{"type": "FeatureCollection", "features": [{"id": "10.1007/s00442-007-0750-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:15:42Z", "type": "Journal Article", "created": "2007-05-09", "title": "Mangrove Growth In New Zealand Estuaries: The Role Of Nutrient Enrichment At Sites With Contrasting Rates Of Sedimentation", "description": "Mangrove forest coverage is increasing in the estuaries of the North Island of New Zealand, causing changes in estuarine ecosystem structure and function. Sedimentation and associated nutrient enrichment have been proposed to be factors leading to increases in mangrove cover, but the relative importance of each of these factors is unknown. We conducted a fertilization study in estuaries with different sedimentation histories in order to determine the role of nutrient enrichment in stimulating mangrove growth and forest development. We expected that if mangroves were nutrient-limited, nutrient enrichment would lead to increases in mangrove growth and forest structure and that nutrient enrichment of trees in our site with low sedimentation would give rise to trees and sediments that converged in terms of functional characteristics on control sites in our high sedimentation site. The effects of fertilizing with nitrogen (N) varied among sites and across the intertidal zone, with enhancements in growth, photosynthetic carbon gain, N resorption prior to leaf senescence and the leaf area index of canopies being significantly greater at the high sedimentation sites than at the low sedimentation sites, and in landward dwarf trees compared to seaward fringing trees. Sediment respiration (CO(2) efflux) was higher at the high sedimentation site than at the low one sedimentation site, but it was not significantly affected by fertilization, suggesting that the high sedimentation site supported greater bacterial mineralization of sediment carbon. Nutrient enrichment of the coastal zone has a role in facilitating the expansion of mangroves in estuaries of the North Island of New Zealand, but this effect is secondary to that of sedimentation, which increases habitat area and stimulates growth. In estuaries with high sediment loads, enrichment with N will cause greater mangrove growth and further changes in ecosystem function.", "keywords": ["nutrient resorption efficiency", "Whangapoua", "0106 biological sciences", "Geologic Sediments", "Nitrogen", "Performance", "soil respiration", "01 natural sciences", "Rhizophora-mangle", "C1", "Oxygen Consumption", "Plant-growth", "Herbivory", "Photosynthesis", "Deposition", "Ecosystem", "580", "photosynthesis", "Avicenna marina", "Ecology", "leaf area index", "Plant Stems", "Phosphorus", "Soil respiration", "Limitation", "15. Life on land", "Carbon", "Plant Leaves", "Leaf area index", "770400 Coastal and Estuarine Environment", "Nutrient resorption efficiency", "Waikopua", "Avicennia", "Seasons", "270402 Plant Physiology", "New Zealand"]}, "links": [{"href": "https://doi.org/10.1007/s00442-007-0750-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-007-0750-y", "name": "item", "description": "10.1007/s00442-007-0750-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-007-0750-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-05-10T00:00:00Z"}}, {"id": "10.1007/s00442-002-1117-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:15:41Z", "type": "Journal Article", "created": "2014-12-22", "title": "Nitrogen Limitation Of Growth And Nutrient Dynamics In A Disturbed Mangrove Forest, Indian River Lagoon, Florida", "description": "The objectives of this study were to determine effects of nutrient enrichment on plant growth, nutrient dynamics, and photosynthesis in a disturbed mangrove forest in an abandoned mosquito impoundment in Florida. Impounding altered the hydrology and soil chemistry of the site. In 1997, we established a factorial experiment along a tree-height gradient with three zones, i.e., fringe, transition, dwarf, and three fertilizer treatment levels, i.e., nitrogen (N), phosphorus (P), control, in Mosquito Impoundment 23 on the eastern side of Indian River. Transects traversed the forest perpendicular to the shoreline, from a Rhizophora mangle-dominated fringe through an Avicennia germinans stand of intermediate height, and into a scrub or dwarf stand of A. germinans in the hinterland. Growth rates increased significantly in response to N fertilization. Our growth data indicated that this site is N-limited along the tree-height gradient. After 2 years of N addition, dwarf trees resembled vigorously growing saplings. Addition of N also affected internal dynamics of N and P and caused increases in rates of photosynthesis. These findings contrast with results for a R. mangle-dominated forest in Belize where the fringe is N-limited, but the dwarf zone is P-limited and the transition zone is co-limited by N and P. This study demonstrated that patterns of nutrient limitation in mangrove ecosystems are complex, that not all processes respond similarly to the same nutrient, and that similar habitats are not limited by the same nutrient when different mangrove forests are compared.", "keywords": ["0106 biological sciences", "Leaves", "Nitrogen", "Fresh-water", "Electron-transport", "01 natural sciences", "Rhizophora-mangle", "Trees", "Sediments", "Random Allocation", "Soil", "Plant-growth", "0502 Environmental Science and Management", "phosphorus", "Photosynthesis", "Vs. Phosphorus Limitation", "Patterns", "Ecosystem", "disturbance", "580", "photosynthesis", "Ecology", "experiment", "Phosphorus", "15. Life on land", "Belize", "Use Efficiency", "Plant Leaves", "fertilization", "Florida", "resorption", "Gradient", "Avicennia"]}, "links": [{"href": "https://doi.org/10.1007/s00442-002-1117-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-002-1117-z", "name": "item", "description": "10.1007/s00442-002-1117-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-002-1117-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-01-08T00:00:00Z"}}, {"id": "10.1007/s00442-012-2484-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:15:43Z", "type": "Journal Article", "created": "2012-12-27", "title": "Herbivore Trampling As An Alternative Pathway For Explaining Differences In Nitrogen Mineralization In Moist Grasslands", "description": "Studies addressing the role of large herbivores on nitrogen cycling in grasslands have suggested that the direction of effects depends on soil fertility. Via selection for high quality plant species and input of dung and urine, large herbivores have been shown to speed up nitrogen cycling in fertile grassland soils while slowing down nitrogen cycling in unfertile soils. However, recent studies show that large herbivores can reduce nitrogen mineralization in some temperate fertile soils, but not in others. To explain this, we hypothesize that large herbivores can reduce nitrogen mineralization in loamy or clay soils through soil compaction, but not in sandy soils. Especially under wet conditions, strong compaction in clay soils can lead to periods of soil anoxia, which reduces decomposition of soil organic matter and, hence, N mineralization. In this study, we use a long-term (37-year) field experiment on a salt marsh to investigate the hypothesis that the effect of large herbivores on nitrogen mineralization depends on soil texture. Our results confirm that the presence of large herbivores decreased nitrogen mineralization rate in a clay soil, but not in a sandy soil. By comparing a hand-mown treatment with a herbivore-grazed treatment, we show that these differences can be attributed to herbivore-induced changes in soil physical properties rather than to above-ground biomass removal. On clay soil, we find that large herbivores increase the soil water-filled porosity, induce more negative soil redox potentials, reduce soil macrofauna abundance, and reduce decomposition activity. On sandy soil, we observe no changes in these variables in response to grazing. We conclude that effects of large herbivores on nitrogen mineralization cannot be understood without taking soil texture, soil moisture, and feedbacks through soil macrofauna into account.", "keywords": ["0106 biological sciences", "IMPACT", "Nitrogen", "01 natural sciences", "Soil fauna", "COMPACTION", "Soil", "SOIL PHYSICAL-PROPERTIES", "SALT-MARSH", "Large herbivores", "Soil texture", "Animals", "Biomass", "Herbivory", "Soil compaction", "Ecosystem", "2. Zero hunger", "UNGULATE", "national", "Water", "DENITRIFICATION", "Nitrogen Cycle", "15. Life on land", "N cycling", "YELLOWSTONE-NATIONAL-PARK", "PLANT-GROWTH", "13. Climate action", "ECOSYSTEM", "Clay", "Aluminum Silicates", "Soil moisture", "BAIT-LAMINA TEST"]}, "links": [{"href": "https://doi.org/10.1007/s00442-012-2484-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-012-2484-8", "name": "item", "description": "10.1007/s00442-012-2484-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-012-2484-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-12-28T00:00:00Z"}}, {"id": "10.1007/s11104-022-05508-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:16:26Z", "type": "Journal Article", "created": "2022-06-22", "title": "Harnessing belowground processes for sustainable intensification of agricultural systems", "description": "Abstract

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.The role of trees in the nitrous oxide (N2O) balance of boreal forests has been neglected despite evidence suggesting their substantial contribution. We measured seasonal changes in N2O fluxes from soil and stems of boreal trees in Finland, showing clear seasonality in stem N2O flux following tree physiological activity, particularly processes of CO2 uptake and release. Stem N2O emissions peak during\uffc2\uffa0the vegetation season, decrease rapidly in October, and remain low but significant to the annual totals during winter dormancy. Trees growing on dry soils even turn to consumption of\uffc2\uffa0N2O from the atmosphere during dormancy, thereby reducing their overall N2O emissions. At an\uffc2\uffa0annual scale, pine, spruce and birch are net N2O sources, with spruce being the strongest emitter. Boreal trees thus markedly contribute to the seasonal dynamics of ecosystem N2O exchange, and their species-specific contribution should be included into forest emission inventories.

", "keywords": ["EDDY COVARIANCE", "Science", "Nitrous Oxide", "NITROUS-OXIDE EMISSIONS", "Article", "CO2 EXCHANGE", "Trees", "CARBON-DIOXIDE", "Soil", "METHANE", "Taiga", "CH4 EMISSIONS", "SCOTS PINE", "Ecosystem", "Finland", "Plant Stems", "Atmosphere", "Q", "Forestry", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "FOREST", "Environmental sciences", "SOIL", "PLANT-GROWTH", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Seasons", "Methane"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-12976-y.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-12976-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-12976-y", "name": "item", "description": "10.1038/s41467-019-12976-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-12976-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-01T00:00:00Z"}}, {"id": "10.1055/s-2001-17730", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-06-25T16:20:37Z", "type": "Journal Article", "created": "2002-07-26", "title": "The Impact Of Sheep Grazing On Net Nitrogen Mineralization Rate In Two Temperate Salt Marshes", "description": "

Abstract: Nitrogen mineralization rate was studied in grazing trials with three different stocking rates (0, 3, 10 sheep ha\uffe2\uff80\uff901) in two man\uffe2\uff80\uff90made salt marshes, viz. a Puccinellia maritima\uffe2\uff80\uff90dominated low salt marsh and a high salt marsh dominated by Festuca rubra. Mineralization rates were derived from the amounts of mineral N which accumulated in situ during six\uffe2\uff80\uff90week incubation periods in tubes containing undisturbed soil cores from the upper 10 cm soil layer. The annual rates of net N mineralization were significantly higher in the better drained, high salt marsh (71 \uffe2\uff80\uff90 81 kg ha\uffe2\uff80\uff901 yr\uffe2\uff80\uff901) than in the low salt marsh (39 \uffe2\uff80\uff90 49 kg ha\uffe2\uff80\uff901 yr\uffe2\uff80\uff901). High amounts of belowground litter accumulated in the low salt marsh due to frequent water logging. Both N mineralization and nitrification rate were negatively correlated with soil water content. In the Puccinellia maritima salt marsh, grazing had neither an effect on N mineralization rates during any of the incubation periods nor on annual mineralization rates. In the Festuca rubra salt marsh, N mineralization rates increased earlier during spring at the intensively grazed site than at the moderately grazed and the ungrazed site. N mineralization and nitrification rates were significantly higher at the ungrazed site than at the intensively grazed site during the period of peak net N mineralization from the end of April until mid\uffe2\uff80\uff90June. Although sheep grazing affected the seasonal pattern of N mineralization in the high marsh, grazing did not affect the annual rate of net N mineralization.

", "keywords": ["2. Zero hunger", "0106 biological sciences", "LIMITATION", "seasonality", "SUCCESSION", "MICROBIAL BIOMASS", "15. Life on land", "grazing experiment", "01 natural sciences", "nitrification", "salt marsh", "zonation", "PSEUDOREPLICATION", "vegetation", "PLANT-GROWTH", "HERBIVORES", "ECOSYSTEM", "VEGETATION", "nitrogen mineralization"]}, "links": [{"href": "https://doi.org/10.1055/s-2001-17730"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1055/s-2001-17730", "name": "item", "description": "10.1055/s-2001-17730", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1055/s-2001-17730"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2001-09-01T00:00:00Z"}}, {"id": "10.3390/agronomy14122979", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-25T16:24:59Z", "type": "Journal Article", "created": "2024-12-16", "title": "Demonstrating Agroecological Practices in Potato Production with Conservation Tillage and Pseudomonas spp., Azotobacter spp., Bacillus spp. Bacterial Inoculants\u2014Evidence from Hungary", "description": "

This study explores agroecological practices designed to improve soil quality and crop yield in small-scale agriculture, focusing on soil inoculation with beneficial bacteria over conventional fertilizers. Conducted at the SZIA Agroecological Garden MATE in G\u00f6d\u00f6ll\u0151, Hungary, the research utilizes 12 plots to evaluate different conservation tillage methods, including minimum and no-tillage, with and without microbial inoculation. Commenced in 2022, this study centers on potato cultivation (Solanum tuberosum L.) and includes comprehensive chemical and physical analyses of soil and harvested potatoes, alongside continuous monitoring of growth. Statistical analysis using One-way Anova in R revealed p-values predominantly above 0.05, indicating no significant differences across most parameters, though variations in soil plasticity and pH (KCl) were noted. Results suggest that substantial treatmeent differences may require a longer observation period. Notably, plots with microbial inoculation exhibited higher harvest weights and tuber sizes compared to control plots. Additionally, trends and interactions were found between weed abundance, total harvest, and plant height. The findings indicate that the benefits of integrated agroecological practices, including conservation tillage, may take time to materialize, emphasizing the necessity for extended observation. This research lays the groundwork for future studies, underscoring the importance of patience in achieving improvements in soil health and crop quality through sustainable agricultural methods.

", "keywords": ["agroecology", "0106 biological sciences", "S", "biofertilizer", "no-tillage", "potato", "0401 agriculture", " forestry", " and fisheries", "Agriculture", "bioinoculant", "04 agricultural and veterinary sciences", "plant-growth-promoting bacteria", "01 natural sciences"]}, "links": [{"href": "https://doi.org/10.3390/agronomy14122979"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agronomy14122979", "name": "item", "description": "10.3390/agronomy14122979", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agronomy14122979"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-12-14T00:00:00Z"}}, {"id": "10.3389/fmicb.2020.562238", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:24:49Z", "type": "Journal Article", "created": "2020-09-22", "title": "The Free-Living Stage Growth Conditions of the Endophytic Fungus Serendipita indica May Regulate Its Potential as Plant Growth Promoting Microbe", "description": "Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica's phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2-20 g L-1 of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica's growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica's potential to promote plant growth: wheat growth promotion by the explorer phenotype was \u00b1 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.", "keywords": ["free-living stage", "symbiosis stage", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "fungal phenotype", "morphology", "physiology", "plant-growth-promoting-microbes", "15. Life on land", "Microbiology", "QR1-502"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2020.562238"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2020.562238", "name": "item", "description": "10.3389/fmicb.2020.562238", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2020.562238"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-22T00:00:00Z"}}, {"id": "10.3390/agronomy12040899", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-25T16:24:58Z", "type": "Journal Article", "created": "2022-04-08", "title": "Effects of Multi-Species Microbial Inoculants on Early Wheat Growth and Litterbag Microbial Activity", "description": "

The use of microbial consortia (MC) with complementing features is considered to be a promising method of sustainable crop intensification, potentially trumping the limited performance of single-strain applications. We assessed the effect of two novel MC on early wheat growth and litterbag microbial activity in heated and unheated soil. Pot experiments were carried out in duplicate in a greenhouse over 63 days using a completely randomized design with six replications. A range of parameters of plant growth and nutrient uptake were regularly assessed and statistically analyzed by ANOVA. The litterbag-NIRS method was used to trace the microbial activity. Averaged over both trials, soil heating resulted in a significant increase in shoot biomass (+53%) and subsequent nitrogen uptake (+307 mg N pot\u22121) but strongly reduced root development (\u221246%) compared with unheated soil. The application of MC had no effect on wheat growth in the heated soil. By contrast, in the unheated soil, shoot (+12%) and root (+15%) biomass and shoot nitrogen uptake (+11%) were significantly increased after double inoculation with MC compared with autoclaved MC. The litterbag-NIRS method confirmed clear effects of soil heating on microbial activity. Differences between MC application and the control were noted, indicating a buffering effect of MC.

", "keywords": ["2. Zero hunger", "Greenhouse", "S", "Litterbag-NIRS method", "microbial consortia inoculants", "plant-microbe interactions", "Agriculture", "04 agricultural and veterinary sciences", "Microbial consortia inoculants", "Plant-growth-promoting microorganisms", "plant-growth-promoting microorganisms; microbial consortia inoculants; microbial fertilizer; plant-microbe interactions; pot experiments; greenhouse; litterbag-NIRS method", "microbial fertilizer", "Pot experiments", "plant-growth-promoting microorganisms", "greenhouse", "0401 agriculture", " forestry", " and fisheries", "pot experiments", "Plant-microbe interactions", "Microbial fertilizer"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/12/4/899/pdf"}, {"href": "https://iris.enea.it/bitstream/20.500.12079/70987/1/Effects%20of%20Multi-Species%20Microbial%20Inoculants%20on%20Early%20Wheat%20Growth%20and%20Litterbag%20Microbial%20Activity.pdf"}, {"href": "https://www.mdpi.com/2073-4395/12/4/899/pdf"}, {"href": "https://doi.org/10.3390/agronomy12040899"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agronomy12040899", "name": "item", "description": "10.3390/agronomy12040899", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agronomy12040899"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-04-08T00:00:00Z"}}, {"id": "10.3390/genes10080601", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-25T16:25:06Z", "type": "Journal Article", "created": "2019-08-09", "title": "Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics", "description": "

The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.

", "keywords": ["COMPARATIVE GENOMICS", "0301 basic medicine", "570", "Antifungal Agents", "Plant-growth promotion", "Biolog\u00eda", "comparative genomics", "Phloroglucinol", "PLANT-GROWTH PROMOTION", "Article", "Rhizoctonia", "transcriptomics", "03 medical and health sciences", "https://purl.org/becyt/ford/1.6", "Genome mining", "Hydrogen Cyanide", "Pseudomonas", "genome mining", "RNA SEQUENCING", "TRANSCRIPTOMICS", "biocontrol", "GENOME MINING", "PSEUDOMONASBRASSICACEARUM", "https://purl.org/becyt/ford/1", "Transcriptomics", "0303 health sciences", "Comparative genomics", "Biocontrol", "RNA sequencing", "Pseudomonas brassicacearum", "BIOCONTROL", "Pseudomonas brassicacearum", "Biological Control Agents", "Genes", " Bacterial", "Transcriptome", "plant-growth promotion"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://doi.org/10.3390/genes10080601"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10080601", "name": "item", "description": "10.3390/genes10080601", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10080601"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-09T00:00:00Z"}}, {"id": "20.500.12079/70987", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-25T16:32:28Z", "type": "Journal Article", "created": "2022-04-08", "title": "Effects of Multi-Species Microbial Inoculants on Early Wheat Growth and Litterbag Microbial Activity", "description": "

The use of microbial consortia (MC) with complementing features is considered to be a promising method of sustainable crop intensification, potentially trumping the limited performance of single-strain applications. We assessed the effect of two novel MC on early wheat growth and litterbag microbial activity in heated and unheated soil. Pot experiments were carried out in duplicate in a greenhouse over 63 days using a completely randomized design with six replications. A range of parameters of plant growth and nutrient uptake were regularly assessed and statistically analyzed by ANOVA. The litterbag-NIRS method was used to trace the microbial activity. Averaged over both trials, soil heating resulted in a significant increase in shoot biomass (+53%) and subsequent nitrogen uptake (+307 mg N pot\u22121) but strongly reduced root development (\u221246%) compared with unheated soil. The application of MC had no effect on wheat growth in the heated soil. By contrast, in the unheated soil, shoot (+12%) and root (+15%) biomass and shoot nitrogen uptake (+11%) were significantly increased after double inoculation with MC compared with autoclaved MC. The litterbag-NIRS method confirmed clear effects of soil heating on microbial activity. Differences between MC application and the control were noted, indicating a buffering effect of MC.

", "keywords": ["2. Zero hunger", "Greenhouse", "S", "Litterbag-NIRS method", "microbial consortia inoculants", "plant-microbe interactions", "Agriculture", "04 agricultural and veterinary sciences", "Microbial consortia inoculants", "Plant-growth-promoting microorganisms", "plant-growth-promoting microorganisms; microbial consortia inoculants; microbial fertilizer; plant-microbe interactions; pot experiments; greenhouse; litterbag-NIRS method", "microbial fertilizer", "Pot experiments", "plant-growth-promoting microorganisms", "greenhouse", "0401 agriculture", " forestry", " and fisheries", "pot experiments", "Plant-microbe interactions", "Microbial fertilizer"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/12/4/899/pdf"}, {"href": "https://iris.enea.it/bitstream/20.500.12079/70987/1/Effects%20of%20Multi-Species%20Microbial%20Inoculants%20on%20Early%20Wheat%20Growth%20and%20Litterbag%20Microbial%20Activity.pdf"}, {"href": "https://www.mdpi.com/2073-4395/12/4/899/pdf"}, {"href": "https://doi.org/20.500.12079/70987"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.12079/70987", "name": "item", "description": "20.500.12079/70987", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.12079/70987"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-04-08T00:00:00Z"}}, {"id": "10451/49641", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:31:23Z", "type": "Journal Article", "created": "2020-09-22", "title": "The Free-Living Stage Growth Conditions of the Endophytic Fungus Serendipita indica May Regulate Its Potential as Plant Growth Promoting Microbe", "description": "Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica's phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2-20 g L-1 of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica's growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica's potential to promote plant growth: wheat growth promotion by the explorer phenotype was \u00b1 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.", "keywords": ["free-living stage", "symbiosis stage", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "fungal phenotype", "morphology", "physiology", "plant-growth-promoting-microbes", "15. Life on land", "Microbiology", "QR1-502"]}, "links": [{"href": "https://repositorio.ulisboa.pt/bitstream/10451/49641/1/Dias%20et%20al%202020%20-The%20Free-Living%20Stage%20Growth%20Conditions%20of%20the%20Endophytic%20Fungus%20Serendipita%20indica.pdf"}, {"href": "https://doi.org/10451/49641"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10451/49641", "name": "item", "description": "10451/49641", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10451/49641"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-22T00:00:00Z"}}, {"id": "11336/151981", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-25T16:31:39Z", "type": "Journal Article", "created": "2019-08-09", "title": "Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics", "description": "

The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.

", "keywords": ["COMPARATIVE GENOMICS", "0301 basic medicine", "570", "Antifungal Agents", "Plant-growth promotion", "Biolog\u00eda", "comparative genomics", "Phloroglucinol", "PLANT-GROWTH PROMOTION", "Article", "Rhizoctonia", "12. Responsible consumption", "transcriptomics", "03 medical and health sciences", "https://purl.org/becyt/ford/1.6", "Genome mining", "Hydrogen Cyanide", "Pseudomonas", "genome mining", "RNA SEQUENCING", "TRANSCRIPTOMICS", "biocontrol", "GENOME MINING", "PSEUDOMONASBRASSICACEARUM", "https://purl.org/becyt/ford/1", "Transcriptomics", "2. Zero hunger", "0303 health sciences", "Comparative genomics", "Biocontrol", "RNA sequencing", "Pseudomonas brassicacearum", "3. Good health", "BIOCONTROL", "Pseudomonas brassicacearum", "Biological Control Agents", "Genes", " Bacterial", "Transcriptome", "plant-growth promotion"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://doi.org/11336/151981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11336/151981", "name": "item", "description": "11336/151981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11336/151981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-09T00:00:00Z"}}, {"id": "1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:32:02Z", "type": "Journal Article", "created": "2023-03-13", "title": "Finding optimal microorganisms to increase crop productivity and sustainability under drought \u2013 a structured reflection", "description": "ABSTRACTConsidering the more frequent and longer drought events due to climate change, improving plant drought tolerance became a priority. The search for plant growth promoting rhizobacteria (PGPR) able to improve plant drought tolerance has been long addressed, but with inconsistent results. Here, we summarize the PGPR mechanisms that improve plant drought tolerance, identify the pitfalls in current PGPR isolation and selection routines, and discuss the key points to define new strategies to get optimal PGPR for plant drought tolerance. Drought and host genotype impact rhizo-communities, and host-mediated selection strategies may be used to obtain a drought-adapted rhizomicrobiome that can be a source for PGPR isolation. Alternatively, an integrated omics-level analysis can improve our knowledge on the mechanisms of rhizomicrobiome construction, and a targeted approach can be designed, which will be focused on key PGP traits. New strategies to build PGPR consortia for improvement of plant drought tolerance are also suggested.", "keywords": ["2. Zero hunger", "Drought; PGPR isolation; PGPR screening; Plant- rhizomicrobiome interactions", "Drought", "MICROBIAL COMMUNITY", "BACILLUS-AMYLOLIQUEFACIENS", "PGPR screening", "Biology and Life Sciences", "Plant culture", "THERMOPHILIC BACTERIA", "15. Life on land", "Plant-rhizomicrobiome interactions", "6. Clean water", "SB1-1110", "PSEUDOMONAS-PUTIDA", "13. Climate action", "PLANT-GROWTH", "ARABIDOPSIS-THALIANA", "QK900-989", "WATER-STRESS", "Plant ecology", "ROOT COLONIZATION", "GROWTH-PROMOTING RHIZOBACTERIA", "GENE-EXPRESSION", "PGPR isolation"]}, "links": [{"href": "https://repositorio.ulisboa.pt/bitstream/10451/59998/1/Rosa%20et%20al%202023.pdf"}, {"href": "https://repositorio.ulisboa.pt/bitstream/10451/59563/1/Finding%20optimal%20microorganisms%20to%20increase%20crop%20productivity%20and%20sustainability%20under%20drought%20%20%20a%20structured%20reflection.pdf"}, {"href": "https://www.tandfonline.com/doi/pdf/10.1080/17429145.2023.2178680"}, {"href": "https://doi.org/1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Plant%20Interactions", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M", "name": "item", "description": "1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-12T00:00:00Z"}}, {"id": "PMC9579094", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:37:26Z", "type": "Journal Article", "created": "2022-06-22", "title": "Harnessing belowground processes for sustainable intensification of agricultural systems", "description": "Abstract

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.