Legume roots can be symbiotically colonized by arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria. In Lotus japonicus, the latter occurs intracellularly by the cognate rhizobial partner Mesorhizobium loti or intercellularly with the Agrobacterium pusense strain IRBG74. Although these symbiotic programs show distinctive cellular and transcriptome signatures, some molecular components are shared. In this study, we demonstrate that 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase 1 (DAHPS1), the first enzyme in the biosynthetic pathway of aromatic amino acids (AAAs), plays a critical role in root hair development and for AM and rhizobial symbioses in Lotus. Two homozygous DAHPS1 mutants (dahps1-1 and dahps1-2) showed drastic alterations in root hair morphology, associated with alterations in cell wall dynamics and a progressive disruption of the actin cytoskeleton. The altered root hair structure was prevented by pharmacological and genetic complementation. dahps1-1 and dahps1-2 showed significant reductions in rhizobial infection (intracellular and intercellular) and nodule organogenesis and a delay in AM colonization. RNAseq analysis of dahps1-2 roots suggested that these phenotypes are associated with downregulation of several cell wall\uffe2\uff80\uff93related genes, and with an attenuated signaling response. Interestingly, the dahps1 mutants showed no detectable pleiotropic effects, suggesting a more selective recruitment of this gene in certain biological processes. This work provides robust evidence linking AAA metabolism to root hair development and successful symbiotic associations.Genomic prediction with special weight of major genes is a valuable tool to populate bio-digital resource centers.
AbstractPhenotypic information of crop genetic resources is a prerequisite for an informed selection that aims to broaden the genetic base of the elite breeding pools. We investigated the potential of genomic prediction based on historical screening data of plant responses against the Barley yellow mosaic viruses for populating the bio-digital resource center of barley. Our study includes dense marker data for 3838 accessions of winter barley, and historical screening data of 1751 accessions for Barley yellow mosaic virus (BaYMV) and of 1771 accessions for Barley mild mosaic virus (BaMMV). Linear mixed models were fitted by considering combinations for the effects of genotypes, years, and locations. The best linear unbiased estimations displayed a broad spectrum of plant responses against BaYMV and BaMMV. Prediction abilities, computed as correlations between predictions and observed phenotypes of accessions, were low for the marker-assisted selection approach amounting to 0.42. In contrast, prediction abilities of genomic best linear unbiased predictions were high, with values of 0.62 for BaYMV and 0.64 for BaMMV. Prediction abilities of genomic prediction were improved by up to\uffe2\uff80\uff89~\uffe2\uff80\uff895% using W-BLUP, in which more weight is given to markers with significant major effects found by association mapping. Our results outline the utility of historical screening data and W-BLUP model to predict the performance of the non-phenotyped individuals in genebank collections. The presented strategy can be considered as part of the different approaches used in genebank genomics to valorize genetic resources for their usage in disease resistance breeding and research.
", "keywords": ["Genetic Markers", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Genotype", "Chromosome Mapping", "Genetic Variation", "Hordeum", "Genomics", "Potyviridae", "Linkage Disequilibrium", "Plant Breeding", "03 medical and health sciences", "Phenotype", "Databases", " Genetic", "Original Article", "Genetic Association Studies", "Disease Resistance", "Plant Diseases"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00122-021-03815-0.pdf"}, {"href": "https://doi.org/10.1007/s00122-021-03815-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Theoretical%20and%20Applied%20Genetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00122-021-03815-0", "name": "item", "description": "10.1007/s00122-021-03815-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00122-021-03815-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-25T00:00:00Z"}}, {"id": "10.1038/s41467-023-42911-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:17:49Z", "type": "Journal Article", "created": "2023-11-07", "title": "Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus", "description": "AbstractLegume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we name SYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.To address the challenge of predicting tomato yields in the field, we used whole-plant functional phenotyping to evaluate water relations under well-irrigated and drought conditions. The genotypes tested are known to exhibit variability in their yields in wet and dry fields. The examined lines included two lines with recessive mutations that affect carotenoid biosynthesis, zetaz2083and tangerinet3406, both isogenic to the processing tomato variety M82. The two mutant lines were reciprocally grafted onto M82, and multiple physiological characteristics were measured continuously, before, during and after drought treatment in the greenhouse. A comparative analysis of greenhouse and field yields showed that the whole-canopy stomatal conductance (gsc) in the morning and cumulative transpiration (CT) were strongly correlated with field measurements of total yield (TY:r2= 0.9 and 0.77, respectively) and plant vegetative weight (PW:r2= 0.6 and 0.94, respectively). Furthermore, the minimum CT during drought and the rate of recovery when irrigation was resumed were both found to predict resilience.
", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "Dehydration", "Genotype", "Genetic Variation", "15. Life on land", "Genes", " Plant", "Adaptation", " Physiological", "6. Clean water", "Droughts", "03 medical and health sciences", "Phenotype", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Mutation", "Plant Physiological Phenomena", "Forecasting"]}, "links": [{"href": "https://doi.org/10.1101/2021.03.18.435447"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2021.03.18.435447", "name": "item", "description": "10.1101/2021.03.18.435447", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2021.03.18.435447"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-19T00:00:00Z"}}, {"id": "10.1101/2023.01.27.525841", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:36Z", "type": "Journal Article", "created": "2023-01-29", "title": "Natural variation in salt-induced root growth phases and their contribution to root architecture plasticity", "description": "AbstractDuring salt stress, the root system architecture of a plant is important for survival. Different accessions ofArabidopsis thalianahave adopted different strategies in remodeling their root architecture during salt stress. Salt induces a multiphase growth response in roots, consisting of a stop phase, quiescent phase, recovery phase and eventually a new level of homeostasis. We explored natural variation in the length of and growth rate during these phases in both main and lateral roots and find that some accessions lack the quiescent phase. Using mathematical models and correlation-based network, allowed us to correlate dynamic traits to overall root architecture and discover that both the main root growth rate during homeostasis and lateral root appearance are the strongest determinants of overall root architecture. In addition, this approach revealed a trade-off between investing in main or lateral root length during salt stress. By studying natural variation in high-resolution temporal root growth using mathematical modeling, we gained new insights in the interactions between dynamic root growth traits and we identified key traits that modulate overall root architecture during salt stress.
Summary statementBy studying natural variation in salt-induced root growth phases inArabidopsis, we show that main root growth rate during homeostasis and lateral root appearance contribute most to root architecture and we reveal a trade-off between investing in main and lateral root growth during salt stress.Due to their broad-spectrum activities, ivermectin and moxidectin are widely used anthelminthics in veterinary and human medicine. However, ivermectin has recently been shown to perturbate gut-microbial growth. Given the macrolide-like structure of both ivermectin and moxidectin, there is a need to characterize the antibiotic spectrum of these anthelminthic drugs and their potential implications in the development of cross-resistance to macrolides and other families of antibiotics. Here, we incubated 59 bacterial isolates representing different clades frequently found in the gut with ivermectin and moxidectin at different concentrations for 16-72h. Further, we challenged 10 bacterial isolates with repeated and gradually increasing concentrations of these two anthelminthics and subsequently characterized their sensitivity to different antibiotics as well as ascending anthelminthic concentrations. We found, that antibacterial activity of the two anthelminthics is comparable to a selection of tested antibiotics, as observed by potency and dose dependence. Bacterial anthelminthic challengingin vitroresulted in decreased anthelminthic sensitivity. Further, adaptation to anthelminthics is associated with decreased antibiotic sensitivity towards three macrolides, a lincosamide, a fluoroquinolone, a tetracycline and two carbapenems. The observed change in bacterial sensitivity profiles is associated with - and likely caused by - repeated anthelminthic exposure. Hence, current and future large-scale administration of ivermectin and moxidectin, respectively, for the control of helminths and malaria raises serious concerns - and hence potential off-target effects should be carefully monitored.During the last few decades, a plethora of sequencing studies provided insight into fungal community composition under various environmental conditions. Still, the mechanisms of species assembly and fungal spread in soil remain largely unknown. While mycelial growth patterns are studied extensively, the abundant formation of asexual spores is often overlooked, though representing a substantial part of the fungal life cycle relevant for survival and dispersal. Here, we explore asexual sporulation (spore abundance, size and shape) in 32 co\uffe2\uff80\uff90occurring soil fungal isolates under varying resource conditions, to answer the question whether resource limitation triggers or inhibits fungal investment into reproduction. We further hypothesized that trade\uffe2\uff80\uff90offs exist in fungal investment towards growth, spore production and size. The results revealed overall increased fungal investment into spore production under resource limitations; however, effect sizes and response types varied strongly among fungal isolates. Such isolate\uffe2\uff80\uff90specific effects were apparent in all measured traits, resulting in unique trait spaces of individual isolates. This comprehensive dataset also elucidated variability in sporulation strategies and trade\uffe2\uff80\uff90offs with fungal growth and reproduction under resource scarcity, as only predicted by theoretical models before. The observed isolate\uffe2\uff80\uff90specific strategies likely underpin mechanisms of co\uffe2\uff80\uff90existence in this diverse group of saprobic soil fungi.
", "keywords": ["0106 biological sciences", "570", "ymp\u00e4rist\u00f6tekij\u00e4t", "Reproduction", "Fungi", "1. No poverty", "500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie", "maaper\u00e4eli\u00f6st\u00f6", "Spores", " Fungal", "15. Life on land", "lis\u00e4\u00e4ntyminen", "01 natural sciences", "Soil", "fungal spread", "Phenotype", "fungal community composition", "Reproduction", " Asexual", "soil fungi", "suvuton lis\u00e4\u00e4ntyminen", "sienet", "iti\u00f6t", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.16012"}, {"href": "https://doi.org/10.1111/1462-2920.16012"}, {"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": "10.1111/1462-2920.16012", "name": "item", "description": "10.1111/1462-2920.16012", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.16012"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-04-27T00:00:00Z"}}, {"id": "10.1111/plb.12400", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:15Z", "type": "Journal Article", "created": "2015-09-25", "title": "Light Compensation Points In Shade-Grown Seedlings Of Deciduous Broadleaf Tree Species With Different Successional Traits Raised Under Elevated Co2", "description": "AbstractWe measured leaf photosynthetic traits in shade\uffe2\uff80\uff90grown seedlings of four tree species native to northern Japan, raised under an elevated CO2 condition, to investigate the effects of elevated CO2 on shade tolerance of deciduous broadleaf tree species with different successional traits. We considered Betula platyphylla var. japonica and Betula maximowicziana as pioneer species, Quercus mongolica var. crispula as a mid\uffe2\uff80\uff90successional species, and Acer mono as a climax species. The plants were grown under shade conditions (10% of full sunlight) in a CO2\uffe2\uff80\uff90regulated phytotron. Light compensation points (LCPs) decreased in all tree species when grown under elevated CO2 (720\uffc2\uffa0\uffce\uffbcmol\uffc2\uffb7mol\uffe2\uff88\uff921), which were accompanied by higher apparent quantum yields but no photosynthetic down\uffe2\uff80\uff90regulation. LCPs in Q.\uffc2\uffa0mongolica and A.\uffc2\uffa0mono grown under elevated CO2 were lower than those in the two pioneer birch species. The LCP in Q.\uffc2\uffa0mongolica seedlings was not different from that of A.\uffc2\uffa0mono in each CO2 treatment. However, lower dark respiration rates were observed in A.\uffc2\uffa0mono than in Q.\uffc2\uffa0mongolica, suggesting higher shade tolerance in A.\uffc2\uffa0mono as a climax species in relation to carbon loss at night. Thus, elevated CO2 may have enhanced shade tolerance by lowering LCPs in all species, but the ranking of shade tolerance related to successional traits did not change among species under elevated CO2, i.e. the highest shade tolerance was observed in the climax species (A.\uffc2\uffa0mono), followed by a gap\uffe2\uff80\uff90dependent species (Q.\uffc2\uffa0mongolica), while lower shade tolerance was observed in the pioneer species (B.\uffc2\uffa0platyphylla and B.\uffc2\uffa0maximowicziana).
", "keywords": ["0106 biological sciences", "CO2 enrichment", "photosynthesis", "Acclimatization", "Acer", "Carbon Dioxide", "15. Life on land", "650", "01 natural sciences", "Carbon", "Apparent quantum yield", "Trees", "shade tolerance", "Plant Leaves", "Quercus", "Phenotype", "Japan", "Seedlings", "Sunlight", "Photosynthesis", "dark respiration", "Betula"]}, "links": [{"href": "https://doi.org/10.1111/plb.12400"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/plb.12400", "name": "item", "description": "10.1111/plb.12400", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/plb.12400"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-10-11T00:00:00Z"}}, {"id": "10.1186/s40168-022-01405-w", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:30Z", "type": "Journal Article", "created": "2022-12-12", "title": "The global distribution and environmental drivers of the soil antibiotic resistome", "description": "Abstract BackgroundLittle is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth\uffe2\uff80\uff99s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs.
ResultsWe show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs.
ConclusionsTogether, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome.
", "keywords": ["Ecolog\u00eda (Biolog\u00eda)", "0301 basic medicine", "SDG-03: Good health and well-being", "550", "Antibiotic resistance", "Edafolog\u00eda (Biolog\u00eda)", "Antibiotic resistance genes (ARGs)", "910", "http://metadata.un.org/sdg/3", "631.4", "Microbial ecology", "2417.14 Gen\u00e9tica Vegetal", "Soil", "03 medical and health sciences", "XXXXXX - Unknown", "Global scale", "Humans", "Global change", "SCALE", "Ensure healthy lives and promote well-being for all at all ages", "2. Zero hunger", "0303 health sciences", "Ecology", "Research", "QR100-130", "Human health", "15. Life on land", "Gen\u00e9tica", "Anti-Bacterial Agents", "3. Good health", "Phenotype", "Mobile genetic elements", "13. Climate action", "BACTERIA", "2511.02 Biolog\u00eda de Suelos", "RESISTANCE GENES"]}, "links": [{"href": "https://doi.org/10.1186/s40168-022-01405-w"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-022-01405-w", "name": "item", "description": "10.1186/s40168-022-01405-w", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-022-01405-w"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-11T00:00:00Z"}}, {"id": "10.3389/fmicb.2020.562238", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:54Z", "type": "Journal Article", "created": "2020-09-22", "title": "The Free-Living Stage Growth Conditions of the Endophytic Fungus Serendipita indica May Regulate Its Potential as Plant Growth Promoting Microbe", "description": "Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica's phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2-20 g L-1 of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica's growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica's potential to promote plant growth: wheat growth promotion by the explorer phenotype was \u00b1 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.", "keywords": ["free-living stage", "symbiosis stage", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "fungal phenotype", "morphology", "physiology", "plant-growth-promoting-microbes", "15. Life on land", "Microbiology", "QR1-502"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2020.562238"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2020.562238", "name": "item", "description": "10.3389/fmicb.2020.562238", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2020.562238"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-22T00:00:00Z"}}, {"id": "10.25491/nvg8-j585", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:45Z", "type": "Dataset", "title": "GTEX-V955-0926-SM-4JBJ8", "description": "Sample ID: GTEX-V955-0926-SM-4JBJ8", "keywords": ["transcriptomics", "annotation", "phenotype", "gtex", "gene regulation"], "contacts": [{"organization": "Consortium, The GTEx", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.25491/nvg8-j585"}, {"rel": "self", "type": "application/geo+json", "title": "10.25491/nvg8-j585", "name": "item", "description": "10.25491/nvg8-j585", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.25491/nvg8-j585"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-01T00:00:00Z"}}, {"id": "10.25491/xydj-cr77", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:45Z", "type": "Dataset", "title": "GTEX-13OW7-1626-SM-5IJDH", "description": "Sample ID: GTEX-13OW7-1626-SM-5IJDH", "keywords": ["transcriptomics", "annotation", "phenotype", "gtex", "gene regulation"], "contacts": [{"organization": "Consortium, The GTEx", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.25491/xydj-cr77"}, {"rel": "self", "type": "application/geo+json", "title": "10.25491/xydj-cr77", "name": "item", "description": "10.25491/xydj-cr77", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.25491/xydj-cr77"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-01T00:00:00Z"}}, {"id": "10.3390/genes11091011", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:07Z", "type": "Journal Article", "created": "2020-08-27", "title": "Phenotyping in Arabidopsis and Crops\u2014Are We Addressing the Same Traits? A Case Study in Tomato", "description": "The convenient model Arabidopsis thaliana has allowed tremendous advances in plant genetics and physiology, in spite of only being a weed. It has also unveiled the main molecular networks governing, among others, abiotic stress responses. Through the use of the latest genomic tools, Arabidopsis research is nowadays being translated to agronomically interesting crop models such as tomato, but at a lagging pace. Knowledge transfer has been hindered by invariable differences in plant architecture and behaviour, as well as the divergent direct objectives of research in Arabidopsis vs. crops compromise transferability. In this sense, phenotype translation is still a very complex matter. Here, we point out the challenges of \uffe2\uff80\uff9ctranslational phenotyping\uffe2\uff80\uff9d in the case study of drought stress phenotyping in Arabidopsis and tomato. After briefly defining and describing drought stress and survival strategies, we compare drought stress protocols and phenotyping techniques most commonly used in the two species, and discuss their potential to gain insights, which are truly transferable between species. This review is intended to be a starting point for discussion about translational phenotyping approaches among plant scientists, and provides a useful compendium of methods and techniques used in modern phenotyping for this specific plant pair as a case study.
", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "9. Industry and infrastructure", "Arabidopsis", "Review", "15. Life on land", "6. Clean water", "Droughts", "03 medical and health sciences", "Phenotype", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Stress", " Physiological", "Arabidopsis; tomato; phenotyping; drought stress; translational phenotyping; osmotic stress; Dehydration; Arabidopsis thaliana; Solanum lycopersicum; Lycopersicon esculentum", "Plant Proteins"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/898415/2/genes-11-01011-v3.pdf"}, {"href": "https://iris.unito.it/bitstream/2318/1757296/1/genes-11-01011-v3.pdf"}, {"href": "https://www.mdpi.com/2073-4425/11/9/1011/pdf"}, {"href": "https://doi.org/10.3390/genes11091011"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes11091011", "name": "item", "description": "10.3390/genes11091011", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes11091011"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-27T00:00:00Z"}}, {"id": "10451/49641", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:24:59Z", "type": "Journal Article", "created": "2020-09-22", "title": "The Free-Living Stage Growth Conditions of the Endophytic Fungus Serendipita indica May Regulate Its Potential as Plant Growth Promoting Microbe", "description": "Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica's phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2-20 g L-1 of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica's growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica's potential to promote plant growth: wheat growth promotion by the explorer phenotype was \u00b1 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.", "keywords": ["free-living stage", "symbiosis stage", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "fungal phenotype", "morphology", "physiology", "plant-growth-promoting-microbes", "15. Life on land", "Microbiology", "QR1-502"]}, "links": [{"href": "https://repositorio.ulisboa.pt/bitstream/10451/49641/1/Dias%20et%20al%202020%20-The%20Free-Living%20Stage%20Growth%20Conditions%20of%20the%20Endophytic%20Fungus%20Serendipita%20indica.pdf"}, {"href": "https://doi.org/10451/49641"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10451/49641", "name": "item", "description": "10451/49641", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10451/49641"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-22T00:00:00Z"}}, {"id": "1959.7/uws:76535", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:36Z", "type": "Journal Article", "created": "2022-12-11", "title": "The global distribution and environmental drivers of the soil antibiotic resistome", "description": "Abstract BackgroundLittle is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth\uffe2\uff80\uff99s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs.
ResultsWe show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs.
ConclusionsTogether, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome.
", "keywords": ["Ecolog\u00eda (Biolog\u00eda)", "0301 basic medicine", "SDG-03: Good health and well-being", "550", "Antibiotic resistance", "Edafolog\u00eda (Biolog\u00eda)", "Antibiotic resistance genes (ARGs)", "910", "631.4", "Microbial ecology", "2417.14 Gen\u00e9tica Vegetal", "Soil", "03 medical and health sciences", "XXXXXX - Unknown", "Global scale", "Humans", "Global change", "SCALE", "2. Zero hunger", "0303 health sciences", "Ecology", "Research", "QR100-130", "Human health", "15. Life on land", "Gen\u00e9tica", "Anti-Bacterial Agents", "3. Good health", "Phenotype", "Mobile genetic elements", "13. Climate action", "BACTERIA", "2511.02 Biolog\u00eda de Suelos", "RESISTANCE GENES"]}, "links": [{"href": "https://doi.org/1959.7/uws:76535"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1959.7/uws:76535", "name": "item", "description": "1959.7/uws:76535", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1959.7/uws:76535"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-11T00:00:00Z"}}, {"id": "36912402", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:26:48Z", "type": "Journal Article", "created": "2023-01-29", "title": "Natural variation in salt-induced root growth phases and their contribution to root architecture plasticity", "description": "AbstractDuring salt stress, the root system architecture of a plant is important for survival. Different accessions ofArabidopsis thalianahave adopted different strategies in remodeling their root architecture during salt stress. Salt induces a multiphase growth response in roots, consisting of a stop phase, quiescent phase, recovery phase and eventually a new level of homeostasis. We explored natural variation in the length of and growth rate during these phases in both main and lateral roots and find that some accessions lack the quiescent phase. Using mathematical models and correlation-based network, allowed us to correlate dynamic traits to overall root architecture and discover that both the main root growth rate during homeostasis and lateral root appearance are the strongest determinants of overall root architecture. In addition, this approach revealed a trade-off between investing in main or lateral root length during salt stress. By studying natural variation in high-resolution temporal root growth using mathematical modeling, we gained new insights in the interactions between dynamic root growth traits and we identified key traits that modulate overall root architecture during salt stress.
Summary statementBy studying natural variation in salt-induced root growth phases inArabidopsis, we show that main root growth rate during homeostasis and lateral root appearance contribute most to root architecture and we reveal a trade-off between investing in main and lateral root growth during salt stress.Due to their broad-spectrum activities, ivermectin and moxidectin are widely used anthelminthics in veterinary and human medicine. However, ivermectin has recently been shown to perturbate gut-microbial growth. Given the macrolide-like structure of both ivermectin and moxidectin, there is a need to characterize the antibiotic spectrum of these anthelminthic drugs and their potential implications in the development of cross-resistance to macrolides and other families of antibiotics. Here, we incubated 59 bacterial isolates representing different clades frequently found in the gut with ivermectin and moxidectin at different concentrations for 16-72h. Further, we challenged 10 bacterial isolates with repeated and gradually increasing concentrations of these two anthelminthics and subsequently characterized their sensitivity to different antibiotics as well as ascending anthelminthic concentrations. We found, that antibacterial activity of the two anthelminthics is comparable to a selection of tested antibiotics, as observed by potency and dose dependence. Bacterial anthelminthic challengingin vitroresulted in decreased anthelminthic sensitivity. Further, adaptation to anthelminthics is associated with decreased antibiotic sensitivity towards three macrolides, a lincosamide, a fluoroquinolone, a tetracycline and two carbapenems. The observed change in bacterial sensitivity profiles is associated with - and likely caused by - repeated anthelminthic exposure. Hence, current and future large-scale administration of ivermectin and moxidectin, respectively, for the control of helminths and malaria raises serious concerns - and hence potential off-target effects should be carefully monitored.Legume roots can be symbiotically colonized by arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria. In Lotus japonicus, the latter occurs intracellularly by the cognate rhizobial partner Mesorhizobium loti or intercellularly with the Agrobacterium pusense strain IRBG74. Although these symbiotic programs show distinctive cellular and transcriptome signatures, some molecular components are shared. In this study, we demonstrate that 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase 1 (DAHPS1), the first enzyme in the biosynthetic pathway of aromatic amino acids (AAAs), plays a critical role in root hair development and for AM and rhizobial symbioses in Lotus. Two homozygous DAHPS1 mutants (dahps1-1 and dahps1-2) showed drastic alterations in root hair morphology, associated with alterations in cell wall dynamics and a progressive disruption of the actin cytoskeleton. The altered root hair structure was prevented by pharmacological and genetic complementation. dahps1-1 and dahps1-2 showed significant reductions in rhizobial infection (intracellular and intercellular) and nodule organogenesis and a delay in AM colonization. RNAseq analysis of dahps1-2 roots suggested that these phenotypes are associated with downregulation of several cell wall\uffe2\uff80\uff93related genes, and with an attenuated signaling response. Interestingly, the dahps1 mutants showed no detectable pleiotropic effects, suggesting a more selective recruitment of this gene in certain biological processes. This work provides robust evidence linking AAA metabolism to root hair development and successful symbiotic associations.Legume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we name SYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.