Establishing Lupinus mutabilis as a protein and oil crop requires improved varieties adapted to EU climates. The genetic regulation of strategic breeding traits, including plant architecture, growing cycle length and yield, is unknown. This study aimed to identify associations between 16 669 single nucleotide polymorphisms (SNPs) and 9 agronomic traits on a panel of 223 L. mutabilis accessions, grown in four environments, by applying a genome wide association study (GWAS). Seven environment-specific QTLs linked to vegetative yield, plant height, pods number and flowering time, were identified as major effect QTLs, being able to capture 6 to 20% of the phenotypic variation observed in these traits. Furthermore, two QTLs across environments were identified for flowering time on chromosome 8. The genes FAF, GAMYB and LNK, regulating major pathways involved in flowering and growth habit, as well as GA30X1, BIM1, Dr1, HDA15, HAT3, interacting with these pathways in response to hormonal and environmental cues, were prosed as candidate genes. These results are pivotal to accelerate the development of L. mutabilis varieties adapted to European cropping conditions by using marker-assisted selection (MAS), as well as to provide a framework for further functional studies on plant development and phenology in this species.Gypsum soils in the Mediterranean Basin house large numbers of edaphic specialists that are adapted to stressful environments. The evolutionary history and standing genetic variation of these taxa have been influenced by the geological and paleoclimatic complexity of this area and the long\uffe2\uff80\uff90standing effect of human activities. However, little is known about the origin of Mediterranean gypsophiles and the factors affecting their genetic diversity and population structure.
METHODSUsing phylogenetic and phylogeographic approaches based on microsatellites and sequence data from nuclear and chloroplast regions, we evaluated the divergence time, genetic diversity, and population structure of 27 different populations of the widespread Iberian gypsophile Lepidium subulatum throughout its entire geographic range.
RESULTSLepidium subulatum diverged from its nearest relatives ~3 million years ago, and ITS and psbA/matK trees supported the monophyly of the species. These results suggest that both geological and climatic changes in the region around the Plio\uffe2\uff80\uff90Pleistocene promoted its origin, compared to other evolutionary processes. We found high genetic diversity in both nuclear and chloroplast markers, but a greater population structure in the chloroplast data. These results suggest that while seed dispersal is limited, pollen flow may be favored by the presence of numerous habitat patches that enhance the movement of pollinators.
CONCLUSIONSDespite being an edaphic endemic, L. subulatum possesses high genetic diversity probably related to its relatively old age and high population sizes across its range. Our study highlights the value of using different markers to fully understand the phylogeographic history of plant species.Soil erosion from agricultural fields is a persistent ecological problem, potentially leading to eutrophication of aquatic habitats in the catchment area. Often used and recommended mitigation measures are vegetated filter strips (VFS) as buffer zones between arable land and water bodies. However, if they are designed and managed poorly, nutrients \uffe2\uff80\uff94 especially phosphorus (P) \uffe2\uff80\uff94 may accumulate in the soil. Ultimately, VFS can switch from being a nutrient sink to a source. This problem is further aggravated if the field runoff does not occur as uniform sheet flow, but rather in concentrated form, as is usually the case. To assess the impact of concentrated flow on VFS performance, we have taken soil core samples from field-VFS transition zones at six sites in Lower Austria. We determined a multitude of physical and chemical soil parameters, focusing on P fractions and indices. Our results revealed that concentrated flow can lead to an accumulation of P in the VFS. P levels in the VFS inside the area of concentrated runoff can be equal to or higher than in the field, even though they receive no direct fertilization. However, the concentration and distribution of nutrients in the fields and VFSs were also site-specific and affected by local factors such as the age of the VFS, cropping, and fertilization. Accordingly, there is a need for more sophisticated, bespoke VFS designs that can cope with site-specific runoff volumes and movements of nutrients that occur.Understanding the role of soil moisture and other controls in runoff generation is important for predicting runoff across scales. This paper aims to identify the degree of non\uffe2\uff80\uff90linearity of the relationship between event peak runoff and potential controls for different runoff generation mechanisms in a small agricultural catchment. The study is set in the 66\uffe2\uff80\uff89ha Hydrological Open Air Laboratory, Austria, where discharge was measured at the catchment outlet and for 11 sub\uffe2\uff80\uff90catchments or hillslopes with different runoff generation mechanisms. Peak runoff of 73 events was related to three potential controls: event precipitation, soil moisture and groundwater levels. The results suggest that the hillslopes dominated by ephemeral overland flow exhibit the most non\uffe2\uff80\uff90linear runoff generation behaviour for its controls; runoff is only generated above a threshold of 95% of the maximum soil moisture. Runoff generation through tile drains and in wetlands is more linear. The largest winter and spring events at the catchment outlet are caused by runoff from hillslopes with shallow flow paths (ephemeral overland flow and tile drainage mechanisms), while the largest summer events are caused by other hillslopes, those with deeper flow paths or with saturation areas throughout the year. Therefore, the response of the entire catchment is a mix of the various mechanisms, and the groundwater contribution makes the response more linear. The implications for hydrological modelling are discussed.Streams and rivers act as landscape-scale bioreactors processing large quantities of terrestrial particulate organic matter (POM). This function is linked to their flow regime, which governs residence times, shapes organic matter reactivity and controls the amount of carbon (C) exported to the atmosphere and coastal oceans. Climate change impacts flow regimes by increasing both flash floods and droughts. Here, we used a modelling approach to explore the consequences of lateral hydrological contraction, that is, the reduction of the wet portion of the streambed, for POM decomposition and transport at the river network scale. Our model integrates seasonal leaf litter input as generator of POM, transient storage of POM on wet and dry streambed portions with associated decomposition and ensuing changes in reactivity, and transport dynamics through a dendritic river network. Simulations showed that the amount of POM exported from the river network and its average reactivity increased with lateral hydrological contraction, due to the combination of (1) low processing of POM while stored on dry streambeds, and (2) large shunting during flashy events. The sensitivity analysis further supported that high lateral hydrological contraction leads to higher export of higher reactivity POM, regardless of transport coefficient values, average reactivity of fresh leaf litter and differences between POM reactivity under wet and dry conditions. Our study incorporates storage in dry streambed areas into the pulse-shunt concept (Raymond and others in Ecology 97(1):5\uffe2\uff80\uff9316, 2016. https://doi.org/10.1890/14-1684.1), providing a mechanistic framework and testable predictions about leaf litter storage, transport and decomposition in fluvial networks.Managing agricultural watersheds in an environmentally friendly manner necessitate the strategic implementation of well-targeted sustainable land management (SLM) practices that limit soil and nonpoint source pollution losses and translocation. Watershed-scale SLM-scenario modeling has the potential to identify efficient and effective management strategies from the field to the integrated landscape level. In a case study targeting a 66-hectare watershed in Petzenkirchen, Lower Austria, the Soil and Water Assessment Tool (SWAT) was utilized to evaluate a variety of locally adoptable SLM practices. SWAT was calibrated and validated (monthly) at the catchment outlet for flow, sediment, nitrate-nitrogen (NO3\uffe2\uff80\uff93N), ammonium nitrogen (NH4\uffe2\uff80\uff93N), and mineralized phosphorus (PO4\uffe2\uff80\uff93P) using SWATplusR. Considering the locally existing agricultural practices and socioeconomic and environmental factors of the research area, four conservation practices were evaluated: baseline scenario, contour farming (CF), winter cover crops (CC), and a combination of no-till and cover crops (NT\uffe2\uff80\uff89+\uffe2\uff80\uff89CC). The NT\uffe2\uff80\uff89+\uffe2\uff80\uff89CC SLM practice was found to be the most effective soil conservation practice in reducing soil loss by around 80%, whereas CF obtained the best results for decreasing the nutrient loads of NO3\uffe2\uff80\uff93N and PO4\uffe2\uff80\uff93P by 11% and 35%, respectively. The findings of this study imply that the setup SWAT model can serve the context-specific performance assessment and eventual promotion of SLM interventions that mitigate on-site land degradation and the consequential off-site environmental pollution resulting from agricultural nonpoint sources.Studies on tree CH4 exchange in boreal forests regarding seasonality and role of tree canopies are rare. We aimed to quantify the contribution of boreal trees to the forest CH4 budget during spring leaf-out and to reveal the role of microbes in the CH4 exchange.
MethodsMethane fluxes of downy birch and Norway spruce (Betula pubescens and Picea abies) growing on fen and upland sites were measured together with soil CH4 flux, environmental variables and microbial abundances involved in the CH4 cycle. Tree CH4 fluxes were studied from three stem heights and from shoots.
ResultsThe trees emitted CH4 with higher stem emissions detected from birch and higher shoot emissions from spruce. The stem CH4 emissions from birches at the fen were high (mean 45\uffc2\uffa0\uffc2\uffb5g\uffc2\uffa0m\uffe2\uff88\uff922\uffc2\uffa0h\uffe2\uff88\uff921), decreasing with stem height. Their dynamics followed soil temperature, suggesting the emitted CH4 originated from methanogenic activity, manifested in high mcrA gene copy numbers, in the peat soil. Methanogens were below the quantification limit in the tree tissues. Upscaled tree CH4 emissions accounted for 22% of the total CH4 emissions at the fen.
ConclusionsThe variation in stem CH4 flux between the trees and habitats is high, and the emissions from high-emitting birches increase as the spring proceeds. The lack of detection of methanogens or methanotrophs in the aboveground plant tissues suggests that these microbes did not have a significant role in the observed tree-derived fluxes. The stem-emitted CH4 from birches at the fen is presumably produced microbially in the soil.
", "keywords": ["0301 basic medicine", "570", "550", "Methanogens", "LIVING TREES", "Trees", "03 medical and health sciences", "Methanotrophs", "METHANE EMISSIONS", "SAP FLOW", "Boreal forest", "Waterlogging", "PRECURSOR", "0303 health sciences", "BIOMASS EQUATIONS", "NORWAY SPRUCE", "Forestry", "Methane fux", "15. Life on land", "Environmental sciences", "METHANOTROPHS", "13. Climate action", "RADIATION", "Methane flux", "VEGETATION", "COMMUNITIES"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s11104-022-05447-9.pdf"}, {"href": "https://doi.org/10.1007/s11104-022-05447-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-022-05447-9", "name": "item", "description": "10.1007/s11104-022-05447-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-022-05447-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-24T00:00:00Z"}}, {"id": "10.1016/j.agrformet.2018.11.031", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:15:18Z", "type": "Journal Article", "created": "2018-11-29", "title": "Partitioning evapotranspiration of a drip-irrigated wheat crop: Inter-comparing eddy covariance-, sap flow-, lysimeter- and FAO-based methods", "description": "Abstract A precise estimate of the evapotranspiration (ET) partitioning is fundamental for determining the crop water needs and optimizing irrigation management. The plant transpiration (T) is generally considered to be the most desirable component, while reducing the soil evaporation (E) could be one of the most important water-saving actions in semi-arid agricultural regions. Given the lack of reference method to estimate the E/T partitioning of wheat crop, this study inter-compares four different methods based on eddy covariance, sap flow and lysimetry measurements and FAO modeling. The objectives are: i) to quantify the systematic and random uncertainty in E and T observations, ii) to evaluate the partitioning ratio (T/ET) at the daily/field scale and iii) to assess the performance of the FAO model over two drip irrigated wheat fields. Results indicate that despite the small surface sensed by mini-lysimeters, the partitioning ratio is evaluated more precisely (19% relative error) with lysimetry than with the other systems (any combination of eddy covariance, lysimetry and sap flow measurements). Moreover, stem-scale T measurements from sap flow sensors are subject to representativeness issues at the field scale, and to systematic errors during water-stress and senescence periods. The lysimeter-derived partitioning ratio increases from about 0.50 to 0.85 during the growth stage and rapidly drops towards 0 during senescence. Its dynamics is found to be significantly correlated (R>0.7) with the 5-cm soil moisture. By comparing FAO simulations with observations, it is found that the FAO method overestimates T and underestimates E, while keeping satisfying ET estimates for drip irrigated wheat. This study suggests that different independent measurement techniques should be implemented to both quantify and reduce uncertainties in the T/ET ratio, and that accurate observations are still needed to improve the modeling of E/T components.", "keywords": ["FAO-56", "0106 biological sciences", "2. Zero hunger", "550", "Lysimeter", "Eddy correlation", "0207 environmental engineering", "02 engineering and technology", "15. Life on land", "01 natural sciences", "[SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces", " environment", "6. Clean water", "Sap flow", "Wheat", "[SDU.STU.HY] Sciences of the Universe [physics]/Earth Sciences/Hydrology", "[SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology", "[SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces", "environment", "Evaporation-transpiration"]}, "links": [{"href": "https://doi.org/10.1016/j.agrformet.2018.11.031"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agricultural%20and%20Forest%20Meteorology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.agrformet.2018.11.031", "name": "item", "description": "10.1016/j.agrformet.2018.11.031", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.agrformet.2018.11.031"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-01T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2017.08.009", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:15:27Z", "type": "Journal Article", "created": "2017-09-18", "title": "Changes in the genetic structure of an invasive earthworm species (Lumbricus terrestris, Lumbricidae) along an urban \u2013 rural gradient in North America", "description": "European earthworms were introduced to North America by European settlers about 400 years ago. Human-mediated introductions significantly contributed to the spread of European species, which commonly are used as fishing bait and are often disposed deliberately in the wild. We investigated the genetic structure of Lumbricus terrestris in a 100 km range south of Calgary, Canada, an area that likely was devoid of this species two decades ago. Genetic relationships among populations, gene flow, and migration events among populations were investigated using seven microsatellite markers and the mitochondrial 16S rDNA gene. Earthworms were collected at different distances from the city and included fishing baits from three different bait distributors. The results suggest that field populations in Alberta established rather recently and that bait and field individuals in the study area have a common origin. Genetic variance within populations decreased outside of the urban area, and the most distant populations likely originated from a single introduction event. The results emphasise the utility of molecular tools to understand the spatial extent and connectivity of populations of exotic species, in particular soil-delling species, that invade native ecosystems and to obtain information on the origin of populations. Such information is crucial for developing management and prevention strategies to limit and control establishment of non-native earthworms in North America.", "keywords": ["0106 biological sciences", "0301 basic medicine", "570", "03 medical and health sciences", "Ecology", " evolutionary biology", "11. Sustainability", "15. Life on land", "Microsatellites", " Exotic earthworms", " Invasion", " Gene flow", " Dispersal", " Population structure", " Soil", "01 natural sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.apsoil.2017.08.009"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2017.08.009", "name": "item", "description": "10.1016/j.apsoil.2017.08.009", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2017.08.009"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-11-01T00:00:00Z"}}, {"id": "10.1016/j.jconhyd.2021.103797", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:19Z", "type": "Journal Article", "created": "2021-03-18", "title": "Dynamics of nitrous oxide with depth in groundwater: Insights from ambient groundwater and laboratory incubation experiments (Hesbaye chalk aquifer, Belgium)", "description": "Aquifers under agricultural areas are considered to be an indirect source of nitrous oxide emission (N2O) to the atmosphere, which is the greenhouse gas (GHGs) characterized with the highest global warning potential and acts as a stratospheric ozone depletion agent. Previous investigations performed in the Cretaceous Hesbaye chalk aquifer in Eastern Belgium suggested that the dynamics of N2O in the aquifer is controlled by overlapping biochemical processes such as nitrification and denitrification. The current study aims to obtain better insight concerning the factors controlling the distribution of N2O concentration along a vertical dimension in the aquifer, and to capture and quantify the occurrence of nitrification and denitrification processes in the groundwater system. Low-flow groundwater sampling technique was undertaken at different depths in the aquifer to collect groundwater samples aiming at obtaining information about ambient aquifer hydrogeochemical conditions and their effect on the accumulation of GHGs. Afterwards, laboratory stable isotope experiments, using NO3- and NH4+ compounds labeled with heavy 15N isotope, were applied to quantify the rates of nitrification and denitrification processes. Ambient studies suggest that the occurrence of N transformation was related to denitrification while laboratory incubation experiments did not detect it. Such controversial results might be explained by the discrepancy between real aquifer conditions and lab design studies. Thus, additional in situ tracer experiments should be carried out in areas where natural groundwater fluxes do not flush the injected tracer too rapidly. In addition, it would be useful to conduct microbiological studies to obtain better insight into the nature of subsurface biofilm biotope.", "keywords": ["2. Zero hunger", "Nitrous Oxide", "N stable isotope analysis", "Nitrification", "01 natural sciences", "Low-flow sampling", "6. Clean water", "Calcium Carbonate", "Greenhouse gases", "Belgium", "13. Climate action", "Denitrification", "Laboratories", "Groundwater", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jconhyd.2021.103797"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Contaminant%20Hydrology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jconhyd.2021.103797", "name": "item", "description": "10.1016/j.jconhyd.2021.103797", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jconhyd.2021.103797"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-01T00:00:00Z"}}, {"id": "10.1016/j.biortech.2018.11.040", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:15:32Z", "type": "Journal Article", "created": "2018-11-10", "title": "Effect of feed glucose and acetic acid on continuous biohydrogen production by Thermotoga neapolitana", "description": "This study focused on the effect of feed glucose and acetic acid on biohydrogen production by Thermotoga neapolitana under continuous-flow conditions. Increasing the feed glucose concentration from 11.1 to 41.6\u202fmM decreased the hydrogen yield from 3.6 (\u00b10.1) to 1.4 (\u00b10.1)\u202fmol\u202fH2/mol glucose. The hydrogen production rate concomitantly increased until 27.8\u202fmM of feed glucose but remained unaffected when feed glucose was further raised to 41.6\u202fmM. Increasing the acetic acid concentration from 0 to 240\u202fmM hampered dark fermentation in batch bioassays, diminishing the cumulative hydrogen production by 45% and the hydrogen production rate by 57%, but induced no negative effect during continuous operation. Indeed, throughout the continuous flow operation the process performance improved considerably, as indicated by the 47% increase of hydrogen yield up to 3.1 (\u00b10.1)\u202fmol\u202fH2/mol glucose on day 110 at 27.8\u202fmM feed glucose.", "keywords": ["Thermotoga neapolitana", "Feed concentration", "Glucose", "Fermentation", "0211 other engineering and technologies", "0202 electrical engineering", " electronic engineering", " information engineering", "Acetic acid; Continuous-flow dark fermentation; Feed concentration; Hydrogen; Inhibition; Thermotoga neapolitana", "02 engineering and technology", "Acetic acid", "Continuous-flow dark fermentation", "Inhibition", "Acetic Acid", "Hydrogen"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/726873/1/Resubmission%20to%20BiTe%202018_11_08.pdf"}, {"href": "https://doi.org/10.1016/j.biortech.2018.11.040"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioresource%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biortech.2018.11.040", "name": "item", "description": "10.1016/j.biortech.2018.11.040", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biortech.2018.11.040"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-01T00:00:00Z"}}, {"id": "10.1016/j.biortech.2019.122033", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:15:32Z", "type": "Journal Article", "created": "2019-08-18", "title": "High rate continuous biohydrogen production by hyperthermophilic Thermotoga neapolitana", "description": "This study focused on continuous-flow hydrogen production by Thermotoga neapolitana at a hydraulic retention time (HRT) decreasing from 24 to 5\u202fh. At each HRT reduction, the hydrogen yield (HY) immediately dropped, but recovered during prolonged cultivation at constant HRT. The final HY in each operating period decreased from 3.4 (\u00b10.1) to 2.0 (\u00b10.0) mol H2/mol glucose when reducing the HRT from 24 to 7\u202fh. Simultaneously, the hydrogen production rate (HPR) and the liquid phase hydrogen concentration (H2aq) increased from 82 (\u00b11) to 192 (\u00b14) mL/L/h and from 9.1 (\u00b10.3) to 15.6 (\u00b10.7) mL/L, respectively. Additionally, the effluent glucose concentration increased from 2.1 (\u00b10.1) to above 10\u202fmM. Recirculating H2-rich biogas prevented the supersaturation of H2aq reaching a value of 9.3 (\u00b10.7) mL/L, resulting in complete glucose consumption and the highest HPR of 277\u202fmL/L/h at an HRT of 5\u202fh.", "keywords": ["0211 other engineering and technologies", "02 engineering and technology", "Acetic acid", "Archaea", "01 natural sciences", "7. Clean energy", "Continuous-flow dark fermentation", "Thermotoga neapolitana", "Acetic acid; Continuous-flow dark fermentation; Gas recirculation; Hydraulic retention time; Hydrogen; Thermotoga neapolitana", "Bioreactors", "Glucose", "Fermentation", "Gas recirculation", "Hydraulic retention time", "Hydrogen", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/758593/1/Post-print%20for%20IRIS.pdf"}, {"href": "https://doi.org/10.1016/j.biortech.2019.122033"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioresource%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biortech.2019.122033", "name": "item", "description": "10.1016/j.biortech.2019.122033", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biortech.2019.122033"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-01T00:00:00Z"}}, {"id": "10.1016/j.ecss.2013.08.021", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:15:43Z", "type": "Journal Article", "created": "2013-08-20", "title": "Effects Of Long-Term Grazing On Sediment Deposition And Salt-Marsh Accretion Rates", "description": "Many studies have attempted to predict whether coastal marshes will be able to keep up with future acceleration of sea-level rise by estimating marsh accretion rates. However, there are few studies focussing on the long-term effects of herbivores on vegetation structure and subsequent effects on marsh accretion. Deposition of fine-grained, mineral sediment during tidal inundations, together with organic matter accumulation from the local vegetation, positively affects accretion rates of marsh surfaces. Tall vegetation can enhance sediment deposition by reducing current flow and wave action. Herbivores shorten vegetation height and this could potentially reduce sediment deposition. This study estimated the effects of herbivores on 1) vegetation height, 2) sediment deposition and 3) resulting marsh accretion after long-term (at least 16 years) herbivore exclusion of both small (i.e. hare and goose) and large grazers (i.e. cattle) for marshes of different ages. Our results firstly showed that both small and large herbivores can have a major impact on vegetation height. Secondly, grazing processes did not affect sediment deposition. Finally, trampling by large grazers affected marsh accretion rates by compacting the soil. In many European marshes, grazing is used as a tool in nature management as well as for agricultural purposes. Thus, we propose that soil compaction by large grazers should be taken in account when estimating the ability of coastal systems to cope with an accelerating sea-level rise. (C) 2013 Elsevier Ltd. All rights reserved.
", "keywords": ["marsh succession", "0106 biological sciences", "Surface elevation change", "Sea-level rise", "FLOW", "Sedimentation rate", "SEA-LEVEL RISE", "SURFACE ELEVATION", "01 natural sciences", "BROWN HARES", "Herbivory", "14. Life underwater", "Marsh succession", "Biology", "Global change", "VEGETATION SUCCESSION", "global change", "COASTAL WETLANDS", "0105 earth and related environmental sciences", "2. Zero hunger", "sedimentation rate", "herbivory", "GEESE", "sea-level rise", "15. Life on land", "PRODUCTIVITY GRADIENT", "surface elevation change", "NORTH-SEA", "13. Climate action", "TIDAL MARSH"]}, "links": [{"href": "https://doi.org/10.1016/j.ecss.2013.08.021"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Estuarine%2C%20Coastal%20and%20Shelf%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ecss.2013.08.021", "name": "item", "description": "10.1016/j.ecss.2013.08.021", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ecss.2013.08.021"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-01T00:00:00Z"}}, {"id": "10.1016/j.ejrh.2021.100882", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:15:45Z", "type": "Journal Article", "created": "2021-07-30", "title": "Surface water and groundwater interaction at long-term exploited riverbank filtration site based on groundwater flow modelling (Mosina-Krajkowo, Poland)", "description": "Study region: Poland, Warta River catchment. Study focus: The study aimed to explain the reasons for spatial variability in chloride concentrations at the Mosina-Krajkowo riverbank filtration (RBF) site located along the river. This variability is attributed to RBF\u2019s different intensity along the river sections, related, among others, to clogging development. The RBF effectiveness was studied using groundwater flow modelling by: examining the water balance in zones established on hydrogeological setting and chloride concentrations; travel time of the bankfiltrate investigation; RBF parametrisation (i.e. infiltration per unit area and specific infiltration per unit of riverbank). New Hydrological Insights for the Region: The study identifies zones of the most favourable RBF conditions and establishes the variability causes. The overall share bankfiltrate was found at 75.8 %. Its spatial variation ranged widely from 41.1\u201389.3%, confirming the usefulness of the RBF performance sectional analysis in managing this type of site. The highest proportion of surface water (>80 %) occurred along the straight river section, where the riverbed was built by fine and medium sands (preventing penetration of organic suspension into the aquifer). In contrast, the lowest values (<42 %) occurred in the meander zone (with the most favourable RBF conditions at the beginning of site operation), where deep erosion reached coarse-grained sediments in the river bottom, followed by the development of clogging processes and a decrease in the RBF efficiency with time.", "keywords": ["Physical geography", "QE1-996.5", "Riverbed clogging", "Numerical modelling", "0208 environmental biotechnology", "0207 environmental engineering", "Geology", "Modflow", "02 engineering and technology", "Riverbank filtration", "6. Clean water", "Modpath", "GB3-5030"]}, "links": [{"href": "https://doi.org/10.1016/j.ejrh.2021.100882"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hydrology%3A%20Regional%20Studies", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ejrh.2021.100882", "name": "item", "description": "10.1016/j.ejrh.2021.100882", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ejrh.2021.100882"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-01T00:00:00Z"}}, {"id": "10.1016/j.jestch.2022.101323", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:21Z", "type": "Journal Article", "created": "2023-01-10", "title": "Multiparametric experimental analysis of the pin disc rotational cavitation generator", "description": "The alarming increase in water pollution is driving research into novel, environmentally friendly treatment solutions such as hydrodynamic cavitation. This study is part of the research on the pin disc rotational generator of hydrodynamic cavitation, which utilises the low pressure wake behind the rotor pins to induce cavitation and the short gap between the rotor and stator pins to enhance cavitation cloud fluctuation. Due to the lack of understanding of the effects of cavitation treatment, a laboratory device was built to investigate the mechanisms of cavitation generation and the effects of various geometric features such as the diameter, number, and shape of the rotor pins and the gap size between the rotor and stator pins. Using simultaneously measured pressure fluctuations and high-speed visualisation, a method was developed to quantify the extent of cavitation, and it was found that throttling the high-pressure side had an order- of- magnitude smaller effect on cavitation than the number of rotor pins. It was found that a smaller number of rotor pins with large downstream area produced the most aggressive cavitation conditions. The weak spectral response and lower mean vapour cloud area, as well as the lower fluctuation in the case without stator, demonstrated the key role of the stator in the onset and aggressiveness of cavitation.", "keywords": ["hydrodynamic cavitation", " cavitation dynamics", " multiparametric analysis", " flow visualization", " waste water treatment", "eksperimentalne analize", "\u010di\u0161\u010denje odpadnih voda", "Cavitation dynamics", "04 agricultural and veterinary sciences", "Multiparametric analysis", "Engineering (General). Civil engineering (General)", "dinamika teko\u010din", "6. Clean water", "Hydrodynamic cavitation pinned disc reactor", "info:eu-repo/classification/udc/532.528", "cavitation dynamics", "0404 agricultural biotechnology", "waste water treatment", "multiparametric analysis", "vizualizacija", "hidrodinamska kavitacija", " dinamika teko\u010din", " eksperimentalne analize", " vizualizacija", " \u010di\u0161\u010denje odpadnih voda", "info:eu-repo/classification/udc/532", "hydrodynamic cavitation", "flow visualization", "hidrodinamska kavitacija", "TA1-2040", "0405 other agricultural sciences", "hydrodynamic cavitation pinned disc reactor", "Flow visualization"]}, "links": [{"href": "https://doi.org/10.1016/j.jestch.2022.101323"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Engineering%20Science%20and%20Technology%2C%20an%20International%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jestch.2022.101323", "name": "item", "description": "10.1016/j.jestch.2022.101323", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jestch.2022.101323"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-01T00:00:00Z"}}, {"id": "10.1016/j.jfoodeng.2020.109973", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:21Z", "type": "Journal Article", "created": "2020-02-13", "title": "Physical and flow properties of pseudocereal-based protein-rich ingredient powders", "description": "Abstract Knowledge of bulk handling properties of food powders is essential in the design of industrial equipment and selection of appropriate powder handling operations. The objectives of this study were to determine the physical and flow properties of plant-based regular and protein-rich flours to establish relationships between powder physical and bulk handling properties as influenced by protein enrichment. A number of physical properties (bulk density, flowability, wall friction and compressibility) were assessed for 11 regular- and protein-rich flours from pseudocereals (amaranth, buckwheat, quinoa) and cereals (rice and maize). Relevant physicochemical properties such as particle size distribution, microstructure and water sorption behaviour were also studied. The protein-rich pseudocereal flours had irregular-shaped, rough surfaces with mean particle diameters ranging from 96.5 to 215\u00a0\u03bcm. The compressibility indices (42.6\u201351.4%) were higher for the former compared to the regular protein content powders and they displayed lesser tendency to uptake water with increasing relative humidity. Analysis of the flow behaviour showed the protein-rich flours to be more cohesive with higher wall friction angle values than the regular protein content powders. The new information obtained in this study is critical in optimising the processing, stability and applications of these value-added high-protein pseudocereal ingredient powders.", "keywords": ["2. Zero hunger", "0404 agricultural biotechnology", "Protein", "Water sorption", "Flowability", "Pseudocereal", "04 agricultural and veterinary sciences", "Powder", "0405 other agricultural sciences", "Microstructure"]}, "links": [{"href": "https://doi.org/10.1016/j.jfoodeng.2020.109973"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Food%20Engineering", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jfoodeng.2020.109973", "name": "item", "description": "10.1016/j.jfoodeng.2020.109973", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jfoodeng.2020.109973"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2010.11.073", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:21Z", "type": "Journal Article", "created": "2010-11-26", "title": "Genotoxic Endpoints In The Earthworms Sub-Lethal Assay To Evaluate Natural Soils Contaminated By Metals And Radionuclides", "description": "Eisenia andrei was exposed, for 56 days, to a contaminated soil from an abandoned uranium mine and to the natural reference soil LUFA 2.2. The organisms were sampled after 0, 1, 2, 7, 14 and 56 days of exposure, to assess metals bioaccumulation, coelomocytes DNA integrity and cytotoxicity. Radionuclides bioaccumulation and growth were also determined at 0 h, 14 and 56 days of exposure. Results have shown the bioaccumulation of metals and radionuclides, as well as, growth reduction, DNA damages and cytotoxicity in earthworms exposed to contaminated soil. The usefulness of the comet assay and flow cytometry, to evaluate the toxicity of contaminants such as metals and radionuclides in earthworms are herein reported. We also demonstrated that DNA strand breakage and immune cells frequency are important endpoints to be employed in the earthworm reproduction assay, for the evaluation of soil geno and cytotoxicity, as part of the risk assessment of contaminated areas. This is the first study that integrates DNA damage and cytotoxicity evaluation, growth and bioaccumulation of metals and radionuclides in a sub lethal assay, for earthworms exposed to soil contaminated with metals and radionuclides.", "keywords": ["Eisenia andrei", "Cytotoxicity", "DNA damages", "Flow Cytometry", "01 natural sciences", "3. Good health", "Metals", "Animals", "Soil Pollutants", "Oligochaeta", "Radionuclides", "DNA Damage", "Mutagens", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2010.11.073"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2010.11.073", "name": "item", "description": "10.1016/j.jhazmat.2010.11.073", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2010.11.073"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-02-01T00:00:00Z"}}, {"id": "10.1016/j.jpowsour.2020.229432", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:24Z", "type": "Journal Article", "created": "2021-01-08", "title": "3D modelling of bioelectrochemical systems with brush anodes under fed-batch and flow conditions", "description": "Abstract A 3D mathematical model of the different processes occurring in a bioelectrochemical system (BES) equipped with carbon fibres brush anodes has been implemented. The model combines equations of electrical charge conservation, with hydrodynamics, convection, diffusion and kinetics of the involved processes, such as biofilm formation, bioelectrochemical and electrochemical reactions. The model has been solved for different scenarios. A system with a single BES cell was simulated under fed-batch and flow conditions, as three cells hydraulically connected in-series have been also considered. Model parameters were derived from the literature or from experimental data obtained with replicate of a single-chamber BES under different conditions. The model solution provides space profiles of potential and current, concentration of substrate and protons and biofilm under transient conditions. Velocity profiles may also be calculated with simulations under flow conditions. The effects of operative conditions on the performance of the process, both for current generation and substrate removal, have been quantified. The model provides a versatile tool to design and optimise BES reactors with fibre brush anodes.", "keywords": ["01 natural sciences", "7. Clean energy", "3D model; Bioelectrochemical systems; Brush anodes; Fed-batch; Flow", "0104 chemical sciences", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://iris.unica.it/bitstream/11584/304704/1/1-s2.0-S0378775320317158-main%20%281%29.pdf"}, {"href": "https://doi.org/10.1016/j.jpowsour.2020.229432"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Power%20Sources", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jpowsour.2020.229432", "name": "item", "description": "10.1016/j.jpowsour.2020.229432", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jpowsour.2020.229432"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-01T00:00:00Z"}}, {"id": "10.1016/j.mne.2022.100125", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:26Z", "type": "Journal Article", "created": "2022-03-10", "title": "Multispectral imaging flow cytometry for process monitoring in microalgae biotechnology", "description": "In the course of efficient development and optimization of biotechnological processes, the need for methods to track morphological and compositional changes of single cells is increasing. So far, the material composition of cells is determined by chemical analysis of a pooled cell sample, which reflects the average composition of the taken cell collection. Conventional flow cytometry enables the analysis of individuals from a population. However, it cannot resolve such valuable information like morphological details and distribution of molecular compounds inside the cells. This gap is bridged by a combination of imaging flow cytometry and multispectral imaging. The potential of this Multispectral Imaging Flow Cytometry (MIFC) approach has been investigated and confirmed in the presented parameter study on the bioproduction of Astaxanthin (Ax) by the microalgae Haematococcus pluvialis (HP). As far as multispectral imaging in transmission mode, only three spectral channels (446\u00a0nm, 532\u00a0nm, 646\u00a0nm) were used to measure the amount of substance and the molecular distribution of the core components chlorophyll (Chl) and Ax. Both could be clearly separated from the phase-contrast information generated from the cellular structures and morphology. In general, the results from the MIFC method comply with the conventional measurements but extend them for details on the morphology and on compositional changes within the cultivated cell population during the cultivation process and in response to the applied stimuli.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Algae", "TK7800-8360", "Multispectral", "Process monitoring", "T1-995", "Chemometrics", "Electronics", "Multispectral imaging flow cytometry", "Technology (General)", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.mne.2022.100125"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Micro%20and%20Nano%20Engineering", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.mne.2022.100125", "name": "item", "description": "10.1016/j.mne.2022.100125", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.mne.2022.100125"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-06-01T00:00:00Z"}}, {"id": "10.1016/j.resconrec.2013.01.014", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:29Z", "type": "Journal Article", "created": "2013-02-21", "title": "Greenhouse Gas Emissions And Energy Balance Of Sunflower Biodiesel: Identification Of Its Key Factors In The Supply Chain", "description": "Abstract The production of first generation biofuels, such as sunflower-based biodiesel, is potentially an option for diversifying the energy matrix in several South American countries. However, biofuels present environmental challenges, especially concerning the reduction of greenhouse gas (GHG) emissions. This study, using a life-cycle approach, evaluates the GHG emissions and energy balance of the future nationwide production of sunflower-based biodiesel in Chile. Direct land use change is included in the analysis. The overall findings indicate that sunflower biodiesel, under the most likely production conditions, will have better environmental performance than fossil diesel in terms of both indicators. The agricultural stage is associated to key factors such as land use change, and nitrogen fertilizers. These factors contribute significantly to GHG emissions or energy demand in the biodiesel life cycle. The sensitivity analysis shows that no GHG emission saving could occur if nitrogen fertilizers rate exceeds 330\u00a0kg\u00a0N/ha. In order to reduce the environmental impacts of this biofuel, improvement measures are suggested.", "keywords": ["2. Zero hunger", "Energy demand", "02 engineering and technology", "15. Life on land", "01 natural sciences", "7. Clean energy", "12. Responsible consumption", "Sunflower", "Life cycle assessment", "13. Climate action", "11. Sustainability", "0202 electrical engineering", " electronic engineering", " information engineering", "Biodiesel", "Chile", "Land use change", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.resconrec.2013.01.014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Resources%2C%20Conservation%20and%20Recycling", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.resconrec.2013.01.014", "name": "item", "description": "10.1016/j.resconrec.2013.01.014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.resconrec.2013.01.014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-04-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2019.134426", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:35Z", "type": "Journal Article", "created": "2019-09-12", "title": "Retention soil filters for the treatment of sewage treatment plant effluent and combined sewer overflow", "description": "Retention soil filters (RSFs) are vertical flow constructed wetlands. They are mainly used for the treatment of combined sewer overflow or stormwater, and not operated during dry weather conditions. However, RSFs have been successfully tested as continuous post treatment for sewage treatment plant effluents. In this paper we present a new approach, namely dual usage of the retention soil filter. During dry weather the RSF is used for the polishing treatment of sewage treatment plant effluent and during overflow events, the retention soil filter treats the combined sewer overflow. This study was conducted at two pilot RSFs that were fed with sewage treatment effluent for four years. Removal of TOC, DOC, nutrients and 21 organic micropollutants was determined during six months at different sequences of regular effluent and overflow treatment conditions. TOC, DOC and nutrients, appearing in high concentration in combined sewer overflow, were effectively removed, and metformin and caffeine micropollutants showed >99% removal. Residues from this combined sewer treatment that were sorbed on filter material or stored in pore water were washed out directly after treatment when STP effluent infiltration was initiated. This effect declined within 20\u202fh after combined sewer overflow treatment. Dry periods of 18\u202fh between combined sewer and sewage treatment plant effluent feeding counteracted the wash out effects. The highest removal efficiency was found in the beginning of the feeding time of 28\u202fh, indicating that shorter feeding cycles enhance the overall efficiency of the RSF. Finally, the results show that a single RSF system can successfully reduce emissions of TOC, DOC, nutrients and micropollutants to surface waters from two different emission pathways, i.e. from regular treated effluents and storm related sewer overflows. In conclusion, the dual usage of RSF is a promising approach and ready for upscaling and implementation.", "keywords": ["Combined sewer overflow treatment", "Waste water treatment", "Micropollutants", "Retention soil filter", "Biologie", "01 natural sciences", "6. Clean water", "Constructed wetland", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2019.134426"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2019.134426", "name": "item", "description": "10.1016/j.scitotenv.2019.134426", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2019.134426"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2023.161600", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:36Z", "type": "Journal Article", "created": "2023-01-18", "title": "Risk reductions during pyrene biotransformation and mobilization in a model plant-bacteria-biochar system", "description": "The productive application of motile microorganisms for degrading hydrophobic contaminants in soil is one of the most promising processes in modern remediation due to its sustainability and low cost. However, the incomplete biodegradation of the contaminants and the formation of the intermediary metabolites in the process may increase the toxicity in soil during bioremediation, and motile inoculants may mobilize the pollutants through biosorption. Therefore, controlling these factors should be a fundamental part of soil remediation approaches. The aim of this study was to evaluate the sources of risk associated with the cometabolism-based transformation of 14C-labeled pyrene by inoculated Pseudomonas putida G7 and identify ways to minimize risk. Our model scenario examined the increase in bioaccessibility to a distant source of contamination facilitated by sunflower (Helianthus annuus L.) roots. A biochar trap for mobilized pollutant metabolites and bacteria has also been employed. The experimental design consisted of pots filled with a layer of sand with 14C-labeled pyrene (88 mg kg-1) as a contamination focus located several centimeters from the inoculation point. Half of the pots included a biochar layer at the bottom. The pots were incubated in a greenhouse with sunflower plants and P. putida G7 bacteria. Pots with sunflower plants showed a higher biodegradation of pyrene, its mobilization as metabolites through the percolate and the roots, and bacterial mobilization toward the source of contamination, also resulting in increased pyrene transformation. In addition, the biochar layer efficiently reduced the concentrations of pyrene metabolites collected in the leachates. Therefore, the combination of plants, motile bacteria and biochar safely reduced the risk caused by the biological transformation of pyrene.", "keywords": ["Risk", "2. Zero hunger", "570", "Pyrenes", "Bacteria", "04 agricultural and veterinary sciences", "Plants", "01 natural sciences", "Polycyclic aromatic hydrocarbons", "6. Clean water", "Sunflower", "Soil", "Biodegradation", " Environmental", "13. Climate action", "Biodegradation", "Soil Pollutants", "0401 agriculture", " forestry", " and fisheries", "Polycyclic Aromatic Hydrocarbons", "Bioremediation", "Biotransformation", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2023.161600"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2023.161600", "name": "item", "description": "10.1016/j.scitotenv.2023.161600", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2023.161600"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-01T00:00:00Z"}}, {"id": "10.1029/2021MS002812", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:17:25Z", "type": "Journal Article", "created": "2022-07-06", "title": "Unsaturated Transport Modeling: Random\u2010Walk Particle\u2010Tracking as a Numerical\u2010Dispersion Free and Efficient Alternative to Eulerian Methods", "description": "AbstractLagrangian methods, such as the random\uffe2\uff80\uff90walk particle\uffe2\uff80\uff90tracking (RWPT), are often qualified as a potentially valuable alternative to error\uffe2\uff80\uff90prone Eulerian methods for simulating solute transport in unsaturated porous media. Yet, the RWPT method has not yet been validated against \uffe2\uff80\uff90 and compared to \uffe2\uff80\uff90 currently used Eulerian solutions for simulating solute transport under a range of typical unsaturated conditions. This paper presents a new implementation of the RWPT approach for advective \uffe2\uff80\uff90 dispersive transport problems under variably saturated conditions. We first show that, as previously demonstrated for a heterogeneous dispersion tensor, using an interpolation scheme in the RWPT algorithm performs well for problems with abrupt changes in the water content. The new model is then compared against a simple 1D uniform transport problem, for which an analytical solution exist, and against a variety of 1D and 3D numerical solutions using the different Eulerian schemes implemented in Hydrus software suite. Results show that, while the Eulerian solutions significantly suffer from numerical dispersion in case of a coarse spatial discretization of the simulation domain, the new Lagrangian model provides accurate solutions for all problems. Furthermore, RWPT reproduces accurately solute transport for typical unsaturated flow conditions (infiltration, evaporation). Moreover, the Lagrangian model appears to be orders of magnitude faster than its Eulerian alternative to solve a 3D heterogeneous problem. Thus, RWPT should be seen as an attractive, stable and efficient alternative for simulating solute transport in the vadose zone, especially in case of complex and large problems.Lagrangian methods, such as the random\uffe2\uff80\uff90walk particle\uffe2\uff80\uff90tracking (RWPT), are often qualified as a potentially valuable alternative to error\uffe2\uff80\uff90prone Eulerian methods for simulating solute transport in unsaturated porous media. Yet, the RWPT method has not yet been validated against \uffe2\uff80\uff90 and compared to \uffe2\uff80\uff90 currently used Eulerian solutions for simulating solute transport under a range of typical unsaturated conditions. This paper presents a new implementation of the RWPT approach for advective \uffe2\uff80\uff90 dispersive transport problems under variably saturated conditions. We first show that, as previously demonstrated for a heterogeneous dispersion tensor, using an interpolation scheme in the RWPT algorithm performs well for problems with abrupt changes in the water content. The new model is then compared against a simple 1D uniform transport problem, for which an analytical solution exist, and against a variety of 1D and 3D numerical solutions using the different Eulerian schemes implemented in Hydrus software suite. Results show that, while the Eulerian solutions significantly suffer from numerical dispersion in case of a coarse spatial discretization of the simulation domain, the new Lagrangian model provides accurate solutions for all problems. Furthermore, RWPT reproduces accurately solute transport for typical unsaturated flow conditions (infiltration, evaporation). Moreover, the Lagrangian model appears to be orders of magnitude faster than its Eulerian alternative to solve a 3D heterogeneous problem. Thus, RWPT should be seen as an attractive, stable and efficient alternative for simulating solute transport in the vadose zone, especially in case of complex and large problems.This study proposes a probabilistic approach for the quantitative assessment of reach- and network-scale hydrological connectivity as dictated by river flow space\uffe2\uff80\uff93time variability. Spatial dynamics of daily streamflows are estimated based on climatic and morphological features of the contributing catchment, integrating a physically based approach that accounts for the stochasticity of rainfall with a water balance framework and a geomorphic recession flow analysis. Ecologically meaningful minimum stage thresholds are used to evaluate the connectivity of individual stream reaches, and other relevant network-scale connectivity metrics. The framework allows a quantitative description of the main hydrological causes and the ecological consequences of water depth dynamics experienced by river networks. The analysis shows that the spatial variability of local-scale hydrological connectivity is strongly affected by the spatial and temporal distribution of climatic variables. Depending on the underlying climatic settings and the critical stage threshold, loss of connectivity can be observed in the headwaters or along the main channel, thereby originating a fragmented river network. The proposed approach provides important clues for understanding the effect of climate on the ecological function of river corridors.
", "keywords": ["streamflow dynamics", "13. Climate action", "Science", "hydrological connectivity", "Q", "0207 environmental engineering", "Earth Science", "02 engineering and technology", "15. Life on land", "ecohydrology", "6. Clean water", "river fragmentation"]}, "links": [{"href": "https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.181428"}, {"href": "https://doi.org/10.1098/rsos.181428"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Royal%20Society%20Open%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1098/rsos.181428", "name": "item", "description": "10.1098/rsos.181428", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1098/rsos.181428"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-01T00:00:00Z"}}, {"id": "10.3389/fenvs.2022.764333", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:20:31Z", "type": "Journal Article", "created": "2022-04-01", "title": "Keeping Up with Phosphorus Dynamics: Overdue Conceptual Changes in Vegetative Filter Strip Research and Management", "description": "Vegetative filter strips (VFS) are best management practices with the primary aim of protecting surface waters from eutrophication resulting from excess nutrient inputs from agricultural sources. However, we argue that there is a substantial time and knowledge lag from the science underpinning VFS to policy and implementation. Focussing on phosphorus (P), we strive to introduce a holistic view on VFS that accounts for the whole functional soil volume, temporal and seasonal effects, the geospatial context, the climatic and physico-chemical basic conditions, and the intricate bio-geochemical processes that govern nutrient retention, transformation, and transport. Specifically, we suggest a step-wise approach to custom VFS designs that links and matches the incoming P from event to multi-annual timescales from the short- and mid-term processes of P retention in the effective soil volume and to the longer-term P retention and offtake coupled to the soil-vegetation system. An a priori assessment of the P export potential should be followed by bespoke VFS designs, in line with local conditions and socio-economic and ecological constraints. To cope with increasingly nutrient saturated or functionally insufficient VFS installed over the last decades, concepts and management strategies need to encompass the transition in understanding of VFS as simple nutrient containers to multifunctional buffer zones that have a complex inner life. We need to address these associated emerging challenges and integrate their implications more thoroughly into VFS research, monitoring, policy, and implementation than ever before. Only then we may get VFS that are effective, sustainable, and persistent.The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.
", "keywords": ["0301 basic medicine", "Evolutionary Biology", "0303 health sciences", "Genome", "Fungi", "Computational Biology", "Eukaryota", "Genomics", "Article", "Workflow", "Evolutionsbiologi", "03 medical and health sciences", "13. Climate action", "Algorithms"]}, "links": [{"href": "https://www.nature.com/articles/s41598-020-58025-3.pdf"}, {"href": "https://doi.org/10.1038/s41598-020-58025-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-020-58025-3", "name": "item", "description": "10.1038/s41598-020-58025-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-020-58025-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-28T00:00:00Z"}}, {"id": "10.1039/d2ee00597b", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:17:40Z", "type": "Journal Article", "created": "2022-05-30", "title": "A plant-like battery: a biodegradable power source ecodesigned for precision agriculture", "description": "A biodegradable battery inspired by the transpiration pull of liquids in plants has been ecodesigned to power wireless sensors and then be safely biodegraded or composted, resembling the way a plant comes back to nature at the end of its lifecycle.
", "keywords": ["GREAT-4PA", "Chemistry", "Evaporation Flow Redox Battery", "13. Climate action", "Biodegradable battery", "Precision Agriculture", "02 engineering and technology", "Marie Sk\u0142odowska-Curie Postodoctoral Fellowship", "0204 chemical engineering", "0210 nano-technology", "Wireless Sensor", "7. Clean energy"]}, "links": [{"href": "http://pubs.rsc.org/en/content/articlepdf/2022/EE/D2EE00597B"}, {"href": "https://doi.org/10.1039/d2ee00597b"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Energy%20%26amp%3B%20Environmental%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1039/d2ee00597b", "name": "item", "description": "10.1039/d2ee00597b", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1039/d2ee00597b"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10.1093/plcell/koac263", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:18:14Z", "type": "Journal Article", "created": "2022-08-26", "title": "Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress", "description": "AbstractWe present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.The metagenome analysis of complex environments with thousands of datasets, such as those in the Sequence Read Archive, requires substantial computational resources for it to be completed within a reasonable time frame. Efficient use of infrastructure is essential, and analyses must be fully reproducible with publicly available workflows to ensure transparency. Here, we introduce the Metagenomics-Toolkit, a scalable, data-agnostic workflow that automates the analysis of short and long metagenomic reads from Illumina and Oxford Nanopore Technology devices, respectively. The Metagenomics-Toolkit provides standard features such as quality control, assembly, binning, and annotation, along with unique capabilities including plasmid identification, recovery of unassembled microbial community members, and discovery of microbial interdependencies through dereplication, co-occurrence, and genome-scale metabolic modeling. Additionally, the Metagenomics-Toolkit includes a machine learning-optimized assembly step that adjusts peak RAM usage to match actual requirements, reducing the need for high-memory hardware. It can be executed on user workstations and includes optimizations for efficient cloud-based cluster execution. We compare the Metagenomics-Toolkit with five widely used metagenomics workflows and demonstrate its capabilities on 757 sewage metagenome datasets to investigate a possible sewage core microbiome. The Metagenomics-Toolkit is open source and available at https://github.com/metagenomics/metagenomics-tk.Wild bee populations are threatened by current agricultural practices in many parts of the world, which may put pollination services and crop yields at risk. Loss of pollination services can potentially be predicted by models that link bee abundances with landscape\uffe2\uff80\uff90scale land\uffe2\uff80\uff90use, but there is little knowledge on the degree to which these statistical models are transferable across time and space. This study assesses the transferability of models for wild bee abundance in a mass\uffe2\uff80\uff90flowering crop across space (from one region to another) and across time (from one year to another). The models used existing data on bumblebee and solitary bee abundance in winter oilseed rape fields, together with high\uffe2\uff80\uff90resolution land\uffe2\uff80\uff90use crop\uffe2\uff80\uff90cover and semi\uffe2\uff80\uff90natural habitats data, from studies conducted in five different regions located in four countries (Sweden, Germany, Netherlands and the UK), in three different years (2011, 2012, 2013). We developed a hierarchical model combining all studies and evaluated the transferability using cross\uffe2\uff80\uff90validation. We found that both the landscape\uffe2\uff80\uff90scale cover of mass\uffe2\uff80\uff90flowering crops and permanent semi\uffe2\uff80\uff90natural habitats, including grasslands and forests, are important drivers of wild bee abundance in all regions. However, while the negative effect of increasing mass\uffe2\uff80\uff90flowering crops on the density of the pollinators is consistent between studies, the direction of the effect of semi\uffe2\uff80\uff90natural habitat is variable between studies. The transferability of these statistical models is limited, especially across regions, but also across time. Our study demonstrates the limits of using statistical models in conjunction with widely available land\uffe2\uff80\uff90use crop\uffe2\uff80\uff90cover classes for extrapolating pollinator density across years and regions, likely in part because input variables such as cover of semi\uffe2\uff80\uff90natural habitats poorly capture variability in pollinator resources between regions and years.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Model predictions", "Transferability in ecology", "Brassica napus", "wild pollinators", "mass flowering crops", "15. Life on land", "Mass flowering crops", "", "transferability in ecology", "03 medical and health sciences", "Permanent seminatural habitats", "model predictions", "ddc:570", "permanent semi-natural habitats", "Wild pollinators"]}, "links": [{"href": "https://centaur.reading.ac.uk/95616/1/ecog.05308.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.05308"}, {"href": "https://doi.org/10.1111/ecog.05308"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecography", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/ecog.05308", "name": "item", "description": "10.1111/ecog.05308", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/ecog.05308"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-19T00:00:00Z"}}, {"id": "10.1111/1758-2229.12119", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-07-26T16:18:28Z", "type": "Journal Article", "created": "2013-11-04", "title": "Grazing Of Heterotrophic Flagellates On Viruses Is Driven By Feeding Behaviour", "description": "SummaryThe trophic interactions between viruses, bacteria and protists play a crucial role in structuring microbial communities and regulating nutrient and organic matter flux. Here, we show that the impact on viral density by heterotrophic flagellates is related to their feeding behaviour (feeding on sedimented particles \uffe2\uff80\uff93 Thaumatomonas coloniensis, filter feeding of suspended particles \uffe2\uff80\uff93 Salpingoeca sp., and actively searching raptorial feeding \uffe2\uff80\uff93 Goniomonas truncata). Phage MS2 was co\uffe2\uff80\uff90incubated with flagellates and the natural bacterial and viral community originating from the same groundwater habitats where the flagellates were isolated. Three complementary assays, i.e. flow cytometry, qPCR and plaque assay, were used for enumeration of total viruses, total MS2 phages, and free and infectious MS2, respectively, to provide insights into the grazing mechanisms of the flagellates on viruses. Phage MS2 was actively removed by the suspension feeders T.\uffe2\uff80\uff89coloniensis and Salpingoeca sp. in contrast with the actively raptoriale grazer G.\uffe2\uff80\uff89truncata. The decline of viral titre was demonstrated to be caused by ingestion rather than random absorption by both qPCR and locating protein fluorescently labelled MS2 inside the flagellates. Further, we indicate that phages can be used as a minor carbon source for flagellates. Collectively, these data demonstrate that eliminating viruses can be an important function of protists in microbial food webs, carbon cycling and potentially water quality control.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Viral Plaque Assay", "Viral Load", "Flow Cytometry", "Real-Time Polymerase Chain Reaction", "7. Clean energy", "Carbon", "6. Clean water", "03 medical and health sciences", "Cercozoa", "Cryptophyta", "Choanoflagellata", "Levivirus"]}, "links": [{"href": "https://doi.org/10.1111/1758-2229.12119"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1758-2229.12119", "name": "item", "description": "10.1111/1758-2229.12119", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1758-2229.12119"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-19T00:00:00Z"}}, {"id": "10.1111/2041-210X.14392", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:18:28Z", "type": "Journal Article", "created": "2024-08-07", "title": "Sap Flow Analyzer: A tool to standardize sap flow estimation and scaling to whole\u2010tree water use using the HFD method", "description": "Abstract
Sap flow measurements are fundamental to understanding water use in trees and could aid in predicting climate change effects on forest function. Deriving knowledge from such measurements requires empirical calibrations and upscaling methods to translate thermometric recordings to tree water use. Here, we developed a user\uffe2\uff80\uff90friendly open\uffe2\uff80\uff90source application, the Sap Flow Analyzer (SFA), which estimates sap flow rates and tree water use from the heat field deformation (HFD) instruments.
The SFA incorporates four key features to ensure maximum accuracy and reproducibility of sap flow estimates: diagnosis diagrams to assess data patterns visually, regression models implemented to increase accuracy when estimating K (the main HFD parameter), three approaches to upscale sap flow rates to whole\uffe2\uff80\uff90tree water use and visualization of the input parameters' uncertainty. Thirteen participants were given three raw datasets and assigned data processing tasks using the SFA user guide, from estimating sapwood depth to scaling sap flow rates to whole\uffe2\uff80\uff90tree water use to assess the reproducibility and applicability of the SFA.
Participants' results were reasonably consistent and independent of their background in using the SFA, R, or HFD method. The results showed lower variability for high flow rates (SD: mean 1% vs. 10%). K estimates and sapwood depth differentiation were the primary sources of variability, which in turn was mainly caused by the user's chosen scaling method.
The SFA provides an easy way to visualize and process sap flow and tree water use data from HFD measurements. It is the first free and open software tool for HFD users. The ability to trace analysis steps ensures reproducibility, increasing transparency and consistency in data processing. Developing tools such as the SFA and masked trials are essential for more precise workflows and improved quality and comparability of HFD sap flow datasets.
Sap flow measurements are fundamental to understanding water use in trees and could aid in predicting climate change effects on forest function. Deriving knowledge from such measurements requires empirical calibrations and upscaling methods to translate thermometric recordings to tree water use. Here, we developed a user\uffe2\uff80\uff90friendly open\uffe2\uff80\uff90source application, the Sap Flow Analyzer (SFA), which estimates sap flow rates and tree water use from the heat field deformation (HFD) instruments.
The SFA incorporates four key features to ensure maximum accuracy and reproducibility of sap flow estimates: diagnosis diagrams to assess data patterns visually, regression models implemented to increase accuracy when estimating K (the main HFD parameter), three approaches to upscale sap flow rates to whole\uffe2\uff80\uff90tree water use and visualization of the input parameters' uncertainty. Thirteen participants were given three raw datasets and assigned data processing tasks using the SFA user guide, from estimating sapwood depth to scaling sap flow rates to whole\uffe2\uff80\uff90tree water use to assess the reproducibility and applicability of the SFA.
Participants' results were reasonably consistent and independent of their background in using the SFA, R, or HFD method. The results showed lower variability for high flow rates (SD: mean 1% vs. 10%). K estimates and sapwood depth differentiation were the primary sources of variability, which in turn was mainly caused by the user's chosen scaling method.
The SFA provides an easy way to visualize and process sap flow and tree water use data from HFD measurements. It is the first free and open software tool for HFD users. The ability to trace analysis steps ensures reproducibility, increasing transparency and consistency in data processing. Developing tools such as the SFA and masked trials are essential for more precise workflows and improved quality and comparability of HFD sap flow datasets.
Extreme weather events can have strong negative impacts on species survival and community structure when surpassing lethal thresholds. Extreme, short\uffe2\uff80\uff90lived, winter warming events in the Arctic rapidly melt snow and expose ecosystems to unseasonably warm air (for instance, 2\uffe2\uff80\uff9310\uffe2\uff80\uff83\uffc2\uffb0C for 2\uffe2\uff80\uff9314 days) but upon return to normal winter climate exposes the ecosystem to much colder temperatures due to the loss of insulating snow. Single events have been shown to reduce plant reproduction and increase shoot mortality, but impacts of multiple events are little understood as are the broader impacts on community structure, growth, carbon balance, and nutrient cycling. To address these issues, we simulated week\uffe2\uff80\uff90long extreme winter warming events \uffe2\uff80\uff93 using infrared heating lamps and soil warming cables \uffe2\uff80\uff93 for 3 consecutive years in a sub\uffe2\uff80\uff90Arctic heathland dominated by the dwarf shrubsEmpetrum hermaphroditum, Vaccinium vitis\uffe2\uff80\uff90idaea(both evergreen) andVaccinium myrtillus(deciduous). During the growing seasons after the second and third winter event, spring bud burst was delayed by up to a week forE. hermaphroditumandV. myrtillus, and berry production reduced by 11\uffe2\uff80\uff9375% and 52\uffe2\uff80\uff9395% forE. hermaphroditumandV. myrtillus, respectively. Greater shoot mortality occurred inE. hermaphroditum(up to 52%),V. vitis\uffe2\uff80\uff90idaea(51%), andV. myrtillus(80%). Root growth was reduced by more than 25% but soil nutrient availability remained unaffected. Gross primary productivity was reduced by more than 50% in the summer following the third simulation. Overall, the extent of damage was considerable, and critically plant responses were opposite in direction to the increased growth seen in long\uffe2\uff80\uff90term summer warming simulations and the \uffe2\uff80\uff98greening\uffe2\uff80\uff99 seen for some arctic regions. Given the Arctic is warming more in winter than summer, and extreme events are predicted to become more frequent, this generates large uncertainty in our current understanding of arctic ecosystem responses to climate change.", "keywords": ["flowering phenology", "0106 biological sciences", "extreme events", "climate change", "13. Climate action", "arctic", "winter warming", "nutrient cycling", "GPP", "15. Life on land", "dwarf shrub", "01 natural sciences", "SDG 15 - Life on Land"]}, "links": [{"href": "https://doi.org/10.1111/j.1365-2486.2011.02424.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1365-2486.2011.02424.x", "name": "item", "description": "10.1111/j.1365-2486.2011.02424.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-2486.2011.02424.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-04-13T00:00:00Z"}}, {"id": "10.1111/j.1654-1103.2012.01472.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:18:53Z", "type": "Journal Article", "created": "2012-08-23", "title": "Advanced Snowmelt Affects Vegetative Growth And Sexual Reproduction Of Vaccinium Myrtillus In A Sub-Alpine Heath", "description": "AbstractQuestionIn cold regions, snow cover duration is expected to decrease, especially in spring, as a consequence of climate warming. We investigated effects of changes in timing of snowmelt in relation to weather conditions on Vaccinium myrtillus, a dominant shrub in heath vegetation. We tested the hypothesis that advanced snowmelt will enhance shrub growth in years with few frosts, but will reduce shrub growth in years with frequent frosts.
LocationA sub\uffe2\uff80\uff90alpine heath in the Northern Apennines (Italy).
MethodsWe carried out two experiments. In the main experiment, snow was added to (+S) or removed from (\uffe2\uff88\uff92S) experimental plots in spring of three growing seasons (2004\uffe2\uff80\uff932006), with a mean delay in snowmelt timing of about 2\uffc2\uffa0wk from \uffe2\uff88\uff92S to +S. In a companion experiment, we simulated a freezing event in late spring 2004.
ResultsDuring the snowmelt period, the \uffe2\uff88\uff92S plants experienced 6\uffe2\uff80\uff9310 more frost events, compared with +S and unmanipulated controls (C) in 2004 and 2005, but not in 2006. In the first 2\uffc2\uffa0yr leaf production, leaf expansion and flowering were all significantly reduced in the \uffe2\uff88\uff92S plants, while shoot elongation was unaffected. In the companion experiment with artificial frost V.\uffc2\uffa0myrtillus presented similar responses. Conversely, the manipulations of snow did not affect either the hydric or nutrient status of plants and soils.
ConclusionsThe results overall support our hypothesis, as shown by the differing effects of snow depth and timing of melt on V.\uffc2\uffa0myrtillus in the 3\uffc2\uffa0yr. Spring frost was the cause of reduced growth and reduced flower production in 2004 and 2005. However, advanced snowmelt will not decrease the cover of this dominant species. Therefore, the structure and species dominance patterns in sub\uffe2\uff80\uff90alpine heath are not expected to change significantly in response to reduced snow cover. Support for this conclusion is provided by the capacity of V.\uffc2\uffa0myrtillus to recover vegetatively from frost injury through stimulated shoot elongation, and by the low importance of sexual reproduction for propagating dominant ericaceous shrubs in closed heath communities.
", "keywords": ["0106 biological sciences", "2. Zero hunger", "570", "13. Climate action", "C; 13; Climate change; Flowering; Frost; N; 15; Nutrient; Snow manipulation; Spring warming; Water;", "15. Life on land", "01 natural sciences"]}, "links": [{"href": "https://doi.org/10.1111/j.1654-1103.2012.01472.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Vegetation%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1654-1103.2012.01472.x", "name": "item", "description": "10.1111/j.1654-1103.2012.01472.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1654-1103.2012.01472.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-08-23T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:19:03Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACTDue to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s V = 0.857, and Theil\uffe2\uff80\uff99s U = 0.316). For species-level community profiling, we found strong correlations ( r s > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average r s = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.
IMPORTANCEA quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.
", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/10.1128/msystems.00859-24"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00859-24", "name": "item", "description": "10.1128/msystems.00859-24", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00859-24"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "10.1186/s12302-024-00873-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:19:12Z", "type": "Journal Article", "created": "2024-03-11", "title": "SWAT\u2009+\u2009input data preparation in a scripted workflow: SWATprepR", "description": "AbstractInput data collection, quality assurance and preparation are central but time_consuming steps in environmental modeling. Errors due to manual processing of model input data can result in an incorrect representation of an environmental system and may consequently lead to implausible model simulations. Correct input data preparation and thorough quality check at an early stage of the model setup procedure are essential to build confidence in model simulation results. Typically, in environmental model applications, many steps in the input data preparation phase have to be repeated with the inflow of new, additional or corrected data. In this study, we selected the widely used SWAT\uffe2\uff80\uff89+\uffe2\uff80\uff89ecohydrological model as an illustrative example to investigate challenges related to input data preparation. To assist in these tasks, we developed an R package named SWATprepR, which provides functions for typical and repeating SWAT\uffe2\uff80\uff89+\uffe2\uff80\uff89model input data preparation tasks. The package supports the preparation of weather input files, atmospheric deposition, soil parameters, crop rotations, and observed (control or calibration) data, to name a few, presently with focus on European applications. The SWATprepR functions are integrated in R script workflows and can help SWAT\uffe2\uff80\uff89+\uffe2\uff80\uff89modelers to avoid repetitive tasks, secure reproducibility and transparently document the data processing steps. Application of the package is illustrated with a test case of a SWAT\uffe2\uff80\uff89+\uffe2\uff80\uff89model for a small catchment in central Poland.
A community effort is needed to move soil modeling forward.
Establishing an international soil modeling consortium is key in this respect.
There is a need to better integrate existing knowledge in soil models.
Integration of data and models is a key challenge in soil modeling.
The remarkable complexity of soil and its importance to a wide range of ecosystem services presents major challenges to the modeling of soil processes. Although major progress in soil models has occurred in the last decades, models of soil processes remain disjointed between disciplines or ecosystem services, with considerable uncertainty remaining in the quality of predictions and several challenges that remain yet to be addressed. First, there is a need to improve exchange of knowledge and experience among the different disciplines in soil science and to reach out to other Earth science communities. Second, the community needs to develop a new generation of soil models based on a systemic approach comprising relevant physical, chemical, and biological processes to address critical knowledge gaps in our understanding of soil processes and their interactions. Overcoming these challenges will facilitate exchanges between soil modeling and climate, plant, and social science modeling communities. It will allow us to contribute to preserve and improve our assessment of ecosystem services and advance our understanding of climate\uffe2\uff80\uff90change feedback mechanisms, among others, thereby facilitating and strengthening communication among scientific disciplines and society. We review the role of modeling soil processes in quantifying key soil processes that shape ecosystem services, with a focus on provisioning and regulating services. We then identify key challenges in modeling soil processes, including the systematic incorporation of heterogeneity and uncertainty, the integration of data and models, and strategies for effective integration of knowledge on physical, chemical, and biological soil processes. We discuss how the soil modeling community could best interface with modern modeling activities in other disciplines, such as climate, ecology, and plant research, and how to weave novel observation and measurement techniques into soil models. We propose the establishment of an international soil modeling consortium to coherently advance soil modeling activities and foster communication with other Earth science disciplines. Such a consortium should promote soil modeling platforms and data repository for model development, calibration and intercomparison essential for addressing contemporary challenges.