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": "10.1016/j.scienta.2025.114006", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-25T16:16:52Z", "type": "Journal Article", "created": "2025-02-08", "title": "Light and substrate composition control root exudation rates at the initial stages of soilless lettuce cultivation", "description": "ABSTRACTPlant root exudation is an inherent metabolic process that enhances various functions of the root system like the mobilization of nutrients and interactions with surrounding microbial communities. The role and extent of root exudation in soilless crop production is poorly investigated. Here, we analyzed soilless lettuce and show that the root exudation rate declines with plant age. Furthermore, the impact of light quality and substrate was assessed by growing soilless lettuce in 100% red light (660 nm), 100% blue light (450 nm), and white light (full-light spectrum) and in 100% perlite, 100% potting soil, or mixtures of both materials. Root exudates were collected at 10, 17 and 24 days after transplanting. The total carbon root exudation rate was influenced by light conditions and substrate composition at the earliest timepoint of the culture but not at later growth stages. The total carbohydrate exudation rate was significantly higher under pure blue and red light compared to white light. The impact of light depended on the presence of perlite in the substrate. The total phenolic compound exudation rate was most strongly influenced by the substrate composition and reached the highest level in either pure potting soil or pure perlite. These findings underscore the importance of root exudation during the initial stages of development. Light and growing media influence the exudation rate at this early stage, suggesting that exudation is an adaptive process of the soilless lettuce culture.
HIGHLIGHTAt an initial stage of development, soilless lettuce exudation rates are high and modulated by light and substrate composition, whereas older plants show lower rates that are not influenced by these environmental conditions.Vegetable production systems are often characterized by excessive nitrogen (N) fertilization and the incorporation of large amounts of post-harvest crop residues. This makes them particularly prone to ammonia (NH3) and nitrous oxide (N2O) emissions. Yet, urgently needed management strategies that can reduce these harmful emissions are missing, because underlying processes are not fully understood. The present study therefore focuses on the effects of residue placement on NH3 and N2O emissions. For this, cauliflower leaf residues (286 kg N/ha) were either applied as surface mulch (mulch) or mixed with the topsoil (mix) and in situ NH3 and N2O emissions were investigated. The experiment took place on a sandy soil in Northeastern Germany during summer 2012. Residue application created a high peak in N2O emissions during the first 2 weeks, irrespective of residue placement. There was no significant difference in the emission sums over the experimental period (65 days) between the mix (5\uffc2\uffb78 \uffc2\uffb1 0\uffc2\uffb768 kg N2O-N/ha) and the mulch (9\uffc2\uffb77 \uffc2\uffb1 1\uffc2\uffb753 kg N2O-N/ha) treatment. This was also the case for NH3 emissions, which exhibited a lower initial peak followed by a prolonged decline. Measured emission sums were 4\uffc2\uffb71 \uffc2\uffb1 0\uffc2\uffb733 (mix) and 5\uffc2\uffb71 \uffc2\uffb1 0\uffc2\uffb773 (mulch) kg NH3-N/ha. It was concluded that substantial NH3 and N2O emissions can occur after high input of available organic carbon and N even in a coarse-textured soil with low water-holding capacity. Other than expected, surface-application does not enhance NH3 emissions at the expense of N2O emissions compared with residue mixing into the soil, at least under the conditions of the present study.
", "keywords": ["2. Zero hunger", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Climate Change and Agriculture Research Papers"]}, "links": [{"href": "https://doi.org/10.1017/s0021859615000027"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Journal%20of%20Agricultural%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1017/s0021859615000027", "name": "item", "description": "10.1017/s0021859615000027", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1017/s0021859615000027"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-02-25T00:00:00Z"}}, {"id": "10.1093/jxb/erad014", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-25T16:18:26Z", "type": "Journal Article", "created": "2023-01-11", "title": "Responses of key root traits in the genusOryzato soil flooding mimicked by stagnant, deoxygenated nutrient solution", "description": "AbstractExcess water can induce flooding stress resulting in yield loss, even in wetland crops such as rice (Oryza). However, traits from species of wild Oryza have already been used to improve tolerance to abiotic stress in cultivated rice. This study aimed to establish root responses to sudden soil flooding among eight wild relatives of rice with different habitat preferences benchmarked against three genotypes of O. sativa. Plants were raised hydroponically, mimicking drained or flooded soils, to assess the plasticity of adventitious roots. Traits included were apparent permeance (PA) to O2 of the outer part of the roots, radial water loss, tissue porosity, apoplastic barriers in the exodermis, and root anatomical traits. These were analysed using a plasticity index and hierarchical clustering based on principal component analysis. For example, O. brachyantha, a wetland species, possessed very low tissue porosity compared with other wetland species, whereas dryland species O. latifolia and O. granulata exhibited significantly lower plasticity compared with wetland species and clustered in their own group. Most species clustered according to growing conditions based on PA, radial water loss, root porosity, and key anatomical traits, indicating strong anatomical and physiological responses to sudden soil flooding.The mountain birch [Betula pubescens var. pumila (L.)] forest in the Subarctic is periodically exposed to insect outbreaks, which are expected to intensify due to climate change. To mitigate abiotic and biotic stresses, plants have evolved chemical defenses, including volatile organic compounds (VOCs) and non-volatile specialized compounds (NVSCs). Constitutive and induced production of these compounds, however, are poorly studied in Subarctic populations of mountain birch. Here, we assessed the joint effects of insect herbivory, elevation and season on foliar VOC emissions and NVSC contents of mountain birch. The VOCs were sampled in situ by an enclosure technique and analyzed by gas chromatography\uffe2\uff80\uff93mass spectrometry. NVSCs were analyzed by liquid chromatography\uffe2\uff80\uff93mass spectrometry using an untargeted approach. At low elevation, experimental herbivory by winter moth larvae (Operophtera brumata) increased emissions of monoterpenes and homoterpenes over the 3-week feeding period, and sesquiterpenes and green leaf volatiles at the end of the feeding period. At high elevation, however, herbivory augmented only homoterpene emissions. The more pronounced herbivory effects at low elevation were likely due to higher herbivory intensity. Of the individual compounds, linalool, ocimene, 4,8-dimethylnona-1,3,7-triene, 2-methyl butanenitrile and benzyl nitrile were among the most responsive compounds in herbivory treatments. Herbivory also altered foliar NVSC profiles at both low and high elevations, with the most responsive compounds likely belonging to fatty acyl glycosides and terpene glycosides. Additionally, VOC emissions from non-infested branches were higher at high than low elevation, particularly during the early season, which was mainly driven by phenological differences. The VOC emissions varied substantially over the season, largely reflecting the seasonal variations in temperature and light levels. Our results suggest that if insect herbivory pressure continues to rise in the mountain birch forest with ongoing climate change, it will significantly increase VOC emissions with important consequences for local trophic interactions and climate.
", "keywords": ["0301 basic medicine", "Volatile Organic Compounds", "0303 health sciences", "secondary metabolites", "VDP::Zoologiske og botaniske fag: 480", "plant\u2013insect interactions", "Moths", "15. Life on land", "geometrid moth", "Plant Leaves", "03 medical and health sciences", "biotic stress", "13. Climate action", "volatile organic compounds", "Larva", "8. Economic growth", "11. Sustainability", "VDP::Zoology and botany: 480", "Animals", "Herbivory", "Seasons", "global change", "Betula", "Research Paper"]}, "links": [{"href": "http://academic.oup.com/treephys/article-pdf/41/6/1019/38497290/tpab023.pdf"}, {"href": "https://doi.org/10.1093/treephys/tpab023"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Tree%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/treephys/tpab023", "name": "item", "description": "10.1093/treephys/tpab023", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/tpab023"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-18T00:00:00Z"}}, {"id": "10.1093/treephys/tpad135", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-25T16:18:28Z", "type": "Journal Article", "created": "2023-11-09", "title": "Carbon dynamics in long-term starving poplar trees\u2014the importance of older carbohydrates and a shift to lipids during survival", "description": "AbstractCarbon (C) assimilation can be severely impaired during periods of environmental stress, like drought or defoliation, making trees heavily dependent on the use of C reserve pools for survival; yet, the dynamics of reserve use during periods of reduced C supply are still poorly understood. We used stem girdling in mature poplar trees (Populus tremula L. hybrids), a lipid-storing species, to permanently interrupt the phloem C transport and induced C shortage in the isolated stem section below the girdle and monitored metabolic activity during three campaigns in the growing seasons of 2018, 2019 and 2021. We measured respiratory fluxes (CO2 and O2), non-structural carbon concentration, the respiratory substrate (based on isotopic analysis and CO2/O2 ratio) and the age of the respiratory substrate (based on radiocarbon analysis). Our study shows that poplar trees can survive long periods of reduced C supply from the canopy by switching in metabolism from recent carbohydrates to older storage pools with a potential mixture of respiratory substrates, including lipids. This mechanism of stress resilience can explain why tree decline may take many years before death occurs.Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.Excess water can induce flooding stress resulting in yield loss, even in wetland crops such as rice (Oryza). However, traits from species of wild Oryza have already been used to improve tolerance to abiotic stress in cultivated rice. This study aimed to establish root responses to sudden soil flooding among eight wild relatives of rice with different habitat preferences benchmarked against three genotypes of O. sativa. Plants were raised hydroponically, mimicking drained or flooded soils, to assess the plasticity of adventitious roots. Traits included were apparent permeance (PA) to O2 of the outer part of the roots, radial water loss, tissue porosity, apoplastic barriers in the exodermis, and root anatomical traits. These were analysed using a plasticity index and hierarchical clustering based on principal component analysis. For example, O. brachyantha, a wetland species, possessed very low tissue porosity compared with other wetland species, whereas dryland species O. latifolia and O. granulata exhibited significantly lower plasticity compared with wetland species and clustered in their own group. Most species clustered according to growing conditions based on PA, radial water loss, root porosity, and key anatomical traits, indicating strong anatomical and physiological responses to sudden soil flooding.Plant root exudation is an inherent metabolic process that enhances various functions of the root system like the mobilization of nutrients and interactions with surrounding microbial communities. The role and extent of root exudation in soilless crop production is poorly investigated. Here, we analyzed soilless lettuce and show that the root exudation rate declines with plant age. Furthermore, the impact of light quality and substrate was assessed by growing soilless lettuce in 100% red light (660 nm), 100% blue light (450 nm), and white light (full-light spectrum) and in 100% perlite, 100% potting soil, or mixtures of both materials. Root exudates were collected at 10, 17 and 24 days after transplanting. The total carbon root exudation rate was influenced by light conditions and substrate composition at the earliest timepoint of the culture but not at later growth stages. The total carbohydrate exudation rate was significantly higher under pure blue and red light compared to white light. The impact of light depended on the presence of perlite in the substrate. The total phenolic compound exudation rate was most strongly influenced by the substrate composition and reached the highest level in either pure potting soil or pure perlite. These findings underscore the importance of root exudation during the initial stages of development. Light and growing media influence the exudation rate at this early stage, suggesting that exudation is an adaptive process of the soilless lettuce culture.
HIGHLIGHTAt an initial stage of development, soilless lettuce exudation rates are high and modulated by light and substrate composition, whereas older plants show lower rates that are not influenced by these environmental conditions.Carbon (C) assimilation can be severely impaired during periods of environmental stress, like drought or defoliation, making trees heavily dependent on the use of C reserve pools for survival; yet, the dynamics of reserve use during periods of reduced C supply are still poorly understood. We used stem girdling in mature poplar trees (Populus tremula L. hybrids), a lipid-storing species, to permanently interrupt the phloem C transport and induced C shortage in the isolated stem section below the girdle and monitored metabolic activity during three campaigns in the growing seasons of 2018, 2019 and 2021. We measured respiratory fluxes (CO2 and O2), non-structural carbon concentration, the respiratory substrate (based on isotopic analysis and CO2/O2 ratio) and the age of the respiratory substrate (based on radiocarbon analysis). Our study shows that poplar trees can survive long periods of reduced C supply from the canopy by switching in metabolism from recent carbohydrates to older storage pools with a potential mixture of respiratory substrates, including lipids. This mechanism of stress resilience can explain why tree decline may take many years before death occurs.Nitrogen (N) fertilization is known to enhance tree biomass production and carbon (C) assimilation in N-limited boreal forests. Yet, the long-term effects of repeated N applications remain limited. Here, we evaluate the impact of repeated N fertilization at 10-year intervals over six decades on a nutrient-poor Scots pine (Pinus sylvestris L.) forest in Central Finland. The analysis encompassed both short-term (single N-addition) and long-term (multi-decadal repeated N-additions) responses of basal area increment (BAI) and carbon isotope composition in tree rings (\uffce\uffb413C) from fertilized and control plots from 1960 to 2022. Furthermore, needle mass and chemistry were investigated, and stand-level nitrogen-use efficiency (NUE, amount of stem volume or tree C increased per unit mass of N added) estimated. We found that a single N-addition had a positive short-term effect on the tree ring \uffce\uffb413C during the first 2\uffc2\uffa0years after fertilization. This suggests a combined effect on increase in photosynthetic activity and stomatal conductance, likely driven by greater needle mass and higher N content. Basal area increment showed a delayed but rapid increase, attributable to enhanced needle mass from improved photosynthesis, reaching its peak 2\uffc2\uffa0years after fertilization, and then persisting for a period of 4\uffe2\uff80\uff937\uffc2\uffa0years. However, by the end of each decadal fertilization cycle, BAI and \uffce\uffb413C values in N treatment reached those of control, demonstrating no lasting site carry-over effects. The mean decadal NUE for the tree stem volume was 0.16\uffc2\uffa0m3 per kg N added, indicating a significant degree of N retention in the forest ecosystem. After six decades, the cumulative impact of repeated fertilization led to a 47% increase in BAI in fertilized plots compared with controls, demonstrating the efficacy of accumulated short-term growth enhancements. Our findings highlight the potential of repeated N fertilization as an effective forest management practice to support the bioeconomy and mitigate climate change in nutrient-poor boreal forests.Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.Plant root exudation is an inherent metabolic process that enhances various functions of the root system like the mobilization of nutrients and interactions with surrounding microbial communities. The role and extent of root exudation in soilless crop production is poorly investigated. Here, we analyzed soilless lettuce and show that the root exudation rate declines with plant age. Furthermore, the impact of light quality and substrate was assessed by growing soilless lettuce in 100% red light (660 nm), 100% blue light (450 nm), and white light (full-light spectrum) and in 100% perlite, 100% potting soil, or mixtures of both materials. Root exudates were collected at 10, 17 and 24 days after transplanting. The total carbon root exudation rate was influenced by light conditions and substrate composition at the earliest timepoint of the culture but not at later growth stages. The total carbohydrate exudation rate was significantly higher under pure blue and red light compared to white light. The impact of light depended on the presence of perlite in the substrate. The total phenolic compound exudation rate was most strongly influenced by the substrate composition and reached the highest level in either pure potting soil or pure perlite. These findings underscore the importance of root exudation during the initial stages of development. Light and growing media influence the exudation rate at this early stage, suggesting that exudation is an adaptive process of the soilless lettuce culture.
HIGHLIGHTAt an initial stage of development, soilless lettuce exudation rates are high and modulated by light and substrate composition, whereas older plants show lower rates that are not influenced by these environmental conditions.