical and veterinary settings. The intensive utilization of sulfonamides has been leading to the widespread contamination of the environment with these xenobiotic compounds. Consequently, in addition to pathogens and commensals, also bacteria inhabiting a wide diversity of environmental compartments have been in contact with sulfonamides for almost 90\u00a0years. This review aims at giving an overview of the effect of sulfonamides on bacterial cells, including the strategies used by bacteria to cope with these bacteriostatic agents. These include mechanisms of antibiotic resistance, co-metabolic transformation, and partial or total mineralization of sulfonamides. Possible implications of these mechanisms on the ecosystems and dissemination of antibiotic resistance are also discussed. KEY POINTS: \u2022 Sulfonamides are widespread xenobiotic pollutants; \u2022 Target alteration is the main sulfonamide resistance mechanism observed in bacteria; \u2022 Sulfonamides can be modified, degraded, or used as nutrients by some bacteria.", "keywords": ["0301 basic medicine", "Sulfonamides", "0303 health sciences", "Bacteria", "Antibiotic resistance", "Drug Resistance", " Microbial", "Anti-Bacterial Agents", "3. Good health", "03 medical and health sciences", "Biodegradation", " Environmental", "Biodegradation", "Xenobiotic", "Biotransformation", "Ecosystem"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s00253-020-10982-5.pdf"}, {"href": "https://doi.org/10.1007/s00253-020-10982-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-020-10982-5", "name": "item", "description": "10.1007/s00253-020-10982-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-020-10982-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-11T00:00:00Z"}}, {"id": "10.1007/s00248-003-0229-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2005-06-17", "title": "Methanogen Communities In A Drained Bog: Effect Of Ash Fertilization", "description": "Forestry practises such has drainage have been shown to decrease emissions of the greenhouse gas methane (CH(4)) from peatlands. The aim of the study was to examine the methanogen populations in a drained bog in northern Finland, and to assess the possible effect of ash fertilization on potential methane production and methanogen communities. Peat samples were collected from control and ash fertilized (15,000 kg/ha) plots 5 years after ash application, and potential CH(4) production was measured. The methanogen community structure was studied by DNA isolation, PCR amplification of the methyl coenzyme-M reductase (mcr) gene, denaturing gradient gel electrophoresis (DGGE), and restriction fragment length polymorphism (RFLP) analysis. The drained peatland showed low potential methane production and methanogen diversity in both control and ash-fertilized plots. Samples from both upper and deeper layers of peat were dominated by three groups of sequences related to Rice cluster-I hydrogenotroph methanogens. Even though pH was marginally greater in the ash-treated site, the occurrence of those sequences was not affected by ash fertilization. Interestingly, a less common group of sequences, related to the Fen cluster, were found only in the fertilized plots. The study confirmed the depth related change of methanogen populations in peatland.", "keywords": ["0301 basic medicine", "0303 health sciences", "Bacteria", "tuhkalannoitus", "metanogeeniset mikrobit", "Biodiversity", "15. Life on land", "03 medical and health sciences", "Genes", " Bacterial", "ojitetut suot", "Fertilizers", "Methane", "Ecosystem", "Phylogeny", "Polymorphism", " Restriction Fragment Length"]}, "links": [{"href": "https://doi.org/10.1007/s00248-003-0229-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-003-0229-2", "name": "item", "description": "10.1007/s00248-003-0229-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-003-0229-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-02-01T00:00:00Z"}}, {"id": "10.1007/s00248-007-9276-4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2007-07-17", "title": "Comparison Of Soil Bacterial Communities Under Diverse Agricultural Land Management And Crop Production Practices", "description": "The composition and structure of bacterial communities were examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Five land management programs were initiated in July 2000: conventional, organic, continuous removal of vegetation (disk fallow), undisturbed (weed fallow), and bahiagrass pasture (Paspalum notatum var Argentine). Similar levels in the diversity of bacterial 16S rDNA amplicons were detected in soil samples collected from organically and conventionally managed plots 3 and 4 years after initiation of land management programs, whereas significantly lower levels of diversity were observed in samples collected from bahiagrass pasture. Differences in diversity were attributed to effects on how the relative abundance of individual amplicons were distributed (evenness) and not on the total numbers of bacterial 16S rDNA amplicons detected (richness). Similar levels of diversity were detected among all land management programs in soil samples collected after successive years of tomato (Lycopersicon esculentum) cultivation. A different trend was observed after a multivariate examination of the similarities in genetic composition among soil bacterial communities. After 3 years of land management, similarities in genetic composition of soil bacterial communities were observed in plots where disturbance was minimized (bahiagrass and weed fallow). The genetic compositions in plots managed organically were similar to each other and distinct from bacterial communities in other land management programs. After successive years of tomato cultivation and damage from two major hurricanes, only the composition of soil bacterial communities within organically managed plots continued to maintain a high degree of similarity to each other and remain distinct from other bacterial communities. This study reveals the effects of agricultural land management practices on soil bacterial community composition and diversity in a large-scale, long-term replicated study where the effect of soil type on community attributes was removed.", "keywords": ["Crops", " Agricultural", "DNA", " Bacterial", "2. Zero hunger", "Analysis of Variance", "Conservation of Natural Resources", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "DNA", " Ribosomal", "Polymerase Chain Reaction", "Solanum lycopersicum", "RNA", " Ribosomal", " 16S", "0401 agriculture", " forestry", " and fisheries", "Cloning", " Molecular", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-007-9276-4"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-007-9276-4", "name": "item", "description": "10.1007/s00248-007-9276-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-007-9276-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-07-07T00:00:00Z"}}, {"id": "10.1007/s00248-007-9295-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2007-08-31", "title": "Plfa Profiling Of Microbial Community Structure And Seasonal Shifts In Soils Of A Douglas-Fir Chronosequence", "description": "The impact and frequency of forest harvesting could significantly affect soil microbial community (SMC) structure and functioning. The ability of soil microorganisms to perform biogeochemical processes is critical for sustaining forest productivity and has a direct impact on decomposition dynamics and carbon storage potential. The Wind River Canopy Crane Research Forest in SW, WA, provided a unique opportunity to study a forest chronosequence and the residual effects of harvesting on the SMC in comparison to old-growth forests. The objective of this study was to determine the effect of clear-cutting and stand age on temporal dynamics of SMC and physiological stress markers using phospholipid fatty acid (PLFA) profiling. Soil microbial PLFA profiles were determined seven times over 22 months (Nov. 02 to Sep. 04) in old-growth coniferous forest stands (300-500 years) and 8 (CC8)- or 25 (CC25)-year-old replanted clear-cuts. PLFA patterns of the SMC shifted because of clear-cutting, but seasonal temporal changes had greater shifts than differences among stand age. The microbial biomass (total PLFA) and bacterial, fungal, and selected other PLFAs were significantly reduced in CC8 but not in CC25 sites relative to the old-growth sites. An increase in stress indicators [PLFA ratios of saturated/monsaturated and (cy17:0 + cy19:0)/(16:1omega7 + 18:1omega7)] in late summer was related to water stress. Although the canopy and litter input are quite different for a 25-year clear-cut compared to virgin old-growth forest, we conclude that the composition of the microbial communities, 25 years after clear-cutting, has recovered sufficiently to be much more similar to old-growth forests than a recent clear-cut at this Pacific Northwest forest site. The study shows the potential of PLFA analysis for profiling microbial communities and their stress status under field conditions, but wide temporal shifts emphasize the need for sampling over seasons to fully interpret ecosystem management impacts on microbial populations.", "keywords": ["Washington", "Time Factors", "Bacteria", "Fatty Acids", "Fungi", "Temperature", "Eukaryota", "Water", "04 agricultural and veterinary sciences", "15. Life on land", "Pseudotsuga", "Trees", "Soil", "13. Climate action", "Animals", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Seasons", "Phospholipids", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-007-9295-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-007-9295-1", "name": "item", "description": "10.1007/s00248-007-9295-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-007-9295-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-08-31T00:00:00Z"}}, {"id": "10.1007/s00248-007-9308-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2007-09-01", "title": "Long-Term Effect Of Municipal Solid Waste Amendment On Microbial Abundance And Humus-Associated Enzyme Activities Under Semiarid Conditions", "description": "Microbial ecology is the key to understanding the function of soil biota for organic matter cycling after a single amendment of organic waste in semiarid soils. Therefore, in this paper, the long-term effect (17 years) of adding different doses of a solid municipal waste to an arid soil on humus-enzyme complexes, a very stable and long-lasting fraction of soil enzymes, as well as on microbial and plant abundance, was studied. Humic substances were extracted by 0.1 M pH 7 sodium pyrophosphate from soil samples collected in experimental plots amended with different doses of a solid municipal waste (0, 65, 130, 195, and 260 t/ha) 17 years before. The activity of different hydrolases related with the C (beta-glucosidase), N (urease), and P (alkaline phosphatase) cycles and with the formation of humic substances (o-diphenol oxidase) were determined in this extract. The density and diversity of plant cover in the plots, as well as the fungal and bacterial biomass (by analyzing phopholipid fatty acids) were also determined. In general, the amended plots showed greater humic substance-related enzymatic activity than the unamended plots. This activity increased with the dose but only up to a certain level, above which it leveled off or even diminished. Plant diversity and cover density followed the same trend. Fungal and bacterial biomass also benefited in a dose-dependent manner. Different signature molecules representing gram+ and gram- bacteria, and those corresponding to monounsaturated and saturated fatty acids showed a similar behavior. The results demonstrate that organic amendment had a noticeable long-term effect on the vegetal development, humic substances-related enzyme activity and on the development of bacteria and fungi in semiarid conditions.", "keywords": ["2. Zero hunger", "Analysis of Variance", "Time Factors", "Bacteria", "Fatty Acids", "Fungi", "04 agricultural and veterinary sciences", "15. Life on land", "01 natural sciences", "6. Clean water", "Enzymes", "Refuse Disposal", "12. Responsible consumption", "Soil", "Ergosterol", "11. Sustainability", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Humic Substances", "Phospholipids", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1007/s00248-007-9308-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-007-9308-0", "name": "item", "description": "10.1007/s00248-007-9308-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-007-9308-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-09-02T00:00:00Z"}}, {"id": "10.1007/s00248-008-9467-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2008-11-21", "title": "Molecular And Functional Assessment Of Bacterial Community Convergence In Metal-Amended Soils", "description": "Species diversity and the structure of microbial communities in soils are thought to be a function of the cumulative selective pressures within the local environment. Shifts in microbial community structure, as a result of metal stress, may have lasting negative effects on soil ecosystem dynamics if critical microbial community functions are compromised. Three soils in the vicinity of a copper smelter, previously contaminated with background, low and high levels of aerially deposited metals, were amended with metal-salts to determine the potential for metal contamination to shape the structural and functional diversity of microbial communities in soils. We hypothesized that the microbial communities native to the three soils would initially be unique to each site, but would converge on a microbial community with similar structure and function, as a result of metal stress. Initially, the three different sites supported microbial communities with unique structural and functional diversity, and the nonimpacted site supported inherently higher levels of microbial activity and biomass, relative to the metal-contaminated sites. Amendment of the soils with metal-salts resulted in a decrease in microbial activity and biomass, as well as shifts in microbial community structure and function at each site. Soil microbial communities from each site were also observed to be sensitive to changes in soil pH as a result of metal-salt amendment; however, the magnitude of these pH-associated effects varied between soils. Microbial communities from each site did not converge on a structurally or functionally similar community following metal-salt amendment, indicating that other factors may be equally important in shaping microbial communities in soils. Among these factors, soil physiochemical parameters like organic matter and soil pH, which can both influence the bioavailability and toxicity of metals in soils, may be critical.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "0303 health sciences", "Bacteria", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Soil", "03 medical and health sciences", "13. Climate action", "Metals", " Heavy", "Soil Pollutants", "Biomass", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-008-9467-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-008-9467-7", "name": "item", "description": "10.1007/s00248-008-9467-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-008-9467-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-11-22T00:00:00Z"}}, {"id": "10.1007/s00248-010-9727-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2010-08-03", "title": "Soil Microbial Abundance And Diversity Along A Low Precipitation Gradient", "description": "The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while \u223c2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (\u223c9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem.", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "0301 basic medicine", "Salinity", "0303 health sciences", "Bacteria", "Mediterranean Region", "Climate", "Rain", "Water", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Soil", "03 medical and health sciences", "Phospholipids", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-010-9727-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-010-9727-1", "name": "item", "description": "10.1007/s00248-010-9727-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-010-9727-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-08-01T00:00:00Z"}}, {"id": "10.1007/s00248-016-0730-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2016-02-02", "title": "Responses Of Soil Bacterial Communities To Nitrogen Deposition And Precipitation Increment Are Closely Linked With Aboveground Community Variation", "description": "It has been predicted that precipitation and atmospheric nitrogen (N) deposition will increase in northern China; yet, ecosystem responses to the interactive effects of water and N remain largely unknown. In particular, responses of belowground microbial community to projected global change and their potential linkages to aboveground macro-organisms are rarely studied. In this study, we examined the responses of soil bacterial diversity and community composition to increased precipitation and multi-level N deposition in a temperate steppe in Inner Mongolia, China, and explored the diversity linkages between aboveground and belowground communities. It was observed that N addition caused the significant decrease in bacterial alpha-diversity and dramatic changes in community composition. In addition, we documented strong correlations of alpha- and beta-diversity between plant and bacterial communities in response to N addition. It was found that N enriched the so-called copiotrophic bacteria, but reduced the oligotrophic groups, primarily by increasing the soil inorganic N content and carbon availability and decreasing soil pH. We still highlighted that increased precipitation tended to alleviate the effects of N on bacterial diversity and dampen the plant-microbe connections induced by N. The counteractive effects of N addition and increased precipitation imply that even though the ecosystem diversity and function are predicted to be negatively affected by N deposition in the coming decades; the combination with increased precipitation may partially offset this detrimental effect.", "keywords": ["0301 basic medicine", "2. Zero hunger", "China", "0303 health sciences", "Bacteria", "Nitrogen", "Climate", "Microbial Consortia", "Water", "Biodiversity", "Plants", "15. Life on land", "Carbon", "6. Clean water", "Soil", "03 medical and health sciences", "13. Climate action", "Chemical Precipitation", "Ecosystem", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-016-0730-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-016-0730-z", "name": "item", "description": "10.1007/s00248-016-0730-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-016-0730-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-02-02T00:00:00Z"}}, {"id": "10.1007/s00248-024-02363-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:34Z", "type": "Journal Article", "created": "2024-03-01", "title": "The Feather Moss Hylocomium splendens Affects the Transcriptional Profile of a Symbiotic Cyanobacterium in Relation to Acquisition and Turnover of Key Nutrients", "description": "AbstractMoss-cyanobacteria symbioses were proposed to be based on nutrient exchange, with hosts providing C and S while bacteria provide N, but we still lack understanding of the underlying molecular mechanisms of their interactions. We investigated how contact between the ubiquitous moss Hylocomium splendens and its cyanobiont affects nutrient-related gene expression of both partners. We isolated a cyanobacterium from H. splendens and co-incubated it with washed H. splendens shoots. Cyanobacterium and moss were also incubated separately. After 1\uffc2\uffa0week, we performed acetylene reduction assays to estimate N2 fixation and RNAseq to evaluate metatranscriptomes. Genes related to N2 fixation and the biosynthesis of several amino acids were up-regulated in the cyanobiont when hosted by the moss. However, S-uptake and the biosynthesis of the S-containing amino acids methionine and cysteine were down-regulated in the cyanobiont while the degradation of selenocysteine was up-regulated. In contrast, the number of differentially expressed genes in the moss was much lower, and almost no transcripts related to nutrient metabolism were affected. It is possible that, at least during the early stage of this symbiosis, the cyanobiont receives few if any nutrients from the host in return for N, suggesting that moss\uffe2\uff80\uff93cyanobacteria symbioses encompass relationships that are more plastic than a constant mutualist flow of nutrients.Pseudomonas putidais a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications ofP. putidaas a cell factory.
Key points\uffe2\uff80\uffa2 Pseudomonas putida advances to a global industrial cell factory.
\uffe2\uff80\uffa2 Novel tools enable system-wide understanding and streamlined genomic engineering.
\uffe2\uff80\uffa2 Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
", "keywords": ["0301 basic medicine", "ddc:500", "0303 health sciences", "Pseudomonas putida", "EDEMP cycle", "PHA", "Systems Biology", "500", "Genomics", "Mini-Review", "Bioeconomy", "Bacterial chassis", "Lignin", "03 medical and health sciences", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "Microbial cell factory", "13. Climate action", "Biocatalysis", "Synthetic Biology", "KT2440", "Metabolic engineering", "Biotransformation", "Synthetic biology", "Biotechnology"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00253-020-10811-9.pdf"}, {"href": "https://doi.org/10.1007/s00253-020-10811-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-020-10811-9", "name": "item", "description": "10.1007/s00253-020-10811-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-020-10811-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-13T00:00:00Z"}}, {"id": "10.1007/s00374-002-0459-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:36Z", "type": "Journal Article", "created": "2003-02-13", "title": "Impact Of A Change In Tillage And Crop Residue Management Practice On Soil Chemical And Microbiological Properties In A Cereal-Producing Red Duplex Soil In Nsw, Australia", "description": "The effect of a change of tillage and crop residue management practice on the chemical and microbiological properties of a cereal-producing red duplex soil was investigated by superimposing each of three management practices (CC: conventional cultivation, stubble burnt, crop conventionally sown; DD: direct-drilling, stubble retained, no cultivation, crop direct-drilled; SI: stubble incorporated with a single cultivation, crop conventionally sown), for a 3-year period on plots previously managed with each of the same three practices for 14 years. A change from DD to CC or SI practice resulted in a significant decline, in the top 0\u20135 cm of soil, in organic C, total N, electrical conductivity, NH4-N, NO3-N, soil moisture holding capacity, microbial biomass and CO2 respiration as well as a decline in the microbial quotient (the ratio of microbial biomass C to organic C; P 0.05). However, there was a significant increase in microbial biomass and the microbial quotient in the top 0\u20135 cm of soil following the change from CC to DD or SI practice and with the change from SI to DD practice (P <0.05). Analysis of ester-linked fatty acid methyl esters (EL-FAMEs) extracted from the 0- to 5-cm and 5- to 10-cm layers of the soils of the various treatments detected changes in the FAME profiles following a change in tillage practice. A change from DD practice to SI or CC practice was associated with a significant decline in the ratio of fungal to bacterial fatty acids in the 0- to 5-cm soil (P <0.05). The results show that a change in tillage practice, particularly the cultivation of a previously minimum-tilled (direct-drilled) soil, will result in significant changes in soil chemical and microbiological properties within a 3-year period. They also show that soil microbiological properties are sensitive indicators of a change in tillage practice.", "keywords": ["2. Zero hunger", "biomass", "cellular organisms", "microbiology", "Australia", "Microbial biomass", "duplex", "04 agricultural and veterinary sciences", "Fatty acid methyl esters", "15. Life on land", "6. Clean water", "Stubble retention", "Tillage", "crop residue", "0401 agriculture", " forestry", " and fisheries", "Organic C", "Bacteria (microorganisms)", "management practice"]}, "links": [{"href": "https://doi.org/10.1007/s00374-002-0459-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-002-0459-3", "name": "item", "description": "10.1007/s00374-002-0459-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-002-0459-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2002-05-01T00:00:00Z"}}, {"id": "10.1007/s00374-006-0139-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:37Z", "type": "Journal Article", "created": "2006-10-10", "title": "Effect Of Intercropping On Crop Yield And Chemical And Microbiological Properties In Rhizosphere Of Wheat (Triticum Aestivum L.), Maize (Zea Mays L.), And Faba Bean (Vicia Faba L.)", "description": "In this study, we investigated crop yield and various chemical and microbiological properties in rhizosphere of wheat, maize, and faba bean grown in the field solely and intercropped (wheat/faba bean, wheat/maize, and maize/faba bean) in the second and third year after establishment of the cropping systems. In both years, intercropping increased crop yield, changed N and P availability, and affected the microbiological properties in rhizosphere of the three species compared to sole cropping. Generally, intercropping increased microbial biomass C, N, and P availability, whereas it reduced microbial biomass N in rhizosphere of wheat. The rhizosphere bacterial community composition was studied by denaturing gradient gel electrophoresis of 16S rRNA. In the third year of different cropping systems, intercropping significantly changed bacterial community composition in rhizosphere compared with sole cropping, and the effects were most pronounced in the wheat/faba bean intercropping system. The effects were less pronounced in the second year. The results show that intercropping has significant effects on microbiological and chemical properties in the rhizosphere, which may contribute to the yield enhancement by intercropping.", "keywords": ["PCR-DGGE", "2. Zero hunger", "Intercropping", "571", "Bacterial community composition", "Rhizosphere", "Microbial biomass", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences"]}, "links": [{"href": "https://doi.org/10.1007/s00374-006-0139-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-006-0139-9", "name": "item", "description": "10.1007/s00374-006-0139-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-006-0139-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-10-11T00:00:00Z"}}, {"id": "10.1007/s00374-012-0721-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:14:39Z", "type": "Journal Article", "created": "2012-07-19", "title": "Grazing Effects On Microbial Community Composition, Growth And Nutrient Cycling In Salt Marsh And Sand Dune Grasslands", "description": "The effect of grazing by large herbivores on the microbial community and the ecosystem functions they provide are relatively unknown in grassland systems. In this study, the impact of grazing upon the size, composition and activity of the soil microbial community was measured in field experiments in two coastal ecosystems: one salt marsh and one sand dune grassland. Bacterial, fungal and total microbial biomass were not systematically affected by grazing across ecosystems, although, within an ecosystem, differences could be detected. Fungal-to-bacterial ratio did not differ with grazing for either habitat. Redundancy analysis showed that soil moisture, bulk density and root biomass significantly explained the composition of phospholipid fatty acid (PLFA) markers, dominated by the distinction between the two grassland habitats, but where the grazing effect could also be resolved. PLFA markers for Gram-positive bacteria were more proportionally abundant in un-grazed, and markers for Gram-negative bacteria in grazed grasslands. Bacterial growth rate (leucine incorporation) was highest in un-grazed salt marsh but did not vary with grazing intensity in the sand dune grassland. We conclude that grazing consistently affects the composition of the soil microbial community in semi-natural grasslands but that its influence is small (7 % of the total variation in PLFA composition), compared with differences between grassland types (89 %). The relatively small effect of grazing translated to small effects on measurements of soil microbial functions, including N and C mineralisation. This study is an early step toward assessing consequences of land-use change for global nutrient cycles driven by the microbial community.", "keywords": ["2. Zero hunger", "bacterial growth rate", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "decomposer ecology", "nutrient cycling", "livestock grazing", "PLFAs", "04 agricultural and veterinary sciences", "15. Life on land"]}, "links": [{"href": "https://doi.org/10.1007/s00374-012-0721-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-012-0721-2", "name": "item", "description": "10.1007/s00374-012-0721-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-012-0721-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-07-19T00:00:00Z"}}, {"id": "10.1016/j.ejsobi.2013.10.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-29T16:15:57Z", "type": "Journal Article", "created": "2013-11-02", "title": "Effect Of Biochar Addition On Soil Microbial Community In A Wheat Crop", "description": "Biochar is known to enhance soil fertility and C sequestration, but relatively little information is currently available about its effect on soil microbial community, a component of terrestrial ecosystems that plays a key role in nutrient cycling. This study tested the effects of soil amendment with two loads of wood-derived biochar (30 and 60 t ha(-1)) in a wheat crop in Tuscany (Italy). Soil samples were collected 3 and 14 months after treatments over two successive growing seasons, and analysed for pH, total organic C (C-org), extractable C (C-ext), microbial biomass-C (C-mic), 25 specific microbial activities, mean substrate-induced respiration (mSIR) for 25 substrates, functional microbial diversity and bacterial genetic diversity. No significant effect of biochar treatment was observed on C-org, C-ext, C-mic, microbial quotient (C-mic % C-org) or genetic diversity. An increase in mSIR, some specific microbial activities and soil pH, and a significant change in functional diversity were observed 3 months after treatment. In contrast, no effect of biochar was detected 14 months after treatment for the parameters considered, except for a small but significant increase in pH. Our data suggest that biochar addition stimulated soil microbial activity without causing any apparent disturbance, but this positive effect was very short-lived. (C) 2013 Published by Elsevier Masson SAS.", "keywords": ["2. Zero hunger", "Soil management", "Wood-derived biochar", "Soil bacterial diversity; Soil management; Soil microbial activity; Soil microbial functional diversity; Wheat crop; Wood-derived biochar;", "Soil microbial functional diversity", "Wheat crop", "Soil microbial activity", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "Soil bacterial diversity", "15. Life on land", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1016/j.ejsobi.2013.10.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/European%20Journal%20of%20Soil%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ejsobi.2013.10.007", "name": "item", "description": "10.1016/j.ejsobi.2013.10.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ejsobi.2013.10.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-01-01T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Bacteria&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=Bacteria&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=Bacteria&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Bacteria&offset=50", "hreflang": "en-US"}], "numberMatched": 708, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-04-30T01:17:50.468673Z"}