Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
", "keywords": ["0301 basic medicine", "570", "Microscopy", "Silicon", "0303 health sciences", "Temperature", "root-microbe interactions", "Equipment Design", "Biological Sciences", "Environment", "15. Life on land", "Plant Roots", "630", "Fluorescence", "Soil", "03 medical and health sciences", "Seedlings", "Calibration", "Rhizosphere", "Image Processing", " Computer-Assisted", "environmental imaging", "rhizosphere", "Soil Microbiology", "Bacillus subtilis", "Lactuca"]}, "links": [{"href": "https://eprints.whiterose.ac.uk/178939/18/e2109176118.full.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.2109176118"}, {"href": "https://doi.org/10.1073/pnas.2109176118"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.2109176118", "name": "item", "description": "10.1073/pnas.2109176118", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.2109176118"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-13T00:00:00Z"}}, {"id": "10.1046/j.1365-2745.1998.00278.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:00Z", "type": "Journal Article", "created": "2003-05-21", "title": "An Experimental Test Of Limits To Tree Establishment In Arctic Tundra", "description": "1 Five treeline species had low seed germination rates and low survivorship and growth of seedlings when transplanted into Alaskan tundra. Seed germination of all species increased with experimental warming, suggesting that the present treeline may in part result from unsuccessful recruitment under cold conditions.
2 Growth, biomass and survivorship of seedlings of treeline species transplanted into tundra were largely unaffected by experimental warming. However, transplanted seedlings of three species (Betula papyrifera, Picea glauca and Populus tremuloides) grew more when below\uffe2\uff80\uff90ground competition with the extant community was reduced. All three measures of transplant performance were greater in shrub tundra than in the less productive tussock or heath tundra. Establishment of trees in tundra may thus be prevented by low resource availability and competition.
3 Two species (Alnus crispa and Populus balsamifera) had low seed germination and survivorship of germinated seeds; transplants of these species did not respond to the manipulations and lost biomass following transplanting into tundra. Isolated populations of these two species north of the present treeline in arctic Alaska probably became established during mid\uffe2\uff80\uff90Holocene warming rather than in recent times.
4 Of all the species studied here, Picea glauca was the most likely to invade intact upland tundra. Its seeds had the highest germination rates and it was the only species whose seedlings survived subsequently. Furthermore, transplanted seedlings of Picea glauca had relatively high survivorship and positive growth in tundra, especially in treatments that increased air temperature or nutrient availability, two factors likely to increase with climate warming.
", "keywords": ["0106 biological sciences", "nutrient-availability", "air-temperature", "tundra", "-Alaska", "Betulaceae-: Dicotyledones-", "Arctic-tundra", "Coniferopsida-: Gymnospermae-", "natural-regeneration", "Environmental-Sciences)", "growth-", "01 natural sciences", "seedlings-", "Picea-glauca", "Betula-papyrifera", "tundra-", "soil-fertility", "Salicaceae-: Dicotyledones-", "Spermatophyta-", "treelines-", "Plantae-", "USA", "tree-establishment", "resource-availability", "Climatology- (Environmental-Sciences)", "Populus-balsamifera (Salicaceae-): seedling-", "Angiosperms-", "transplanting-", "Angiospermae-", "15. Life on land", "Plant-ecology:-communities", "Populus-balsamifera", "Betula-papyrifera (Betulaceae-): seedling-", "Populus-tremuloides", "climate-", "interspecific-competition", "germination", "Populus-tremuloides (Salicaceae-): seedling-", "Terrestrial-Ecology (Ecology-", "Picea-glauca (Coniferopsida-): seedling-", "Dicots-", "seed-germination", "Alnus-crispa", "plant-competition", "Alnus-crispa (Betulaceae-): seedling-", "survival-", "establishment-"]}, "links": [{"href": "https://doi.org/10.1046/j.1365-2745.1998.00278.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1046/j.1365-2745.1998.00278.x", "name": "item", "description": "10.1046/j.1365-2745.1998.00278.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1046/j.1365-2745.1998.00278.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1998-06-01T00:00:00Z"}}, {"id": "10.1093/treephys/22.7.435", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:31Z", "type": "Journal Article", "created": "2012-01-20", "title": "Responses Of Deciduous Broadleaf Trees To Defoliation In A Co2 Enriched Atmosphere", "description": "Relatively little is known about the implications of atmospheric CO2 enrichment for tree responses to biotic disturbances such as folivory. We examined the combined effects of elevated CO2 concentration ([CO2]) and defoliation on growth and physiology of sugar maple (Acer saccharum Marsh.) and trembling aspen (Populus tremuloides Michx.). Seedlings were planted in the ground in eight open-top chambers. Four chambers were ventilated with CO2-enriched air (ambient + 283 micromol mol-1) and four chambers were supplied with ambient air. After 6 weeks of growth, half of the leaf area was removed on a subset of seedlings of each species in each CO2 treatment. We monitored subsequent biomass gain and allocation, along with leaf gas exchange and chemistry. Defoliation did not significantly affect final seedling biomass in either species or CO2 treatment. Growth recovery following defoliation was associated with increased allocation to leaf mass in maple and a slight enhancement of mean photosynthesis in aspen. Elevated [CO2] did not significantly affect aspen growth, and the observed stimulation of maple growth was significant only in mid-season. Correspondingly, simulated responses of whole-tree photosynthesis to elevated [CO2] were constrained by a decrease in photosynthetic capacity in maple, and were partially offset by reductions in specific leaf area and biomass allocation to foliage in aspen. There was a significant interaction between [CO2] and defoliation on only a few of the measured traits. Thus, the data do not support the hypothesis that atmospheric CO2 enrichment will substantially alter tree responses to folivory. However, our findings do provide further indication that regeneration-stage growth rates of certain temperate tree species may respond only moderately to a near doubling of atmospheric [CO2].", "keywords": ["defoliation-", "0106 biological sciences", "Ecophysiology", "Quaking aspen", "biomass-allocation", "growth-response", "Growth", "Environmental-Sciences)", "01 natural sciences", "plant-composition", "Trees", "biomass-", "Spermatophyta-", "Biomass", "Photosynthesis", "plant-physiology", "defoliation", "Angiospermae-", "leaf-area", "GLOBAL-ECOLOGY", "seedling-growth", "source-sink-relations", "Populus-tremuloides", "gas-exchange", "Populus", "broadleaves-", "deciduous-tree", "forest-trees", "atmosphere-", "trees-", "biomass-production", "Acer saccharum", "Nitrogen", "Carbohydrates", "Acer", "carbon-dioxide-enrichment", "photosynthesis-", "growth-", "species-differences", "seedlings-", "wisconsin-", "Populus tremuloides", "photosynthesis", "Climatic changes", "Carbon Dioxide", "15. Life on land", "Plant Leaves", "leaves-", "Aceraceae-: Dicotyledones-", "Carbon dioxide", "Sugar maple", "Seedlings", "Terrestrial-Ecology (Ecology-", "Acer-saccharum"], "contacts": [{"organization": "Volin, John C., Kruger, Eric L., Lindroth, Richard L.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1093/treephys/22.7.435"}, {"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/22.7.435", "name": "item", "description": "10.1093/treephys/22.7.435", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/22.7.435"}, {"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": "10.1093/treephys/24.3.323", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:31Z", "type": "Journal Article", "created": "2012-01-20", "title": "Effects Of Elevated Carbon Dioxide Concentration On Growth And N-2 Fixation Of Young Robinia Pseudoacacia", "description": "Effects of elevated CO2 concentration ([CO2]) on carbon (C) and nitrogen (N) uptake and N source partitioning (N2 fixation versus mineral soil N uptake) of 1-year-old Robinia pseudoacacia were determined in a dual 13C and 15N continuous labeling experiment. Seedlings were grown for 16 weeks in ambient (350 ppm) or elevated [CO2] (700 ppm) with 15NH4 15NO3 as the only mineral nitrogen source. Elevated [CO2] increased the fraction of new C in total C, but it did not alter C partitioning among plant compartments. Elevated [CO2] also increased the fraction of new N in total N and this was coupled with a shift in N source partitioning toward N2 fixation. Soil N uptake was unaffected by elevated [CO2], whereas N2 fixation was markedly increased by the elevated [CO2] treatment, mainly because of increased specific fixation (mg N mg(-1) nodule). As a result of increased N2 fixation, the C/N ratio of tree biomass tended to decrease in the elevated [CO2] treatment. Partitioning of N uptake among plant compartments was unaffected by elevated [CO2]. Total dry mass of root nodules doubled in response to elevated [CO2], but this effect was not significant because of the great variability of root nodule formation. Our results show that, in the N2-fixing R. pseudoacacia, increased C uptake in response to increased [CO2] is matched by increased N2 fixation, indicating that enhanced growth in elevated [CO2] might not be restricted by N limitations.", "keywords": ["0106 biological sciences", "Seedlings", "Nitrogen Fixation", "Robinia", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "01 natural sciences", "Trees"], "contacts": [{"organization": "Feng, Zhe, Dyckmans, Jens, Flessa, Heiner,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1093/treephys/24.3.323"}, {"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/24.3.323", "name": "item", "description": "10.1093/treephys/24.3.323", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/24.3.323"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2004-03-01T00:00:00Z"}}, {"id": "10.1093/treephys/tpp079", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:32Z", "type": "Journal Article", "created": "2009-09-30", "title": "Low Moisture Availability Inhibits The Enhancing Effect Of Increased Soil Temperature On Net Photosynthesis Of White Birch (Betula Papyrifera) Seedlings Grown Under Ambient And Elevated Carbon Dioxide Concentrations", "description": "White birch (Betula papyrifera Marsh.) seedlings were grown under two carbon dioxide concentrations (ambient: 360 micromol mol(-1) and elevated: 720 micromol mol(-1)), three soil temperatures (5, 15 and 25 degrees C initially, increased to 7, 17 and 27 degrees C, respectively, 1 month later) and three moisture regimes (low: 30-40%; intermediate: 45-55% and high: 60-70% field water capacity) in greenhouses. In situ gas exchange and chlorophyll fluorescence were measured after 2 months of treatments. Net photosynthetic rate (A(n)) of seedlings grown under the intermediate and high moisture regimes increased from low to intermediate T(soil) and then decreased to high T(soil). There were no significant differences between the low and high T(soil), with the exception that A(n) was significantly higher under high than low T(soil) at the high moisture regime. No significant T(soil) effect on A(n) was observed at the low moisture regime. The intermediate T(soil) increased stomatal conductance (g(s)) only at intermediate and high but not at low moisture regime, whereas there were no significant differences between the low and high T(soil) treatments. Furthermore, the difference in g(s) between the intermediate and high T(soil) at high moisture regime was not statistically significant. The low moisture regime significantly reduced the internal to ambient CO2 concentration ratio at all T(soil). There were no significant individual or interactive effects of treatment on maximum carboxylation rate of Rubisco, light-saturated electron transport rate, triose phosphate utilization or potential photochemical efficiency of photosystem II. The results of this study suggest that soil moisture condition should be taken into account when predicting the responses of white birch to soil warming.", "keywords": ["0106 biological sciences", "0301 basic medicine", "Ribulose-Bisphosphate Carboxylase", "Temperature", "Water", "Carbon Dioxide", "15. Life on land", "01 natural sciences", "Soil", "03 medical and health sciences", "Seedlings", "Stress", " Physiological", "Photosynthesis", "Betula"], "contacts": [{"organization": "Qing-Lai Dang, Titus Fondo Ambebe,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1093/treephys/tpp079"}, {"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/tpp079", "name": "item", "description": "10.1093/treephys/tpp079", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/tpp079"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-09-28T00:00:00Z"}}, {"id": "10.1093/treephys/tpq080", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:32Z", "type": "Journal Article", "created": "2010-10-18", "title": "Green Spruce Aphid Infestations Cause Larger Growth Reductions To Sitka Spruce Under Shade", "description": "Light availability and infestation by the green spruce aphid (Elatobium abietinum) are key factors affecting the growth of Sitka spruce (Picea sitchensis) seedlings under a mature tree canopy, but their combined effect on seedling growth has not previously been quantified. A controlled outdoor experiment in which light levels (high light (HL): 100%, intermediate light (IL): 24%) and aphid infestation (absence/presence) were manipulated was conducted over 2 years to look at the effects on seedling growth and biomass distribution patterns. Aphid population assessments showed a significantly increased population density under IL, with three to four times higher cumulative aphid densities than that under HL. Defoliation rates of infested seedlings were directly related to aphid density. Total seedling biomass was strongly reduced in IL, and aphid infestation caused additional reductions in the biomass of particular components of the seedlings. Dry weight (DW) of older (\u22651-year-old) needles in infested trees was significantly decreased in both years. Total root DW at the end of the second year was significantly affected by aphid infestation, and the reduction (14-18%) was similar in IL and HL treatments despite large differences in aphid density. Biomass distribution patterns in infested trees were similar to that of uninfested trees within each light treatment, indicating that the relative decreases in root biomass were accompanied by similar reductions in distribution to the above-ground parts of the seedlings. Leader extension growth of infested seedlings was reduced by 15-17% compared with uninfested seedlings under IL, whereas only a 2-3% reduction in leader extension of infested seedlings under HL was observed. The results showed that the response of seedlings to E. abietinum were primarily dependent on the light environment. The significant reduction caused by aphids on the total DW of older needles and roots, and on leader extension growth, does suggest the potential for effects to accumulate over time.", "keywords": ["Population Density", "0106 biological sciences", "Time Factors", "Light", "15. Life on land", "Plant Roots", "01 natural sciences", "Host-Parasite Interactions", "Plant Leaves", "Seedlings", "13. Climate action", "Aphids", "Animals", "Biomass", "Picea", "Ecosystem"]}, "links": [{"href": "https://doi.org/10.1093/treephys/tpq080"}, {"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/tpq080", "name": "item", "description": "10.1093/treephys/tpq080", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/tpq080"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-10-12T00:00:00Z"}}, {"id": "10.1093/treephys/tps051", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:32Z", "type": "Journal Article", "created": "2012-06-14", "title": "Effects Of Predicted Future And Current Atmospheric Temperature And [Co2] And High And Low Soil Moisture On Gas Exchange And Growth Of Pinus Taeda Seedlings At Cool And Warm Sites In The Species Range", "description": "Predicted future changes in air temperature and atmospheric CO(2) concentration ([CO(2)]), coupled with altered precipitation, are expected to substantially affect tree growth. Effects on growth may vary considerably across a species range, as temperatures vary from sub-optimal to supra-optimal for growth. We performed an experiment simultaneously at two locations in the current range of loblolly pine, a cool site and a warm site, to examine the effect of future climate conditions on growth of loblolly pine seedlings in contrasting regions of the species range. At both sites 1-year-old loblolly pine seedlings were grown in current (local ambient temperature and [CO(2)]) and predicted future atmospheric conditions (ambient +2 \u00b0C temperature and 700 \u03bcmol mol(-1) [CO(2)]). Additionally, high and low soil moisture treatments were applied within each atmospheric treatment at each site by altering the amount of water provided to the seedlings. Averaged across water treatments, photosynthesis (A(net)) was 31% greater at the cool site and 34% greater at the warm site in elevated temperature and [CO(2)] compared with ambient temperature. Biomass accumulation was also stimulated by 38% at the cool site and by 24% at the warm site in that treatment. These results suggest that a temperature increase of 2 \u00b0C coupled with an increase in [CO(2)] (predicted future climate) will create conditions favorable for growth of this species. Reduced soil moisture decreased growth in both current and predicted atmospheric conditions. Biomass accumulation and A(net) were reduced by \u223c39 and 17%, respectively, in the low water treatment. These results suggest that any benefit of future atmospheric conditions may be negated if soil moisture is reduced by altered precipitation patterns.", "keywords": ["0106 biological sciences", "Analysis of Variance", "Atmosphere", "Temperature", "Humidity", "Pinus taeda", "Carbon Dioxide", "15. Life on land", "01 natural sciences", "6. Clean water", "Soil", "Species Specificity", "Seedlings", "13. Climate action", "Plant Stomata", "Biomass", "Seasons", "Photosynthesis"]}, "links": [{"href": "https://doi.org/10.1093/treephys/tps051"}, {"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/tps051", "name": "item", "description": "10.1093/treephys/tps051", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/tps051"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-06-12T00:00:00Z"}}, {"id": "10.1093/treephys/tps133", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:32Z", "type": "Journal Article", "created": "2013-02-01", "title": "Nitrogen Nutrition And Drought Hardening Exert Opposite Effects On The Stress Tolerance Of Pinus Pinea L. Seedlings", "description": "Functional attributes determine the survival and growth of planted seedlings in reforestation projects. Nitrogen (N) and water are important resources in the cultivation of forest species, which have a strong effect on plant functional traits. We analyzed the influence of N nutrition on drought acclimation of Pinus pinea L. seedlings. Specifically, we addressed if high N fertilization reduces drought and frost tolerance of seedlings and whether drought hardening reverses the effect of high N fertilization on stress tolerance. Seedlings were grown under two N fertilization regimes (6 and 100 mg N per plant) and subjected to three drought-hardening levels (well-watered, moderate and strong hardening). Water relations, gas exchange, frost damage, N concentration and growth at the end of the drought-hardening period, and survival and growth of seedlings under controlled xeric and mesic outplanting conditions were measured. Relative to low-N plants, high-N plants were larger, had higher stomatal conductance (27%), residual transpiration (11%) and new root growth capacity and closed stomata at higher water potential. However, high N fertilization also increased frost damage (24%) and decreased plasmalemma stability to dehydration (9%). Drought hardening reversed to a great extent the reduction in stress tolerance caused by high N fertilization as it decreased frost damage, stomatal conductance and residual transpiration by 21, 31 and 24%, respectively, and increased plasmalemma stability to dehydration (8%). Drought hardening increased tissue non-structural carbohydrates and N concentration, especially in high-fertilized plants. Frost damage was positively related to the stability of plasmalemma to dehydration (r\u2009=\u20090.92) and both traits were negatively related to the concentration of reducing soluble sugars. No differences existed between moderate and strong drought-hardening treatments. Neither N nutrition nor drought hardening had any clear effect on seedling performance under xeric outplanting conditions. However, fertilization increased growth under mesic conditions, whereas drought hardening decreased growth. We conclude that drought hardening and N fertilization applied under typical container nursery operational conditions exert opposite effects on the physiological stress tolerance of P. pinea seedlings. While drought hardening increases overall stress tolerance, N nutrition reduces it and yet has no effect on the drought acclimation capacity of seedlings.", "keywords": ["0106 biological sciences", "2. Zero hunger", "Nitrogen", "Acclimatization", "Water", "Plant Transpiration", "15. Life on land", "Pinus", "Plant Roots", "01 natural sciences", "6. Clean water", "Droughts", "Trees", "Cold Temperature", "Plant Leaves", "Seedlings", "Stress", " Physiological", "Plant Stomata", "Photosynthesis", "Fertilizers", "Plant Shoots"]}, "links": [{"href": "https://doi.org/10.1093/treephys/tps133"}, {"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/tps133", "name": "item", "description": "10.1093/treephys/tps133", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/tps133"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-01-30T00:00:00Z"}}, {"id": "10.1093/treephys/tpt019", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:32Z", "type": "Journal Article", "created": "2013-03-23", "title": "Synergistic, Additive And Antagonistic Impacts Of Drought And Herbivory On Pinus Sylvestris: Leaf, Tissue And Whole-Plant Responses And Recovery", "description": "Forests typically experience a mix of anthropogenic, natural and climate-induced stressors of different intensities, creating a mosaic of stressor combinations across the landscape. When multiple stressors co-occur, their combined impact on plant growth is often greater than expected based on single-factor studies (i.e., synergistic), potentially causing catastrophic dysfunction of physiological processes from an otherwise recoverable situation. Drought and herbivory are two stressors that commonly co-occur in forested ecosystems, and have the potential to 'overlap' in their impacts on various plant traits and processes. However, the combined impacts from these two stressors may not be predictable based on additive models from single-stressor studies. Moreover, the impacts and subsequent recovery may be strongly influenced by the relative intensities of each stressor. Here, we applied drought stress and simulated bark-feeding herbivory at three levels of intensity (control, moderate and severe) in a full factorial design on young Pinus sylvestris L. seedlings. We assessed if the combined effects from two stressors were additive (responses were equal to the sum of the single-factor effects), synergistic (greater than expected) or antagonistic (less than expected) on a suite of morphological and physiological traits at the leaf-, tissue- and whole-plant level. We additionally investigated whether recovery from herbivory was dependent on relief from drought. The two stressors had synergistic impacts on specific leaf area and water-use efficiency, additive effects on height and root-to-shoot ratios, but antagonistic effects on photosynthesis, conductance and, most notably, on root, shoot and whole-plant biomass. Nevertheless, the magnitude and direction of the combined impacts were often dependent on the relative intensities of each stressor, leading to many additive or synergistic responses from specific stressor combinations. Also, seedling recovery was far more dependent on the previous year's drought compared with the previous year's herbivory, demonstrating the influence of one stressor over another during recovery. Our study reveals for the first time, the importance of not only the presence or absence of drought and herbivory stressors, but also shows that their relative intensities are critical in determining the direction and magnitude of their impacts on establishing seedlings.", "keywords": ["0106 biological sciences", "Water", "Pinus sylvestris", "Plant Transpiration", "15. Life on land", "Plant Roots", "01 natural sciences", "6. Clean water", "Droughts", "Trees", "Plant Leaves", "Seedlings", "Stress", " Physiological", "Biomass", "Herbivory", "Photosynthesis", "Ecosystem", "Plant Shoots"]}, "links": [{"href": "https://doi.org/10.1093/treephys/tpt019"}, {"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/tpt019", "name": "item", "description": "10.1093/treephys/tpt019", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/tpt019"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-03-21T00:00:00Z"}}, {"id": "10.1099/mic.0.001477", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:35Z", "type": "Journal Article", "created": "2024-08-06", "title": "Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere", "description": "The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12\uffe2\uff80\uff9324\uffe2\uff80\uff89h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700\uffe2\uff80\uff931000\uffe2\uff80\uff89\uffc2\uffb5m from the tip. Bacteria accumulated predominantly in confined pore spaces within 200\uffe2\uff80\uff89\uffc2\uffb5m from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.We 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": "10.1371%2fjournal.pone.0028601", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:36Z", "type": "Journal Article", "created": "2011-12-14", "title": "Effects Of Increased Nitrogen Deposition And Precipitation On Seed And Seedling Production Of Potentilla Tanacetifolia In A Temperate Steppe Ecosystem", "description": "The responses of plant seeds and seedlings to changing atmospheric nitrogen (N) deposition and precipitation regimes determine plant population dynamics and community composition under global change.In a temperate steppe in northern China, seeds of P. tanacetifolia were collected from a field-based experiment with N addition and increased precipitation to measure changes in their traits (production, mass, germination). Seedlings germinated from those seeds were grown in a greenhouse to examine the effects of improved N and water availability in maternal and offspring environments on seedling growth. Maternal N-addition stimulated seed production, but it suppressed seed mass, germination rate and seedling biomass of P. tanacetifolia. Maternal N-addition also enhanced responses of seedlings to N and water addition in the offspring environment. Maternal increased-precipitation stimulated seed production, but it had no effect on seed mass and germination rate. Maternal increased-precipitation enhanced seedling growth when grown under similar conditions, whereas seedling responses to offspring N- and water-addition were suppressed by maternal increased-precipitation. Both offspring N-addition and increased-precipitation stimulated growth of seedlings germinated from seeds collected from the maternal control environment without either N or water addition. Our observations indicate that both maternal and offspring environments can influence seedling growth of P. tanacetifolia with consequent impacts on the future population dynamics of this species in the study area.The findings highlight the importance of the maternal effects on seed and seedling production as well as responses of offspring to changing environmental drivers in mechanistic understanding and projecting of plant population dynamics under global change.", "keywords": ["0106 biological sciences", "2. Zero hunger", "China", "Nitrogen", "Science", "Rain", "Q", "R", "Water", "Germination", "15. Life on land", "01 natural sciences", "Seedlings", "Potentilla", "Seeds", "Medicine", "Biomass", "Ecosystem", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371%2fjournal.pone.0028601"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371%2fjournal.pone.0028601", "name": "item", "description": "10.1371%2fjournal.pone.0028601", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371%2fjournal.pone.0028601"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-12-14T00:00:00Z"}}, {"id": "10.1371%2fjournal.pone.0030754", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:36Z", "type": "Journal Article", "created": "2012-02-08", "title": "Effects Of Soil Water And Nitrogen On Growth And Photosynthetic Response Of Manchurian Ash (Fraxinus Mandshurica) Seedlings In Northeastern China", "description": "Soil water and nitrogen (N) are considered to be the main environmental factors limiting plant growth and photosynthetic capacity. However, less is known about the interactive effects of soil water and N on tree growth and photosynthetic response in the temperate ecosystem.We applied N and water, alone and in combination, and investigated the combined effect of different water and N regimes on growth and photosynthetic responses of Fraxinus mandshurica seedlings. The seedlings were exposed to three water regimes including natural precipitation (CK), higher precipitation (HW) (CK +30%) and lower precipitation (LW) (CK -30%), and both with and without N addition for two growing seasons. We demonstrated that water and N supply led to a significant increase in the growth and biomass production of the seedlings. LW treatment significantly decreased biomass production and leaf N content, but they showed marked increases in N addition. N addition could enhance the photosynthetic capability under HW and CK conditions. Leaf chlorophyll content and the initial activity of Rubisco were dramatically increased by N addition regardless of soil water condition. The positive relationships were found between photosynthetic capacity, leaf N content, and SLA in response to water and N supply in the seedling. Rubisco expression was up-regulated by N addition with decreasing soil water content. Immunofluorescent staining showed that the labeling for Rubisco was relatively low in leaves of the seedlings under LW condition. The accumulation of Rubisco was increased in leaf tissues of LW by N addition.Our study has presented better understanding of the interactions between soil water and N on the growth and photosynthetic response in F. mandschurica seedlings, which may provide novel insights on the potential responses of the forest ecosystem to climate change associated with increasing N deposition.", "keywords": ["0106 biological sciences", "China", "Nitrogen", "Science", "Q", "R", "Water", "04 agricultural and veterinary sciences", "15. Life on land", "01 natural sciences", "Soil", "Fraxinus", "Seedlings", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Photosynthesis", "Ecosystem", "Research Article"], "contacts": [{"organization": "Ping Jiang, Zhanqing Hao, Guanhua Dai, Shuai Shi, Miao Wang, Fei Lin,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371%2fjournal.pone.0030754"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371%2fjournal.pone.0030754", "name": "item", "description": "10.1371%2fjournal.pone.0030754", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371%2fjournal.pone.0030754"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-02-08T00:00:00Z"}}, {"id": "10.1371/journal.pone.0028601", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:37Z", "type": "Journal Article", "created": "2011-12-14", "title": "Effects Of Increased Nitrogen Deposition And Precipitation On Seed And Seedling Production Of Potentilla Tanacetifolia In A Temperate Steppe Ecosystem", "description": "The responses of plant seeds and seedlings to changing atmospheric nitrogen (N) deposition and precipitation regimes determine plant population dynamics and community composition under global change.In a temperate steppe in northern China, seeds of P. tanacetifolia were collected from a field-based experiment with N addition and increased precipitation to measure changes in their traits (production, mass, germination). Seedlings germinated from those seeds were grown in a greenhouse to examine the effects of improved N and water availability in maternal and offspring environments on seedling growth. Maternal N-addition stimulated seed production, but it suppressed seed mass, germination rate and seedling biomass of P. tanacetifolia. Maternal N-addition also enhanced responses of seedlings to N and water addition in the offspring environment. Maternal increased-precipitation stimulated seed production, but it had no effect on seed mass and germination rate. Maternal increased-precipitation enhanced seedling growth when grown under similar conditions, whereas seedling responses to offspring N- and water-addition were suppressed by maternal increased-precipitation. Both offspring N-addition and increased-precipitation stimulated growth of seedlings germinated from seeds collected from the maternal control environment without either N or water addition. Our observations indicate that both maternal and offspring environments can influence seedling growth of P. tanacetifolia with consequent impacts on the future population dynamics of this species in the study area.The findings highlight the importance of the maternal effects on seed and seedling production as well as responses of offspring to changing environmental drivers in mechanistic understanding and projecting of plant population dynamics under global change.", "keywords": ["0106 biological sciences", "2. Zero hunger", "China", "Nitrogen", "Science", "Rain", "Q", "R", "Water", "Germination", "15. Life on land", "01 natural sciences", "Seedlings", "Potentilla", "Seeds", "Medicine", "Biomass", "Ecosystem", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0028601"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0028601", "name": "item", "description": "10.1371/journal.pone.0028601", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0028601"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-12-14T00:00:00Z"}}, {"id": "10.1371/journal.pone.0029642", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:37Z", "type": "Journal Article", "created": "2012-01-04", "title": "Carbon Stocks And Fluxes In Tropical Lowland Dipterocarp Rainforests In Sabah, Malaysian Borneo", "description": "Deforestation in the tropics is an important source of carbon C release to the atmosphere. To provide a sound scientific base for efforts taken to reduce emissions from deforestation and degradation (REDD+) good estimates of C stocks and fluxes are important. We present components of the C balance for selectively logged lowland tropical dipterocarp rainforest in the Malua Forest Reserve of Sabah, Malaysian Borneo. Total organic C in this area was 167.9 Mg C ha\u207b\u00b9\u00b13.8 (SD), including: Total aboveground (TAGC: 55%; 91.9 Mg C ha\u207b\u00b9\u00b12.9 SEM) and belowground carbon in trees (TBGC: 10%; 16.5 Mg C ha\u207b\u00b9\u00b10.5 SEM), deadwood (8%; 13.2 Mg C ha\u207b\u00b9\u00b13.5 SEM) and soil organic matter (SOM: 24%; 39.6 Mg C ha\u207b\u00b9\u00b10.9 SEM), understory vegetation (3%; 5.1 Mg C ha\u207b\u00b9\u00b11.7 SEM), standing litter (<1%; 0.7 Mg C ha\u207b\u00b9\u00b10.1 SEM) and fine root biomass (<1%; 0.9 Mg C ha\u207b\u00b9\u00b10.1 SEM). Fluxes included litterfall, a proxy for leaf net primary productivity (4.9 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b10.1 SEM), and soil respiration, a measure for heterotrophic ecosystem respiration (28.6 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b11.2 SEM). The missing estimates necessary to close the C balance are wood net primary productivity and autotrophic respiration.Twenty-two years after logging TAGC stocks were 28% lower compared to unlogged forest (128 Mg C ha\u207b\u00b9\u00b113.4 SEM); a combined weighted average mean reduction due to selective logging of -57.8 Mg C ha\u207b\u00b9 (with 95% CI -75.5 to -40.2). Based on the findings we conclude that selective logging decreased the dipterocarp stock by 55-66%. Silvicultural treatments may have the potential to accelerate the recovery of dipterocarp C stocks to pre-logging levels.", "keywords": ["0106 biological sciences", "1000 Multidisciplinary", "Tropical Climate", "Science", "Rain", "Q", "R", "1100 General Agricultural and Biological Sciences", "Biodiversity", "15. Life on land", "01 natural sciences", "Carbon", "Dipterocarpaceae", "Trees", "10127 Institute of Evolutionary Biology and Environmental Studies", "Soil", "1300 General Biochemistry", " Genetics and Molecular Biology", "Borneo", "Seedlings", "13. Climate action", "570 Life sciences; biology", "590 Animals (Zoology)", "Medicine", "Biomass", "Research Article"], "contacts": [{"organization": "Saner, Philippe, Loh, Yen Yee, Ong, Robert C., Hector, Andy,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0029642"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0029642", "name": "item", "description": "10.1371/journal.pone.0029642", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0029642"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-01-03T00:00:00Z"}}, {"id": "10.3732/ajb.1300163", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:27Z", "type": "Journal Article", "created": "2013-11-19", "title": "Soil Nitrogen, And Not Phosphorus, Promotes Cluster-Root Formation In A South American Proteaceae, Embothrium Coccineum", "description": "\uffe2\uff80\uffa2 Premise of the study: Cluster roots are a characteristic root adaptation of Proteaceae species. In South African and Australian species, cluster roots promote phosphorus (P) acquisition from poor soils. In a South American Proteaceae species, where cluster roots have been scarcely studied and their function is unknown, we tested whether cluster\uffe2\uff80\uff90root formation is stimulated by low soil nutrition, in particular low P\uffe2\uff80\uff90availability.
\uffe2\uff80\uffa2 Methods: Small and large seedlings (< 6\uffe2\uff80\uff90 and > 6\uffe2\uff80\uff90months old, respectively) of Embothrium coccineum and soil were collected across four different sites in Patagonia (Chile). We determined cluster\uffe2\uff80\uff90root number and relative mass, and leaf Pi concentration per mass (Pimass) and per area (Piarea) for each seedling, and tested relationships with Olsen\uffe2\uff80\uff93P (OP), sorbed\uffe2\uff80\uff93P (sP) and total nitrogen (N) using generalized linear mixed\uffe2\uff80\uff90effects models and model selection to assess the relative strength of soil and plant drivers.
\uffe2\uff80\uffa2 Key results: Best\uffe2\uff80\uff90fit models showed a negative logarithmic relationship between cluster\uffe2\uff80\uff90root number and soil nitrogen (N), and between cluster\uffe2\uff80\uff90root relative mass and both leaf Piarea and soil N, and a positive logarithmic relationship between cluster\uffe2\uff80\uff90root number and leaf Piarea. Cluster\uffe2\uff80\uff90root relative mass was higher in small than in large seedlings.
\uffe2\uff80\uffa2 Conclusions: Contrary to that found in South African and Australian Proteaceae, cluster roots of E. coccineum do not appear to be driven by soil P, but rather by soil N and leaf Piarea. We suggest that cluster roots are a constitutive and functional trait that allows plants to prevail in poor N soils.
", "keywords": ["Plant Leaves", "0106 biological sciences", "2. Zero hunger", "Soil", "Nitrogen", "Seedlings", "Phosphorus", "Chile", "15. Life on land", "Adaptation", " Physiological", "Plant Roots", "01 natural sciences", "Proteaceae"]}, "links": [{"href": "https://doi.org/10.3732/ajb.1300163"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/American%20Journal%20of%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3732/ajb.1300163", "name": "item", "description": "10.3732/ajb.1300163", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3732/ajb.1300163"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-12-01T00:00:00Z"}}, {"id": "10.5061/dryad.6q573n5wf", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:40Z", "type": "Dataset", "title": "Identifying functional impacts of heat-resistant fungi on boreal forest recovery after wildfire", "description": "Open AccessFungi were isolated into pure culture from heat-treated soils that had burned the previous year. These were inoculated on to litter of paper birch and black spruce to assess decomposition (mass lost) under controlled conditions. Fungi were also inoculated on to roots of seedlings of paper birch, black spruce, and jack pine to assess impacts on biomass (grams after dried). Sanger sequences of cultured fungi were matched with that of sequences from high throughput amplicon sequencing (MiSeq Illumina) at 47 plots. In situ decomposition (mass lost) of black spruce and paper birch litter was assessed after 12 and 24 months from 5 litterbags 30 plots in the field 2-4 years after fire. Seedlings were counted in 3, 1 by 1 m quadrats per plot one year after fire at 47 plots.", "keywords": ["Northwest Territories", "Seedlings", "Earth and Environmental Sciences", "Extremophile", "Taiga plains", "15. Life on land", "Mycorrhiza", "Boreal", "extremophile"], "contacts": [{"organization": "Day, Nicola, Cumming, Steve, Dunfield, Kari, Johnstone, Jill, Mack, Michelle, Reid, Kirsten, Turetsky, Merritt, Walker, Xanthe, Baltzer, Jennifer L.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.6q573n5wf"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.6q573n5wf", "name": "item", "description": "10.5061/dryad.6q573n5wf", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.6q573n5wf"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-12T00:00:00Z"}}, {"id": "10.5061/dryad.926nd", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:41Z", "type": "Dataset", "title": "Data from: Do plant traits explain tree seedling survival in bogs?", "description": "unspecifiedSeedlingtraitdataexperiment2Experiment 2 Morphological traits were assessed independently of Experiment 1. We grew tree seedlings under optimal conditions by planting pre-grown 4 weeks old tree seedlings ( see plant material) into the center of a (10 cm wide) pot, using a density of one seedling per pot. The pots were filled with sterilized organic soil, watered daily and kept under the same glasshouse light and humidity conditions as Experiment 1. Pots were arranged in five replicated blocks. Both the blocks and the pots within a block were randomly moved once a week. For more information on columnheadings see Table 1 in the associated MSMotherfile.xlsTraitsandsurvivalTraits assessed in Experiment 2 were used to relate to seedling survival in Experiment 1. This file contains trait data from experiment 2 and seedling survival of seven conifer species in experiment 1 kept under contrasting moisture conditions (Dry, Wet)traitsandsurvival.xlsxTraitplasticityseedlingsmosssoilTo assess the plasticity of the morphological traits, we compared the morphological traits based on seedlings from Experiment 2 (grown on soil) with values measured on seedlings in Experiment 1 under contrasting moisture conditionsTraitflexibilitymosssoil.xlsxgerminationTo assess germination, we introduced seeds to Experiment 1 in the third week, corresponding to the time when pot water contents had stabilized. Three seeds were placed around the seedling of the same species, on the capitulum of a moss individual, using 3 x 140 = 420 seeds in total. Germination was checked twice a week until harvest, 5 weeks later. We considered a seed germinated when the integument had broken and a \u2018shoot\u2019 of at least 1 mm had emerged from the seed.Mossgrowth and seedling performanceThe file contains growth and survival of seedlings grown on moss in experiment 1 as well as the moss growth itselfRelatie tussen mosgroei en seedling performance.xlsx", "keywords": ["2. Zero hunger", "(Pinus sylvestris L.", "tree encroachment", "Holocene", "mires", "Picea sitchensis (Bong.) Carri\u00e8re", "15. Life on land", "Pinus sylvestris L.", "Picea rubens Sarg.", "Picea glauca (Moench) Voss", "Bogs", "Pinus banksiana Lamb", "Seedlings", "Picea glauca (Moench) Voss)", "Picea mariana (Mill.) Britton", "Picea mariana (Mill.) Britton Sterns & Poggenb.", "Sterns & Poggenb.", "peatlands", "Pinus nigra Arnold"], "contacts": [{"organization": "Limpens, Juul, van Egmond, Emily, Li, Bingxi, Holmgren, Milena,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.926nd"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.926nd", "name": "item", "description": "10.5061/dryad.926nd", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.926nd"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-06-24T00:00:00Z"}}, {"id": "10.5061/dryad.h1123/1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:44Z", "type": "Dataset", "title": "Stable isotope abundance and nitrogen concentration data of adult orchids, orchid seedlings and autotrophic references.", "description": "Single and mean \u03b415N, \u03b413C, \u03b42H values, enrichment factors \u03b515N, \u03b513C, \u03b52H and total nitrogen concentration data of adult green leaves of 7 Orchidaceae species, fully mycoheterotrophic protocorms of 5 Orchidaceae species and 15 autotrophic reference plant species (n = 105).", "keywords": ["NE Bavaria", "Epipactis palustris", "Orchis militaris", "carbon (C)", "orchid seedlings", "hydrogen (H)", "stable isotopes", "orchid mycorrhiza", "Dactylorhiza majalis", "Ophrys insectifera", "mycoheterotrophy", "Platanthera bifolia", "Gymnadenia conopsea", "Neottia ovata", "Germany", "rhizoctonia", "fungi"], "contacts": [{"organization": "Schweiger, Julienne Marie-Isabelle, Bidartondo, Martin I., Gebauer, Gerhard,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.h1123/1"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.h1123/1", "name": "item", "description": "10.5061/dryad.h1123/1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.h1123/1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-01-01T00:00:00Z"}}, {"id": "10.5061/dryad.z08kprrnc", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:49Z", "type": "Dataset", "created": "2024-04-19", "title": "Data from: Water level drawdown induces a legacy effect on the seed bank and retains sediment chemistry in a eutrophic clay wetland", "description": "Open Access2.1 Study site The study was conducted in Oostvaardersplassen in the Netherlands (coordinates: 52.456857, 5.355935). This eutrophic clay wetland of about 5600 ha consists of a 3600 ha marsh and a 2000 ha dryer border zone. This study took place in the marsh part. The marsh is characterized by large water bodies, reed vegetation and willow forests. Oostvaardersplassen is part of the polder Zuidelijk Flevoland, which is located in the former Zuiderzee estuary, a marine habitat (see van Leeuwen et al., 2021 for a detailed description). For water safety reasons the decision was made to separate the inland Zuiderzee from the North Sea through the construction of a dike, named the Afsluitdijk. After completion of the construction and within five years, the Zuiderzee transformed into a freshwater lake, IJsselmeer. In this freshwater lake, several polders were established to create land for agriculture; Zuidelijk Flevoland was reclaimed in 1968. Since Oostvaardersplassen is located in, what was then, the lowest part of the polder, it remained wet during the first years after reclamation and no actions were taken to develop this area into the industrial site as it was planned to be (Cornelissen et al., 2014). The marine clay soil and its associated high nutrient concentrations (eutrophic) in combination with the unmanaged and wet conditions, led nature to develop quickly. This made the area into an important breeding and resting area for many wetland birds and therefore became a protected wetland nature reserve in 1974. In 1989 it became a protected area within the European Bird directive and under the Ramsar agreement. Additionally, it was qualified as a Natura 2000 area in 2009. Later on, the relatively high water levels at the end of winter, due to the height of the weir, in combination with high grazing pressure by moulting greylag geese (Anser anser) from May to July, resulted in the loss of reed cover (Phragmites australis) (Vulink and Van Eerden, 1998). This in turn resulted in decreasing bird numbers due to lower food and habitat availability (Beemster et al., 2010). To restore reed-dominated wetlands and to increase food and habitat availability for birds, a complete multi-year water level drawdown was induced in the western part of the marsh from 1987 till 1991\u00a0(Vulink and Van Eerden, 1998). The eastern part was hydrologically separated from the western part by a low dike\u00a0and water levels and dynamics remained unchanged in this area. The implemented water level drawdown resulted in the development of c. 600 ha of reed-dominated vegetation in the western part, after which typical wetland birds, e.g., bearded reedling (Paranrus biarmicus), marsh harrier (Circus aeruginosus) and Eurasian bittern (Botaurus stellaris), increased in numbers (Beemster et al., 2012; Vulink and Van Eerden, 1998). The study area experiences seasonal variation in water level, but lacks long-term dynamics in water level that would be caused by extreme climatological periods. As the marsh is rainwater fed, natural water level dynamics occur with a high water level at the end of winter (March) and low levels at the end of summer (September;). The surplus of water in winter leaves the marsh via a weir. The average difference in water level between summer and winter is approximately 30 cm. During \u2018dry\u2019 summers the water level can drop 50 cm at the end of the growing season. Due to both the climate conditions in combination with the height of the weir, set as to pertain high water levels in the reed beds during late winter and spring, these naturally occurring \u2018dry\u2019 summers did not result in enough mudflat exposure throughout the area to allow extensive marsh recovery. At the time of sampling, both the water level drawdown and the non-water level drawdown area were characterized by a sharp border between vegetation and open water. The vegetation on the shores was similar in both areas and dominated by Phragmites australis, Salix spp. and, to a lesser extent, Convolvulus spp.. At drier sites, with greater proximity to the lake, Urtica dioica and Carduus spp. were present in higher abundances.\u00a0The shores of the lake, that sometimes fall dry during dry summers, are colonized quickly by species among which Tephroseris palustris (also known as Senecio congestus), Epilobium hirsutum and Ranunculus sceleratus. 2.2 Experimental design We examined the legacy effects of a water level drawdown, a water level gradient and water level fluctuations on seed bank germination and nutrient availability using field sampling and mesocosm experiment. The unique field situation consisting of areas with and without a water level drawdown history allows to explore legacy effects on seed bank properties (Part 1.1) and nutrient availability (Part 2.1). This approach focusses on the long-term effects of inducing a four-year water level drawdown, in this case 30 years after the event, by sampling 20 locations in each subarea that have been inundated since the last water level drawdown. In addition, soil samples have been taken in these two hydrologically distinct areas, along a water level gradient that is dictated by elevational differences of about 20 cm. With this approach, we used the elevational gradient to distinguish between higher locations, that would fall dry more often due to for example dry summers, and lower locations. The latter had not fallen dry for 30 years in case of the water level drawdown area and 50 years in case of the non\u2013water level drawdown area. By taking soil samples on 7 (germination) or 5 (nutrient) locations along this water level gradient, we were able to research how changes in water level alter seed bank properties (Part 2.1) and nutrient availability (Part 2.2) on a smaller seasonal time scale. In addition to the above two sampling campaigns, a mesocosm experiment was conducted to study the effects of water level on germination (Part 3.1) and nutrient availability (Part 3.2) . With this approach it was possible to determine effects of a specified water level (inundated, saturated, dry) on an even smaller time scale of weeks/months and how such a response might be influenced by events in the past, in this case drawdown history.\u00a0 2.2.1 Part 1: Water level drawdown history To investigate the legacy effects of a previously induced water level drawdown on the seed bank (part 1.1) and on nutrient availability (part 1.2), we compared seed bank properties (density, diversity, species composition) and sediment nutrient concentrations between an area with water level drawdown history and an area without. For the method on sediment nutrient concentrations we would like to refer to the section on water level gradient (2.2.2) for field sampling and lab protocols. 2.2.1.1 Seed bank properties (part 1.1) We collected sediment samples from both areas in Oostvaardersplassen in June 2021, when both areas were still inundated. To cover the spatial heterogeneity of the area, 40 locations were sampled. 20 Sample points were located in the area that was continuously inundated for 50 years (non-water level drawdown history, n = 20) and 20 in the area that had undergone a water level drawdown from 1987 till 1991 and was subsequently inundated for 30 years (water level drawdown history, n = 20). In June 2021, we took ten sediment cores of 23.8 cm2 (diameter = 5.5 cm) to a depth of 10 cm and pooled the 0-5 cm and 5-10 cm depth in separate plastic bags at each location (Verhofstad et al., 2017). The bags were stored in the dark at 4\u00b0C for approximately one month to allow seed stratification, after which the sediment was sieved (mesh width: 150 \u00b5m) and the residue, containing the seeds, was spread across a tray (37\u00d727 cm) containing sediment for propagation and germination (Lensli substrates; pH = ~5.3; electrical conductivity = ~0.5mS/cm). The trays were placed in a greenhouse with supplementary light from 6:00-22:00h so that light conditions on plant level corresponded with 250 \u03bcmol.m2/s. The temperature in the greenhouse was on average 21\u00b0C between 6:00-22:00 and 16\u00b0C between 22:00-6:00. The relative humidity (Rh) in the greenhouse was on average 60% (-5/+5%). To ensure optimal sediment moisture, the trays were watered at least once a week with rainwater. The germinating plants were then identified to species level and removed afterwards. This was done to minimize possible competition effects between seedlings. Unidentified plants were transferred from the trays to individual pots, providing the space for them to grow and/or flower until their identification could be determined. When germination stopped, the sediment was mixed to allow seeds deeper in the sediment to germinate. The trays were kept in the greenhouse until germination stopped again, which lasted up to 5 months. 2.2.2 Part 2: Water level gradient To determine how a water level gradient, induced through a gradient in soil elevation of around 20 cm, affects seed bank properties (density, diversity, species composition; Part 2.1) and nutrient availability (part 2.2), we collected sediment samples in the field. Sample collection occurred at seven locations (seed bank) and five locations (nutrient availability) along four transects perpendicular to the border of the reed vegetation. The indicated direction was chosen to cover differences in soil elevation, with locations on a relatively higher elevation falling dry more often due to small fluctuations in the water level and locations on a lower elevation falling dry less often. 2.2.2.1 Seed bank properties (part 2.1) To assess how a water level gradient alters seed bank properties, we collected sediment samples in June 2021 along four transects, each consisting of seven sampling points (n = 28). The sampling points cover a gradient of soil elevation, where the locations indicated by a 1 are located at the highest elevation, and thus fall dry the most, while locations indicated by a higher number (2-7) are decreasing in soil elevation and thus fall dry less often or never. Each transect covered around 777.5 \u00b1 418.7 meter. Two transects were located in the area without water level drawdown history and two in the area with water level drawdown history. The sampling and germination protocol was identical to the one described in section 2.2.1. 2.2.2.2 Nutrient availability (part 2.2) To examine how a water level gradient affect nutrient availability, sediment samples were collected along four transects (different from the transects in 2.2.2.1) in November 2021. Each transect consists of five sampling points that were sampled in duplicate (n = 40). The sampling points cover a gradient of soil elevation, where the locations indicated by a 1 are located at the highest elevation, and thus fall dry the most, while locations indicated by a higher number (2-5) are decreasing in soil elevation and thus fall dry less often or never. Each transect covered around 237.5 \u00b1 17.9 meter. Two transects were situated in the area without water level drawdown history and two in the area with water level drawdown history. At each sampling location, four sediment cores of 23.8 cm2 (diameter = 5.5 cm) to a depth of 0-10 cm and 20-30 cm were collected for pore-water extraction and one sediment core of 23.8 cm2 (diameter = 5.5 cm) to a depth of 0-10 and 20-30 cm was collected for sediment nutrient analyses. Soil elevation measurements were conducted with a dGPS (Topcon, HiPer SR). At each location, we took three measurements which were averaged. Pore-water extraction was initiated in the lab on the same day as sediment collection and collected the next morning. Pore-water samples were extracted using vacuum syringes attached to rhizons (Rhizon SMS; Rhizosphere Research Products; Eijkelkamp Agrisearch Equipment, Giesbeek, The Netherlands). The pore-water was analyzed for pH, alkalinity (Metrohm, 877 Titrino plus), total inorganic carbon (TIC; infrared carbon Analyser, IRGA; ABB Analytical, Frankfurt, Germany) and nutrient concentrations. Sediment samples were analyzed on water content, bulk density loss of ignition (LOI; proxy for organic matter content) and bioavailable phosphorus and NH4+ and NO3-. The elaborated method can be found in the supplementary material S1. Nitrite (NO2-) concentrations were barely detectable and therefore left out of the analysis. 2.2.3 Part 3: Water level fluctuations Experimental setup To unravel how water level influences germination (part 3.1) and nutrient availability (part 3.2), we performed a mesocosm experiment with different water levels on intact sediment cores from sites with and without water level drawdown history from Oostvaardersplassen. The different water levels reflect the different stages the system goes through during the first phase (drying) of a water level drawdown cycle: (1) Dry, the water level was 20 cm below sediment surface level (\u2018dry\u2019 for brevity), (2) saturated, the water level was equal to the sediment surface level (\u2018saturated\u2019 for brevity), and (3) wet, the water level was eight cm above sediment surface level (\u2018wet\u2019 for brevity). The experiment ran for eight consecutive weeks in which each core experienced one of the water level treatments (inundated, saturated or dry) following Vonk et al. (2017). In November 2020, intact sediment cores were collected from Oostvaardersplassen at ten locations that were inundated. Half of these locations were situated in an area with a water level drawdown history (n = 5, water level = 13.8 +/- 3.9 cm), while the other half were situated in a continuously inundated area (n = 5, water level = 17 +/- 5.4 cm). At each location, four sediment cores with a diameter of 16 cm and a depth of 40 cm were collected by pressing a PVC-tube in the sediment and sealing it with a cap on the bottom. Three of the intact cores for each location were placed in a climate room for an acclimation period of six days, after which the experiment started. The cores were placed in the climate room with a temperature regime of 20\u00b0C from 6:00-22:00 and 15\u00b0C from 22:00-6:00. The average humidity in the climate chamber was 45% and the average light conditions at sediment level were 554 \u03bcmol.m2/s (LI-COR LI-250 photometer) with 16 hours light and 8 hours dark. The cores were placed using a randomized block design (n = 5), each block consisted of six sediment cores. The treatments were applied by drilling holes in the PVC-tube at the corresponding water level treatment height (-20 cm, 0 cm, +8 cm relative to the sediment height). To regulate the water level in the core, we placed the PVC-tube in a larger water-proof PVC-core (diameter = 20 cm, length = 50 cm). Water collected from the Oostvaardersplassen was used to initiate the treatments. During the experiment, water was replenished till treatment level with rainwater (pH = 5.18, alkalinity = 0.33 mEQ/L). The fourth core was used to determine sediment nutrient starting conditions by taking two sediment samples of 40 cm deep (23.8 cm2) after which it was split in two sections of 10 cm (0-10, 20-30). The two sediment samples from the sediment core were pooled per location and per depth and stored in the freezer at -20\u00b0C until further analyses. The same analysis protocol was used as in approach 2 (section 2.2.2.2). 2.2.3.1 Seed bank properties(part 3.1) Through the use of intact soil cores in an experimental setup, we could identify possible environmental filters that would exert selection on the type of plants that were able to germinate during different phases of a water level drawdown cycle. During the 8-week experiment, the mesocosms were checked weekly for plant germination. Germinated plants were counted and identified to species level if possible. Plants were not removed during the experiment. 2.2.3.2 Nutrient availability (part 3.2) The experimental setup allowed us to assess how a certain water level regime impacts nutrient availability in the system, in this case, we selected three water levels to mimic different phases of the water level drawdown cycle. By monitoring these changes it would be possible to identify possible nutrient depletion in the system upon repeated water level drawdown implementation. Nutrient concentrations were determined in both the pore-water and the sediment. To collect pore-water samples during the experiment, rhizons (Rhizon SMS; Rhizosphere Research Products; Eijkelkamp Agrisearch Equipment, Giesbeek, The Netherlands) were installed in the sediment core at a depth of 10 cm and a vacuum syringe could be attached to extract pore-water. This was done at the start of the experiment (day 0), and repeated five times on day 7, 14, 21, 35 and 56. Pore-water samples were analyzed in the same way as in approach 2. At the end of the experiment, sediment samples were taken from the sediment cores at two different depths (0-10 cm and 20-30 cm) following the same sampling strategy as at the start of the experiment. These samples were stored in the freezer at -20\u00b0C until further analyses, following the analysis protocol as described in approach 2 (section 2.2.2.2). 2.3 Statistical analyses Data were analyzed in RStudio version 4.0.3 (R Core Team, 2023). For all hypotheses testing procedures the significance level was set at \u03b1 = 0.05. All data are shown with their average \u00b1 standard deviation (sd). Part 1: Water level drawdown history Part 1.1 Seed bank properties To determine the effect of water level drawdown history (Yes or No) on mean Shannon-Wiener diversity, mean species richness, and mean germination densities (log transformed), we used mixed linear models from the GlmmTMB package (Mollie et al., 2017), using location ID as a random effect. Differences in the total sum of germinated individuals between the water level drawdown and non-water level drawdown area were tested using a Chi-Square test. Shannon-Wiener diversity was calculated using the \u2018vegan package\u2019 (Oksanen et al., 2022). To assess the effect of water level drawdown history on species composition a permanova analysis with a Bray-Curtis dissimilarity index was used, in combination with non-metric multidimensional scaling (NMDS) (vegan package: Oksanen et al., 2022). Part 1.2 Nutrient availability To determine the effect of water level drawdown history and sampling depth (independent variables) on the nutrient availability (dependent variables) along the transect survey (method section 2.2.2.2), we used mixed linear models from the GlmmTMB package (Mollie et al., 2017). The model was performed for both the sediment- and the pore-water nutrient concentrations. Location ID was used as a random effect to correct for the duplicate measurements. Tukey-adjusted comparisons were done using \u201cemmeans\u201d (Russell, 2022). Normality and heterogeneity of the residuals of the models were assessed using histograms, and transformed if necessary. Additionally, we used the nutrient starting concentrations from the experimental water level experiment (part 3) to determine differences in nutrient concentrations due to the water level drawdown history. To determine the effect of water level drawdown history (independent variable) on nutrient availability (dependent variables), we used mixed linear models from the GlmmTMB package (Mollie et al., 2017). Starting nutrient concentrations (day 0; field conditions) were used as the dependent variable. Field location ID was used as a random effect to correct for samples taken at the same location. Part 2: Water level gradient Part 2.1 Seed bank properties To determine the best fit of the relation between germination and distance to the reed border, we compared the AIC of linear, parabolic, hyperbolic and exponential decay functions. An \u0394AIC \u2265 2 was used to differentiate models ( \u2018stats\u2019 package (R Core Team, 2023). To assess the effect of water level drawdown history and location along soil elevation gradient on species composition, a permanova analysis with a Bray-Curtis dissimilarity index was used in combination with non-metric multidimensional scaling (NMDS) (Oksanen et al., 2022). To determine differences in Shannon-Wiener diversity, species richness and germination densities (dependent variables) along the transect survey (location within transect as independent variable), we used mixed linear models from the GlmmTMB package with location ID as a random effect (Mollie et al., 2017). Species richness was fitted with a Poisson distribution. This approach was done separately for the water level drawdown and the non-water level drawdown area. Tukey-adjusted comparisons were done using \u201cemmeans\u201d (Russell, 2022). Shannon-Wiener diversity was calculated using the \u2018vegan package\u2019 (Oksanen et al., 2022). Differences in the sum of germinated individuals per location along the water level gradient were tested using a Chi-Square test. Part 2.2 Nutrient availability To test for differences in nutrient availability along the elevational gradient of current water level fluctuations in the transect survey, we performed Spearman correlations. The Spearman correlations were done between nutrient concentration as the dependent variable and elevation in meters NAP as the independent variable. Part 3: Water level fluctuations Part 3.1: Seed bank properties Due to the low germination rate, no statistical analysis were performed on seed bank properties in relation to any of the water level treatments. Part 3.2: Nutrient availability To determine the effect of water level treatment (independent variable) on nutrient availability (dependent variables), we used mixed linear models from the GlmmTMB package (Mollie et al., 2017). Nutrient concentrations from the end of the experiment (day 56) were used as dependent variable. Nutrient starting concentrations were used as a covariate into the model and the blocking factor was used as a random effect. Additionally, nutrient concentrations were tested for changes over time during the eight-week experiment using mixed linear models from the GlmmTMB package (Mollie et al., 2017). Nutrient concentrations were used as the dependent variable, the blocking factor was used as a covariate in the model and date was used as the independent variable. To test for differences among the independent variables, Tukey-adjusted comparisons were done using \u201cemmeans\u201d for all models (Russell, 2022). All models were fitted with a Gaussian-error distribution. Normality and heterogeneity of the residuals of the models were assessed using histograms, and were transformed if necessary. For more details we would like to refer to\u00a0Figure 1 in the related manuscript.", "keywords": ["fluctuating water level", "nutrients", "Seedlings", "Wetlands", "seedlings", "Fluctuating water level", "Nutrients", "mesocosms", "natural sciences", "Mesocosms", "FOS: Natural sciences", "wetlands"]}, "links": [{"href": "https://doi.org/10.5061/dryad.z08kprrnc"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.z08kprrnc", "name": "item", "description": "10.5061/dryad.z08kprrnc", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.z08kprrnc"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "10029/626877", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:24:40Z", "type": "Journal Article", "created": "2023-07-21", "title": "Species-dependent responses of crop plants to polystyrene microplastics", "description": "Only recently there has been a strong focus on the impacts of microplastics on terrestrial crop plants. This study aims to examine and compare the effects of microplastics on two monocotyledonous (barley, Hordeum vulgare and wheat, Triticum aestivum), and two dicotyledonous (carrot, Daucus carota and lettuce, Lactuca sativa) plant species through two complimentary experiments. First, we investigated the effects of low, medium, and high (103, 105, 107 particles per mL) concentrations of 500\u00a0nm polystyrene microplastics (PS-MPs) on seed germination and early development. We found species-dependent effects on the early development, with microplastics only significantly affecting lettuce and carrot. When acutely exposed during germination, PS-MPs significantly delayed the germination of lettuce by 24%, as well as promoted the shoot growth of carrot by 71% and decreased its biomass by 26%. No effect was recorded on monocot species. Secondly, we performed a chronic (21\u00a0d) hydroponic experiment on lettuce and wheat. We observed that PS-MPs significantly reduced the shoot growth of lettuce by up to 35% and increased its biomass by up to 64%, while no record was reported on wheat. In addition, stress level indicators and defence mechanisms were significantly up-regulated in both lettuce and wheat seedlings. Overall, this study shows that PS-MPs affect plant development: impacts were recorded on both germination and growth for dicots, and responses identified by biochemical markers of stress were increased in both lettuce and wheat. This highlights species-dependent effects as the four crops were grown under identical conditions to allow direct comparison. For future research, our study emphasizes the need to focus on crop specific effects, while also working towards knowledge of plastic-induced impacts at environmentally relevant conditions.", "keywords": ["2. Zero hunger", "Microplastics", "Microplastic", "ta1183", "Biochemical indicators of stress", "Agriculture", "Germination", "15. Life on land", "Seed germination", "Seedlings", "Polystyrenes", "microplastic", "Plastics", "Triticum", "agriculture", "Plant growth", "Lactuca"]}, "links": [{"href": "https://doi.org/10029/626877"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10029/626877", "name": "item", "description": "10029/626877", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10029/626877"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-01T00:00:00Z"}}, {"id": "3130873339", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:26:31Z", "type": "Journal Article", "created": "2021-02-13", "title": "Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere", "description": "AbstractOur understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12\uffe2\uff80\uff9324\uffe2\uff80\uff89h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700\uffe2\uff80\uff931000\uffe2\uff80\uff89\uffc2\uffb5m from the tip. Bacteria accumulated predominantly in confined pore spaces within 200\uffe2\uff80\uff89\uffc2\uffb5m from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.