Legume roots can be symbiotically colonized by arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria. In Lotus japonicus, the latter occurs intracellularly by the cognate rhizobial partner Mesorhizobium loti or intercellularly with the Agrobacterium pusense strain IRBG74. Although these symbiotic programs show distinctive cellular and transcriptome signatures, some molecular components are shared. In this study, we demonstrate that 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase 1 (DAHPS1), the first enzyme in the biosynthetic pathway of aromatic amino acids (AAAs), plays a critical role in root hair development and for AM and rhizobial symbioses in Lotus. Two homozygous DAHPS1 mutants (dahps1-1 and dahps1-2) showed drastic alterations in root hair morphology, associated with alterations in cell wall dynamics and a progressive disruption of the actin cytoskeleton. The altered root hair structure was prevented by pharmacological and genetic complementation. dahps1-1 and dahps1-2 showed significant reductions in rhizobial infection (intracellular and intercellular) and nodule organogenesis and a delay in AM colonization. RNAseq analysis of dahps1-2 roots suggested that these phenotypes are associated with downregulation of several cell wall\uffe2\uff80\uff93related genes, and with an attenuated signaling response. Interestingly, the dahps1 mutants showed no detectable pleiotropic effects, suggesting a more selective recruitment of this gene in certain biological processes. This work provides robust evidence linking AAA metabolism to root hair development and successful symbiotic associations.Forests provide important ecological, economic, and social services, and recent interest has emerged in the potential for using residue from timber harvest as a source of renewable woody bioenergy. The long\uffe2\uff80\uff90term consequences of such intensive harvest are unclear, particularly as forests face novel climatic conditions over the next century. We used a simulation model to project the long\uffe2\uff80\uff90term effects of management and climate change on above\uffe2\uff80\uff90 and belowground forest carbon storage in a watershed in northwestern Oregon. The multi\uffe2\uff80\uff90ownership watershed has a diverse range of current management practices, including little\uffe2\uff80\uff90to\uffe2\uff80\uff90no harvesting on federal lands, short\uffe2\uff80\uff90rotation clear\uffe2\uff80\uff90cutting on industrial land, and a mix of practices on private nonindustrial land. We simulated multiple management scenarios, varying the rate and intensity of harvest, combined with projections of climate change. Our simulations project a wide range of total ecosystem carbon storage with varying harvest rate, ranging from a 45% increase to a 16% decrease in carbon compared to current levels. Increasing the intensity of harvest for bioenergy caused a 2\uffe2\uff80\uff933% decrease in ecosystem carbon relative to conventional harvest practices. Soil carbon was relatively insensitive to harvest rotation and intensity, and accumulated slowly regardless of harvest regime. Climate change reduced carbon accumulation in soil and detrital pools due to increasing heterotrophic respiration, and had small but variable effects on aboveground live carbon and total ecosystem carbon. Overall, we conclude that current levels of ecosystem carbon storage are maintained in part due to substantial portions of the landscape (federal and some private lands) remaining unharvested or lightly managed.\uffc2\uffa0Increasing the intensity of harvest for bioenergy on currently harvested land, however,\uffc2\uffa0led to a relatively small reduction in the ability of forests to store carbon. Climate change is unlikely to substantially alter carbon storage in these forests, absent shifts in disturbance regimes.
", "keywords": ["0106 biological sciences", "Carbon dioxide mitigation", "Forest ecology -- Oregon -- Oregon Coast Range", "Forest biomass", "13. Climate action", "Carbon cycle (Biogeochemistry)", "Biomass energy", "Forest Biology", "15. Life on land", "01 natural sciences", "7. Clean energy", "Climatic change", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1111/gcbb.12255"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/GCB%20Bioenergy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/gcbb.12255", "name": "item", "description": "10.1111/gcbb.12255", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcbb.12255"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-05-25T00:00:00Z"}}, {"id": "10.2139/ssrn.5084742", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:18:44Z", "type": "Journal Article", "created": "2025-05-25", "title": "ZnO-nanostructured electrochemical sensor for efficient detection of glyphosate in water", "description": "Glyphosate is a widely used broad-spectrum herbicide for controlling grassy weeds, despite having potential health hazards. Herein, we report on a solid-state electrochemical sensor based on ZnO nanoparticles (ZnO NPs) for on-site detection of glyphosate. Accordingly, ZnO NPs was drop-cast on the surface of a disposable screen-printed carbon electrode. Eco-friendly ZnO NPs of only 7 nm crystallite sizes were obtained by green sol-gel synthesis using lemon (Citrus limon) waste aqueous extract as the green reducing and capping/stabilizing agent and Zn nitrate precursor as evidenced by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction and diffuse reflectance. SEM confirmed successful electrode functionalization with the synthesized nanoparticles. Under laboratory conditions in acetate buffer (pH 5), the sensor demonstrated excellent selectivity and sensitivity, with a detection limit of 0.648 \u00b5M, a wide linear detection range (0.5 \u00b5M to 7.5 mM), and a rapid detection time of 30 min. When tested in river water, the sensor achieved a detection limit of 0.96 \u00b5M using differential pulse voltammetry. It also exceptionally tolerated interference from similar organophosphorus compounds and ions commonly found in river water. The excellent detection performance of the sensor was attributed to the strong coordination interactions between Zn atoms and phosphonate/carboxylate groups that are enhanced by a hydrogen bond at acidic pH, as determined by chemical calculations. This disposable sensor offers a cost-effective, efficient, and environmentally friendly solution for monitoring glyphosate in water systems.", "keywords": ["QD71-142", "Environmental water", "Eco-friendly ZnO nanoparticles", "Computational modeling", "Pesticides", "Eco-friendly ZnO nanoparticles;", "[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology", "Analytical chemistry", "Sensor"]}, "links": [{"href": "https://doi.org/10.2139/ssrn.5084742"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Talanta%20Open", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2139/ssrn.5084742", "name": "item", "description": "10.2139/ssrn.5084742", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2139/ssrn.5084742"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-01-01T00:00:00Z"}}, {"id": "10.3389/fmicb.2016.01446", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:18:57Z", "type": "Journal Article", "created": "2016-09-14", "description": "Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.", "keywords": ["Soil nutrients", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "long-term fertilization", "microbial biomass", "15. Life on land", "microbial activity", "Microbiology", "QR1-502", "03 medical and health sciences", "13. Climate action", "soil microbial communities", "soil nutrients", "454 pyrosequencing"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2016.01446"}, {"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.2016.01446", "name": "item", "description": "10.3389/fmicb.2016.01446", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2016.01446"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-09-14T00:00:00Z"}}, {"id": "10.3389/fmicb.2019.02597", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:18:57Z", "type": "Journal Article", "created": "2019-11-08", "title": "New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni.", "description": "Some strains of Oenococcus oeni possess cinnamoyl esterase activity that can be relevant in the malolactic stage of wine production liberating hydroxycinnamic acids that are precursors of volatile phenols responsible for sensory faults. The objective of this study was to better understand the basis of the differential activity between strains. After initial screening, five commercial strains of O. oeni were selected, three were found to exhibit cinnamoyl esterase activity (CE+) and two not (CE-). Although the use of functional annotation of genes revealed genotypic variations between the strains, no specific genes common only to the three CE+ strains could explain the different activities. Pasteurized wine was used as a natural source of tartrate esters in growth and metabolism experiments conducted in MRS medium, whilst commercial trans-caftaric acid was used as substrate for enzyme assays. Detoxification did not seem to be the main biological mechanism involved in the activity since unlike its phenolic cleavage products and their immediate metabolites (trans-caffeic acid and 4-ethylcatechol), trans-caftaric acid was not toxic toward O. oeni. In the case of the two CE+ strains OenosTM and CiNeTM, wine-exposed samples showed a more rapid degradation of trans-caftaric acid than the unexposed ones. The CE activity was present in all cell-free extracts of both wine-exposed and unexposed strains, except in the cell-free extracts of the CE- strain CH11TM. This activity may be constitutive rather than induced by exposure to tartrate esters. Trans-caftaric acid was totally cleaved to trans-caffeic acid by cell-free extracts of the three CE+ strains, whilst cell-free extracts of the CE- strain CH16TM showed significantly lower activity, although higher for the strains in experiments with no prior wine exposure. The EstB28 esterase gene, found in the genomes of the 5 strains, did not reveal any difference on the upstream regulation and transport functionality between the strains. This study highlights the complexity of the basis of this activity in wine related O. oeni population. Variable cinnamoyl esterases or/and membrane transport activities in the O. oeni strains analyzed and a possible implication of wine molecules could explain this phenomenon.", "keywords": ["0301 basic medicine", "0303 health sciences", "tartrate esters", "cinnamoyl esterase", "Tartrate esters", "Hydroxycinnamic acids", "Wine", "hydroxycinnamic acids", "[SDV.IDA] Life Sciences [q-bio]/Food engineering", "Microbiology", "QR1-502", "03 medical and health sciences", "Cinnamoyl esterase", "wine", "Oenococcus oeni"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2019.02597"}, {"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.2019.02597", "name": "item", "description": "10.3389/fmicb.2019.02597", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2019.02597"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-08T00:00:00Z"}}, {"id": "10.3389/fmicb.2021.758395", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:18:57Z", "type": "Journal Article", "created": "2022-01-12", "title": "Fresh rumen liquid inoculant enhances the rumen microbial community establishment in pre-weaned dairy calves", "description": "The development of the functional rumen in calves involves a complex interplay between the host and host-related microbiome. Attempts to modulate rumen microbial community establishment may therefore have an impact on weaning success, calf health, and animal performance later in life. In this experiment, we aimed to elucidate how rumen liquid inoculum from an adult cow, provided to calves during the pre-weaning period, influences the establishment of rumen bacterial, archaeal, fungal, and ciliate protozoan communities in monozygotic twin calves (n = 6 pairs). The calves were divided into treatment (T-group) and control (C-group) groups, where the T-group received fresh rumen liquid as an oral inoculum during a 2\uffe2\uff80\uff938-week period. The C-group was not inoculated. The rumen microbial community composition was determined using bacterial and archaeal 16S ribosomal RNA (rRNA) gene, protozoal 18S rRNA gene, and fungal ITS1 region amplicon sequencing. Animal weight gain and feed intake were monitored throughout the experiment. The T-group tended to have a higher concentrate intake (Treatment: p < 0.08) and had a significantly higher weekly weight gain (Treatment: p < 0.05), but no significant difference in volatile fatty acid concentrations between the groups was observed. In the T-group, the inoculum stimulated the earlier establishment of mature rumen-related bacterial taxa, affecting significant differences between the groups until 6 weeks of age. The inoculum also increased the archaeal operational taxonomic unit (OTU) diversity (Treatment: p < 0.05) but did not affect the archaeal quantity. Archaeal communities differed significantly between groups until week 4 (p = 0.02). Due to the inoculum, ciliate protozoa were detected in the T-group in week 2, while the C-group remained defaunated until 6 weeks of age. In week 8, Eremoplastron dilobum was the dominant ciliate protozoa in the C-group and Isotricha sp. in the T-group, respectively. The Shannon diversity of rumen anaerobic fungi reduced with age (Week: p < 0.01), and community establishment was influenced by a change of diet and potential interaction with other rumen microorganisms. Our results indicate that an adult cow rumen liquid inoculum enhanced the maturation of bacterial and archaeal communities in pre-weaning calves\uffe2\uff80\uff99 rumen, whereas its effect on eukaryotic communities was less clear and requires further investigation.
", "keywords": ["0301 basic medicine", "570", "Anaerobic fungi", "microbiome establishment", "archaea", "Rumen function", "Microbiome manipulation", "Microbiology", "630", "Microbiome establishment", "ciliate protozoa", "03 medical and health sciences", "Dairy calf", "anaerobic fungi", "bacteria", "[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology", "2. Zero hunger", "0303 health sciences", "ta412", "Bacteria", "dairy calf", "Animal science", " dairy science", "Archaea", "Ciliate protozoa", "QR1-502", "rumen function", "[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology", "microbiome manipulation"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2021.758395"}, {"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.2021.758395", "name": "item", "description": "10.3389/fmicb.2021.758395", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2021.758395"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-12T00:00:00Z"}}, {"id": "10.3389/fmicb.2022.983823", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:18:58Z", "type": "Journal Article", "created": "2022-11-08", "title": "Long-term effects of early-life rumen microbiota modulation on dairy cow production performance and methane emissions", "description": "Rumen microbiota modulation during the pre-weaning period has been suggested as means to affect animal performance later in life. In this follow-up study, we examined the post-weaning rumen microbiota development differences in monozygotic twin-heifers that were inoculated (T-group) or not inoculated (C-group) (n\uffe2\uff80\uff89=\uffe2\uff80\uff894 each) with fresh adult rumen liquid during their pre-weaning period. We also assessed the treatment effect on production parameters and methane emissions of cows during their 1st lactation period. The rumen microbiota was determined by the 16S rRNA gene, 18S rRNA gene, and ITS1 amplicon sequencing. Animal weight gain and rumen fermentation parameters were monitored from 2 to 12\uffe2\uff80\uff89months of age. The weight gain was not affected by treatment, but butyrate proportion was higher in T-group in month 3 (p\uffe2\uff80\uff89=\uffe2\uff80\uff890.04). Apart from archaea (p\uffe2\uff80\uff89=\uffe2\uff80\uff890.084), the richness of bacteria (p\uffe2\uff80\uff89<\uffe2\uff80\uff890.0001) and ciliate protozoa increased until month 7 (p\uffe2\uff80\uff89=\uffe2\uff80\uff890.004) and anaerobic fungi until month 11 (p\uffe2\uff80\uff89=\uffe2\uff80\uff890.005). The microbiota structure, measured as Bray\uffe2\uff80\uff93Curtis distances, continued to develop until months 3, 6, 7, and 10, in archaea, ciliate protozoa, bacteria, and anaerobic fungi, respectively (for all: p\uffe2\uff80\uff89=\uffe2\uff80\uff890.001). Treatment or age \uffc3\uff97 treatment interaction had a significant (p\uffe2\uff80\uff89<\uffe2\uff80\uff890.05) effect on 18 bacterial, 2 archaeal, and 6 ciliate protozoan taxonomic groups, with differences occurring mostly before month 4 in bacteria, and month 3 in archaea and ciliate protozoa. Treatment stimulated earlier maturation of prokaryote community in T-group before month 4 and earlier maturation of ciliate protozoa at month 2 (Random Forest: 0.75\uffe2\uff80\uff89month for bacteria and 1.5\uffe2\uff80\uff89month for protozoa). No treatment effect on the maturity of anaerobic fungi was observed. The milk production and quality, feed efficiency, and methane emissions were monitored during cow\uffe2\uff80\uff99s 1st lactation. The T-group had lower variation in energy-corrected milk yield (p\uffe2\uff80\uff89<\uffe2\uff80\uff890.001), tended to differ in pattern of residual energy intake over time (p\uffe2\uff80\uff89=\uffe2\uff80\uff890.069), and had numerically lower somatic cell count throughout their 1st lactation period (p\uffe2\uff80\uff89=\uffe2\uff80\uff890.081), but no differences between the groups in methane emissions (g/d, g/kg DMI, or g/kg milk) were observed. Our results demonstrated that the orally administered microbial inoculant induced transient changes in early rumen microbiome maturation. In addition, the treatment may influence the later production performance, although the mechanisms that mediate these effects need to be further explored.
", "keywords": ["microbiome modulation", "0301 basic medicine", "570", "ta412", "microbiome establishment", "Heifer", "dairy cow", "Rumen function", "Animal science", " dairy science", "Microbiology", "630", "Microbiome modulation", "QR1-502", "rumen function", "Microbiome establishment", "03 medical and health sciences", "Dairy cow", "heifer"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2022.983823"}, {"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.2022.983823", "name": "item", "description": "10.3389/fmicb.2022.983823", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2022.983823"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-08T00:00:00Z"}}, {"id": "11585/996230", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:21:58Z", "type": "Journal Article", "created": "2023-10-10", "title": "Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities", "description": "The analysis of phospholipid fatty acids (PLFAs) is one of the most common methods used to quantify the abundance, and analyse the community structure, of soil microbes. The PLFA extraction method can yield two additional lipid fractions\u2014neutral lipids and glycolipids\u2014which potentially hold additional, valuable information on soil microbial communities. Yet its quantitative sensitivity on complete neutral lipid (NLFA) and glycolipid fatty acid (GLFA) profiles has never been validated. In this study we tested (i) if the high-throughput PLFA method can be expanded to concurrently extract complete NLFA and GLFA profiles, as well as sterols, (ii) whether taxonomic specificities of signature fatty acids are retained across the three lipid fractions in pure culture strains, and (iii) whether NLFAs and GLFAs allow soil-specific fingerprinting to the same extent as PLFA analysis. By adjusting the polarity of chloroform with 2% ethanol for solid phase extraction, pure lipid standards were fully fractionated into neutral lipids, glycolipids, and phospholipids. Sterols eluted in the neutral lipid fraction, and a betaine lipid co-eluted with phospholipids. We found consistent taxonomic specificities of fatty acid markers across the three lipid fractions by analysing pure culture extracts representative of soil microbes. Fatty acid profiles from soil extracts, however, showed stronger differences between PLFAs, NLFAs, and GLFAs than between soil types. This indicates that PLFAs and NLFAs signify different community properties (biomass vs. carbon storage, putatively), and that GLFAs are sensitive markers for community traits which behave differently than PLFAs. Although we consistently found high abundances of characteristic sterols in fungal extracts, the PLFA extraction method only yielded miniscule amounts of ergosterol from soil extracts. We argue that concomitant measurement of fatty acid profiles from all three lipid fractions is a low-effort and potentially information-rich addition to the PLFA method, and discuss its applicability for soil microbial community analyses.", "keywords": ["0301 basic medicine", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "15. Life on land", "Soil lipids", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "NLFA", "Ergosterol", "Ergosterol; GLFA; NLFA; Phospholipid fatty acids; Soil lipids", "Phospholipid fatty acid", "soil lipids", "Phospholipid fatty acids", "106022 Microbiology", "GLFA", "106026 Ecosystem research"]}, "links": [{"href": "https://doi.org/11585/996230"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11585/996230", "name": "item", "description": "11585/996230", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11585/996230"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "1854/LU-8732814", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:22:04Z", "type": "Journal Article", "created": "2021-11-09", "title": "Litter quality, mycorrhizal association, and soil properties regulate effects of tree species on the soil fauna community", "description": "Abstract Forest management, including selection of appropriate tree species to mitigate climate change and sustain biodiversity, requires a better understanding of factors that affect the composition of soil fauna communities. These communities are an integral part of the soil ecosystem and play an essential role in forest ecosystem functioning related to carbon and nitrogen cycling. Here, by performing a field study across six common gardens in Denmark, we evaluated the effects of tree species identity and mycorrhizal association (i.e., arbuscular mycorrhiza (AM) and ectomycorrhiza (ECM)) on soil fauna (meso- and macrofauna) taxonomic and functional community composition by using diversity, abundance, and biomass as proxies. We found that (1) tree species identity and mycorrhizal association both showed significant effects on soil fauna communities, but the separation between community characteristics in AM and ECM tree species was not entirely consistent; (2) total soil fauna abundance, biomass, as well as taxonomic and functional diversity were generally significantly higher under AM tree species, as well as lime, with higher litter quality (high N and base cation and low lignin:N ratio); (3) tree species significantly influenced the properties of litter, forest floor, and soil, among which litter and/or forest floor N, P, Ca, and Mg concentrations, soil pH, and soil moisture predominantly affected soil fauna abundance, biomass, and taxonomic and functional diversity. Our results from this multisite common garden experiment provide strong and consistent evidence of positive effects of tree species with higher litter quality on soil fauna communities in general, which helps to better understand the effects of tree species selection on soil biodiversity and its functions related to forest soil carbon sequestration.", "keywords": ["DECOMPOSITION", "EARTHWORMS", "Diversity", "PH", "FOREST FLOOR", "Common garden experiment", "Soil meso- and macrofauna", "DIVERSITY", "Biology and Life Sciences", "04 agricultural and veterinary sciences", "15. Life on land", "NITROGEN", "CARBON", "Taxonomic group", "FUNCTIONAL TRAITS", "Abundance", "13. Climate action", "Earth and Environmental Sciences", "Functional group", "0401 agriculture", " forestry", " and fisheries", "BIODIVERSITY", "ABUNDANCE", "Biomass"]}, "links": [{"href": "https://doi.org/1854/LU-8732814"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Geoderma", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1854/LU-8732814", "name": "item", "description": "1854/LU-8732814", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1854/LU-8732814"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-01T00:00:00Z"}}, {"id": "10.1016/j.eja.2021.126318", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:15:25Z", "type": "Journal Article", "created": "2021-06-05", "title": "Designing a model to investigate cropping systems aiming to control both parasitic plants and weeds", "description": "Abstract Branched broomrape (Phelipanche ramosa (L.) Pomel) is a parasitic plant, which causes severe yield losses in major crops worldwide. Because of its broad host range, including numerous non-parasitic weed species, the persistence of its seeds in the soil, and the poor efficiency of available management techniques, broomrape management is complex. The objective of the present paper was to develop a broomrape-dynamics model to support the design of management strategies combining multiple techniques aiming at long-term control of broomrape. Towards this goal, we developed a simulation model with formalisms and parameters based on data from our own experiments and the literature. This model called PheraSys combines 1) a demographic submodel to predict broomrape seed bank dynamics, 2) a trophic-relationships submodel to predict the effect of parasitism on crops and weeds, and 3) a submodel of weed dynamics in agroecosystems to predict the growth of crops and weeds from cropping techniques and pedoclimate. Thanks to an individual representation of each host plant, PheraSys is able to simulate complex heterogeneous canopies. This model can be used as a tool to test management strategies including crop mixtures and relying on biological regulations by weeds.", "keywords": ["[SDV.SA.AGRO] Life Sciences [q-bio]/Agricultural sciences/Agronomy", "0106 biological sciences", "2. Zero hunger", "Cropping systems", "Branched broomrape", "[SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy", "Biological regulation", "04 agricultural and veterinary sciences", "Phelipanche ramose", "15. Life on land", "Weed", "01 natural sciences", "630", "Modelling", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "0401 agriculture", " forestry", " and fisheries", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Agroecology", "PheraSys"]}, "links": [{"href": "https://doi.org/10.1016/j.eja.2021.126318"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/European%20Journal%20of%20Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.eja.2021.126318", "name": "item", "description": "10.1016/j.eja.2021.126318", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.eja.2021.126318"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-01T00:00:00Z"}}, {"id": "10.1002/ecm.1507", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:04Z", "type": "Journal Article", "created": "2022-01-09", "title": "Lessons learned from a long\u2010term irrigation experiment in a dry Scots pine forest: Impacts on traits and functioning", "description": "AbstractClimate change exposes ecosystems to strong and rapid changes in their environmental boundary conditions mainly due to the altered temperature and precipitation patterns. It is still poorly understood how fast interlinked ecosystem processes respond to altered environmental conditions, if these responses occur gradually or suddenly when thresholds are exceeded, and if the patterns of the responses will reach a stable state. We conducted an irrigation experiment in the Pfynwald, Switzerland from 2003\uffe2\uff80\uff932018. A naturally dry Scots pine (Pinus sylvestris L.) forest was irrigated with amounts that doubled natural precipitation, thus releasing the forest stand from water limitation. The aim of this study was to provide a quantitative understanding on how different traits and functions of individual trees and the whole ecosystem responded to increased water availability, and how the patterns and magnitudes of these responses developed over time. We found that the response magnitude, the temporal trajectory of responses, and the length of initial lag period prior to significant response largely varied across traits. We detected rapid and stronger responses from aboveground tree traits (e.g., tree\uffe2\uff80\uff90ring width, needle length, and crown transparency) compared to belowground tree traits (e.g., fine\uffe2\uff80\uff90root biomass). The altered aboveground traits during the initial years of irrigation increased the water demand and trees adjusted by increasing root biomass during the later years of irrigation, resulting in an increased survival rate of Scots pine trees in irrigated plots. The irrigation also stimulated ecosystem\uffe2\uff80\uff90level foliar decomposition rate, fungal fruit body biomass, and regeneration abundances of broadleaved tree species. However, irrigation did not promote the regeneration of Scots pine trees, which are reported to be vulnerable to extreme droughts. Our results provide extensive evidence that tree\uffe2\uff80\uff90 and ecosystem\uffe2\uff80\uff90level responses were pervasive across a number of traits on long\uffe2\uff80\uff90term temporal scales. However, after reaching a peak, the magnitude of these responses either decreased or reached a new stable state, providing important insights into how resource alterations could change the system functioning and its boundary conditions.Anthropogenic pressures on tropical forests are rapidly intensifying, but our understanding of their implications for biological diversity is still very limited, especially with regard to soil biota, and in particular soil bacterial communities. Here we evaluated bacterial community composition and diversity across a gradient of land use intensity in the eastern Amazon from undisturbed primary forest, through primary forests varyingly disturbed by fire, regenerating secondary forest, pasture, and mechanized agriculture. Soil bacteria were assessed by paired\uffe2\uff80\uff90end Illumina sequencing of 16S rRNA gene fragments (V4 region). The resulting sequences were clustered into operational taxonomic units (OTU) at a 97% similarity threshold. Land use intensification increased the observed bacterial diversity (both OTU richness and community heterogeneity across space) and this effect was strongly associated with changes in soil pH. Moreover, land use intensification and subsequent changes in soil fertility, especially pH, altered the bacterial community composition, with pastures and areas of mechanized agriculture displaying the most contrasting communities in relation to undisturbed primary forest. Together, these results indicate that tropical forest conversion impacts soil bacteria not through loss of diversity, as previously thought, but mainly by imposing marked shifts on bacterial community composition, with unknown yet potentially important implications for ecological functions and services performed by these communities.
", "keywords": ["Rios de composi\u00e7\u00e3o de comunidade bacteriana", "2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "550", "Bacteria", "Biodiversidade subterr\u00e2nea", "Agriculture", "Biodiversity", "Forests", "15. Life on land", "Below\u2010ground biodiversity", "High\u2010throughput sequencing", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Sequenciamento de alto rendimento", "Rivers of bacterial community composition", "Soil Microbiology"]}, "links": [{"href": "https://eprints.lancs.ac.uk/id/eprint/82660/1/de_Carvalho_et_al_2016_raw_pdf.pdf"}, {"href": "https://doi.org/10.1002/ecy.1513"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ecy.1513", "name": "item", "description": "10.1002/ecy.1513", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecy.1513"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-09-09T00:00:00Z"}}, {"id": "10.1002/etc.5400", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:05Z", "type": "Journal Article", "created": "2022-06-09", "title": "Arbuscular Mycorrhizal Fungi and the Need for a Meaningful Regulatory Plant Protection Product Testing Strategy", "description": "AbstractArbuscular mycorrhizal fungi (AMF) perform key soil ecosystem services and, because of their symbiotic relationship with plant roots, may be exposed to the plant protection products (PPPs) applied to soils and crops. In 2017, the European Food Safety Authority (EFSA) released a scientific opinion addressing the state of the science on risk assessment of PPPs for in-soil organisms, recommending the inclusion of AMF ecotoxicological testing in the PPP regulatory process. However, it is not clear how this can be implemented in a tiered, robust, and ecologically relevant manner. Through a critical review of current literature, we examine the recommendations made within the EFSA report and the methodologies available to integrate AMF into the PPP risk assessment and provide perspective and commentary on their agronomic and ecological relevance. We conclude that considerable research questions remain to be addressed prior to the inclusion of AMF into the in-soil organism risk assessment, many of which stem from the unique challenges associated with including an obligate symbiont within the PPP risk assessment. Finally, we highlight critical knowledge gaps and the further research required to enable development of relevant, reliable, and robust scientific tests alongside pragmatic and scientifically sound guidance to ensure that any future risk-assessment paradigm is adequately protective of the ecosystem services it aims to preserve. Environ Toxicol Chem 2022;41:1808\uffe2\uff80\uff931823. \uffc2\uffa9 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.Global warming is accompanied by increasing water stress across much of our planet. We studied soil biological processes and changes in soil organic carbon (SOC) storage in 30 Hungarian oak forest sites in the Carpathian Basin along a climatic gradient (mean annual temperature (MAT) 9.6\uffe2\uff80\uff9312.1\uffc2\uffa0\uffc2\uffb0C, mean annual precipitation (MAP) 545\uffe2\uff80\uff93725\uffc2\uffa0mm) but on similar gently sloped hillsides where the parent materials are loess and weathered dust inputs dating from the end of the ice age. The purpose of this research was to understand how a drying climate, predicted for this region, might regulate long-term SOC sequestration. To examine the effects of decreasing water availability, we compared soil parameters and processes in three categories of forest that represented the moisture extremes along our gradient and that were defined using a broken-stick regression model. Soil biological activity was significantly lower in the driest (\uffe2\uff80\uff9cdry\uffe2\uff80\uff9d) forests, which had more than double the SOC concentration in the upper 30\uffc2\uffa0cm layer (3.28\uffc2\uffa0g C/100\uffc2\uffa0g soil\uffe2\uff80\uff89\uffc2\uffb1\uffe2\uff80\uff890.11 SE) compared to soils of the wettest (\uffe2\uff80\uff9chumid\uffe2\uff80\uff9d) forests (1.32\uffc2\uffa0g C/100\uffc2\uffa0g soil\uffe2\uff80\uff89\uffc2\uffb1\uffe2\uff80\uff890.09 SE), despite the fact that annual surface litter production in humid forests was\uffe2\uff80\uff89~\uffe2\uff80\uff8937% higher than in dry forests. A two-pool SOM model constrained to fit radiocarbon data indicates that turnover times for fast and slow pools are about half as long in the humid soil compared to the dry soil, and humid soils transfer C twice as efficiently from fast to slow pools. Enzyme activity and fungal biomass data also imply shorter turnover times associated with faster degradation processes in the soils of humid forests. Thermogravimetry studies suggest that more chemically recalcitrant compounds are accumulating in the soils of dry forests. Taken together, our results suggest that the predicted climate drying in this region might increase SOC storage in Central European mesic deciduous forests even as litter production decreases.50% higher in the organic than the inorganic fertilizer-based system (P < 0.05). Crop yields in 2008 were generally lower in the low-input organic rotations than in the high-input inorganic fertilizer-based system; only spring barley in rotations with pig slurry application and incorporation of a catch crop prior to sowing obtained grain yields similar to levels achieved in the system where inorganic fertilizer was applied. These results suggest that within organic cropping systems, both microbial activity and crop yields could be enhanced through inclusion of catch crops. However, the timing of catch crop incorporation is critical.", "keywords": ["2. Zero hunger", "microbial biomass", "Nutrient turnover", "inorganic fertilizer", "15. Life on land", "potential ammonium oxidation", "Air and water emissions", "6. Clean water", "12. Responsible consumption", "denitrifier enzyme activity", "Soil biology", "/dk/atira/pure/core/keywords/Life", "13. Climate action", "potential mineralizable nitrogen", "catch drop", "gas diffusivity", "11. Sustainability", "Former LIFE faculty"]}, "links": [{"href": "https://doi.org/10.1016/j.agee.2010.10.001"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agriculture%2C%20Ecosystems%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.agee.2010.10.001", "name": "item", "description": "10.1016/j.agee.2010.10.001", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.agee.2010.10.001"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-12-01T00:00:00Z"}}, {"id": "10.1016/j.agrformet.2022.108823", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-09-20T16:15:06Z", "type": "Journal Article", "created": "2022-01-20", "title": "Timing leaf senescence : a generalized additive models for location, scale and shape approach", "description": "Accurate estimations of phenophases in deciduous trees are important to understand forest ecosystems and their feedback on the climate. In particular, the timing of leaf senescence is of fundamental importance to trees' nutrient stoichiometry and drought tolerance and therefore to trees' vigor and fecundity. Nevertheless, there is no integrated view on the significance, and direction, of seasonal trends in leaf senescence, especially for years characterized by extreme weather events. Difficulties in the acquisition and analyses of hierarchical data can account for this. We collected four years of chlorophyll content index (CCI) measurements in thirty-eight individuals of four deciduous tree species (Betula pendula, Fagus sylvatica, Populus tremula and Quercus robur) in Belgium, Norway and Spain, and analyzed these data using generalized additive models for location, scale and shape (GAMLSS). As a result, (I) the phenological strategy and seasonal trend of leaf senescence in these tree species could be clarified for exceptionally dry and warm years, and (II) the daily average (air) temperature, global radiation, and vapor pressure deficit could be established as main drivers behind the variation in the timing of the senescence transition date. Our results show that the onset of the re-organization phase in the leaf senescence, which we approximated and defined as local minima in the second derivative of a CCI graph, was in all species mainly negatively affected by the average temperature, global radiation and vapor pressure deficit. All together the variables explained 89 to 98% of the variability in the leaf senescence timing. An additional finding is that the generalized beta type 2 and generalized gamma distributions are well suited to model the chlorophyll content index, while the senescence transition date can be modeled using the normal-exponential-student-t, generalized gamma and zero-inflated Box-Cox Cole and Green distributions for beech, oak and birch, and poplar, respectively.", "keywords": ["0106 biological sciences", "Physics", "ta1183", "Silver birch", "15. Life on land", "01 natural sciences", "Generalized additive models for location", "Scale and shape", "European beech", "Pedunculate oak", "Chemistry", "Leaf senescence", "13. Climate action", "European aspen", "ta1181", "0101 mathematics", "Biology"]}, "links": [{"href": "https://doi.org/10.1016/j.agrformet.2022.108823"}, {"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.2022.108823", "name": "item", "description": "10.1016/j.agrformet.2022.108823", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.agrformet.2022.108823"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2011.08.031", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:15:19Z", "type": "Journal Article", "created": "2011-09-22", "title": "Impact Of Biochar Application To A Mediterranean Wheat Crop On Soil Microbial Activity And Greenhouse Gas Fluxes", "description": "Biochar has been recently proposed as a management strategy to improve crop productivity and global warming mitigation. However, the effect of such approach on soil greenhouse gas fluxes is highly uncertain and few data from field experiments are available. In a field trial, cultivated with wheat, biochar was added to the soil (3 or 6 kg m(-2)) in two growing seasons (2008/2009 and 2009/2010) so to monitor the effect of treatments on microbial parameters 3 months and 14 months after char addition. N(2)O, CH(4) and CO(2) fluxes were measured in the field during the first year after char addition. Biochar incorporation into the soil increased soil pH (from 5.2 to 6.7) and the rates of net N mineralization, soil microbial respiration and denitrification activity in the first 3 months, but after 14 months treated and control plots did not differ significantly. No changes in total microbial biomass and net nitrification rate were observed. In char treated plots, soil N(2)O fluxes were from 26% to 79% lower than N(2)O fluxes in control plots, excluding four sampling dates after the last fertilization with urea, when N(2)O emissions were higher in char treated plots. However, due to the high spatial variability, the observed differences were rarely significant. No significant differences of CH(4) fluxes and field soil respiration were observed among different treatments, with just few exceptions. Overall the char treatments showed a minimal impact on microbial parameters and GHG fluxes over the first 14 months after biochar incorporation.", "keywords": ["Crops", " Agricultural", "Greenhouse Effect", "Nitrous Oxide", "Biochar; CH; 4; CO; 2; Denitrification; N; 2; O; Nitrification;", "630", "12. Responsible consumption", "Fertilizers", "Soil Microbiology", "Triticum", "2. Zero hunger", "CH4", "Bacteria", "N2O", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "Nitrification", "6. Clean water", "Biochar", "13. Climate action", "Charcoal", "Denitrification", "0401 agriculture", " forestry", " and fisheries", "CO2", "Gases", "Methane", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2011.08.031"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2011.08.031", "name": "item", "description": "10.1016/j.chemosphere.2011.08.031", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2011.08.031"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-11-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2016.03.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:16:12Z", "type": "Journal Article", "created": "2016-03-26", "title": "Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland", "description": "
Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA. Microbial respiration was 28-37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland.
", "keywords": ["FUNGAL", "2. Zero hunger", "106022 Mikrobiologie", "Nitrogen addition", "BACTERIAL", "NITROGEN DEPOSITION", "GROWTH EFFICIENCY", "FOREST FLOOR", "Nutrients", "04 agricultural and veterinary sciences", "15. Life on land", "Stoichiometry", "ORGANIC-MATTER", "RESPIRATION", "106026 \u00d6kosystemforschung", "13. Climate action", "Nutrient limitation", "Microbial growth yield", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Mean residence time", "STOICHIOMETRIC CONTROLS", "ENZYME-ACTIVITY", "106026 Ecosystem research", "COMMUNITY STRUCTURE"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2016.03.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2016.03.008", "name": "item", "description": "10.1016/j.soilbio.2016.03.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2016.03.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2023.161600", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:16:02Z", "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": "10.1016/j.soilbio.2012.04.004", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:16:09Z", "type": "Journal Article", "created": "2012-04-23", "title": "Biochar But Not Earthworms Enhances Rice Growth Through Increased Protein Turnover", "description": "The aim of this work was to compare the effects of biochar and earthworms on rice growth and to investigate the possible interactions between both. In addition to classic macroscopic variables we also monitored some leaf-level cellular processes involved in protein turnover. Both biochar and earthworms significantly increased shoot biomass production. However, biochar had a higher effect on the number of leaves (\u00fe87%) and earthworms on leaf area (\u00fe89%). Biochar also significantly increased the leaf turnover. At the cellular level, biochar but not earthworms enhanced protein catabolism by an increase in leaf proteolytic activities. This could be related to the increased expression of three of the six genes tested related to protein catabolism, one serine protease gene OsSP2 (\u00fe24%), one aspartic acid protease gene, Oryzasin (\u00fe162%) and one cysteine protease gene OsCatB (\u00fe257%). Furthermore, biochar also enhanced the expression level of two genes linked to protein anabolism, coding for the small and large subunits of rubisco (\u00fe33% and \u00fe30%, for rbcS and rbcL, respectively), the most abundant protein in leaves. In conclusion, our data gives evidence that biochar increased rice biomass production through increased leaf protein turnover (both catabolism and anabolism) whereas earthworms also increased rice biomass production but not through changes in the rate of protein turnover. We hypothesize that earthworms increase nitrogen uptake at a low cost for the plant through a simultaneous increase in mineralization rate and root biomass, probably through the release in the soil of plant growth factors. This could allow plants to accumulate more biomass without an increase in nitrogen metabolism at the leaf level, and without having to support the consecutive energy cost that must bear plants in the biochar treatment. 2012 Elsevier Ltd. All rights reserved.", "keywords": ["0106 biological sciences", "0301 basic medicine", "earthworms", "FAUNE DU SOL", "7. Clean energy", "01 natural sciences", "03 medical and health sciences", "AZOTE", "PROTEINE", "CROISSANCE", "ETUDE COMPARATIVE", "lombriz de tierra", "2. Zero hunger", "BIOMASSE", "BIOCHAR", "biomass", "carbon", "microbiology", "MACROFAUNE", "CHARBON DE BOIS", "carbono", "RIZICULTURE", "biomasa", "oryza sativa", "METABOLISME", "FERTILISATION DU SOL", "carb\u00f3n vegetal", "LOMBRIC", "FEUILLE", "charcoal"], "contacts": [{"organization": "Kam-Rigne Laossi, Juan Andr\u00e9s Cardoso, Patrick Lavelle, Patrick Lavelle, Diana Cristina Noguera, Diana Cristina Noguera, Diana Cristina Noguera, M.H. Cruz de Carvalho, S\u00e9bastien Barot,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2012.04.004"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2012.04.004", "name": "item", "description": "10.1016/j.soilbio.2012.04.004", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2012.04.004"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-09-01T00:00:00Z"}}, {"id": "10.1111/j.1461-0248.2010.01570.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:40Z", "type": "Journal Article", "created": "2010-12-22", "title": "Enhanced Root Exudation Induces Microbial Feedbacks To N Cycling In A Pine Forest Under Long-Term Co2 Fumigation", "description": "Ecology Letters (2011) 14: 187\uffe2\uff80\uff93194
AbstractThe degree to which rising atmospheric CO2 will be offset by carbon (C) sequestration in forests depends in part on the capacity of trees and soil microbes to make physiological adjustments that can alleviate resource limitation. Here, we show for the first time that mature trees exposed to CO2 enrichment increase the release of soluble C from roots to soil, and that such increases are coupled to the accelerated turnover of nitrogen (N) pools in the rhizosphere. Over the course of 3\uffe2\uff80\uff83years, we measured in situ rates of root exudation from 420 intact loblolly pine (Pinus taeda L.) roots. Trees fumigated with elevated CO2 (200 p.p.m.v. over background) increased exudation rates (\uffce\uffbcg\uffe2\uff80\uff83C\uffe2\uff80\uff83cm\uffe2\uff88\uff921\uffe2\uff80\uff83root\uffe2\uff80\uff83h\uffe2\uff88\uff921) by 55% during the primary growing season, leading to a 50% annual increase in dissolved organic inputs to fumigated forest soils. These increases in root\uffe2\uff80\uff90derived C were positively correlated with microbial release of extracellular enzymes involved in breakdown of organic N (R2\uffe2\uff80\uff83=\uffe2\uff80\uff830.66; P\uffe2\uff80\uff83=\uffe2\uff80\uff830.006) in the rhizosphere, indicating that exudation stimulated microbial activity and accelerated the rate of soil organic matter (SOM) turnover. In support of this conclusion, trees exposed to both elevated CO2 and N fertilization did not increase exudation rates and had reduced enzyme activities in the rhizosphere. Collectively, our results provide field\uffe2\uff80\uff90based empirical support suggesting that sustained growth responses of forests to elevated CO2 in low fertility soils are maintained by enhanced rates of microbial activity and N cycling fuelled by inputs of root\uffe2\uff80\uff90derived C. To the extent that increases in exudation also stimulate SOM decomposition, such changes may prevent soil C accumulation in forest ecosystems.
", "keywords": ["0106 biological sciences", "Nitrogen", "Plant Exudates", "Pinus taeda", "04 agricultural and veterinary sciences", "15. Life on land", "Carbon Dioxide", "01 natural sciences", "Plant Roots", "Carbon", "Trees", "Soil", "13. Climate action", "Rhizosphere", "North Carolina", "0401 agriculture", " forestry", " and fisheries", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/j.1461-0248.2010.01570.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology%20Letters", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1461-0248.2010.01570.x", "name": "item", "description": "10.1111/j.1461-0248.2010.01570.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1461-0248.2010.01570.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-12-22T00:00:00Z"}}, {"id": "10.1016/j.envpol.2018.09.128", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:15:29Z", "type": "Journal Article", "created": "2018-09-28", "title": "A rationale for the high limits of quantification of antibiotic resistance genes in soil", "description": "The determination of values of abundance of antibiotic resistance genes (ARGs) per mass of soil is extremely useful to assess the potential impacts of relevant sources of antibiotic resistance, such as irrigation with treated wastewater or manure application. Culture-independent methods and, in particular, quantitative PCR (qPCR), have been regarded as suitable approaches for such a purpose. However, it is arguable if these methods are sensitive enough to measure ARGs abundance at levels that may represent a risk for environmental and human health. This study aimed at demonstrating the range of values of ARGs quantification that can be expected based on currently used procedures of DNA extraction and qPCR analyses. The demonstration was based on the use of soil samples spiked with known amounts of wastewater antibiotic resistant bacteria (ARB) (Enterococcus faecalis, Escherichia coli, Acinetobacter johnsonii, or Pseudomonas aeruginosa), harbouring known ARGs, and also on the calculation of expected values determined based on qPCR. The limits of quantification (LOQ) of the ARGs (vanA, qnrS, blaTEM, blaOXA, blaIMP, blaVIM) were observed to be approximately 4 log-units per gram of soil dry weight, irrespective of the type of soil tested. These values were close to the theoretical LOQ values calculated based on currently used DNA extraction methods and qPCR procedures. The observed LOQ values can be considered extremely high to perform an accurate assessment of the impacts of ARGs discharges in soils. A key message is that ARGs accumulation will be noticeable only at very high doses. The assessment of the impacts of ARGs discharges in soils, of associated risks of propagation and potential transmission to humans, must take into consideration this type of evidence, and avoid the simplistic assumption that no detection corresponds to risk absence.", "keywords": ["0301 basic medicine", "2. Zero hunger", "LOD - Limit of detection", "0303 health sciences", "Acinetobacter", "Drug Resistance", " Microbial", "Wastewater", "Real-Time Polymerase Chain Reaction", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "Manure", "Quantitative PCR", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "13. Climate action", "Pseudomonas aeruginosa", "Enterococcus faecalis", "Escherichia coli", "LOQ - Limit of quantification", "Soil Microbiology", "Risk assessment"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2018.09.128"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envpol.2018.09.128", "name": "item", "description": "10.1016/j.envpol.2018.09.128", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2018.09.128"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-01T00:00:00Z"}}, {"id": "10.1101/2023.06.28.546105", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:20Z", "type": "Journal Article", "created": "2023-06-29", "title": "Construction and Characterisation of a Structured, Tuneable, and Transparent 3D Culture Platform for Soil Bacteria", "description": "2.AbstractWe have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the metabolic profile of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms,Bacillus subtilisandStreptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of other difficult-to-culture bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as interaction, competition, and warfare.
3.Graphical AbstractA step-by-step method for creating a tailored 3D culture medium for study of soil microbes.
The complete workflow can be split into three parts: Growth and observation, metabolic profiling to provide a stable refractive index matching solution, and production of the 3D soil environment. The 3D culture scaffold was created by cryomilling Nafion\uffe2\uff84\uffa2 resin pellets and size filtration. Chemical processing altered the surface chemistry of Nafion\uffe2\uff84\uffa2 particles and facilitated nutrient binding by titration of a defined liquid culture medium. Metabolic profiling determined non-metabolisable sugars and provided an inert refractive index matching substrate, which was added to the final nutrient titration. Inoculation and growth of the test strain allowed for downstream assessment of colonisation behaviours and community dynamicsin situby, for example, optical microscopy.Measurements of nitrous oxide (N2O) emissions from agriculture are essential for understanding the complex soil\uffe2\uff80\uff93crop\uffe2\uff80\uff93climate processes, but there are practical and economic limits to the spatial and temporal extent over which measurements can be made. Therefore, N2O models have an important role to play. As models are comparatively cheap to run, they can be used to extrapolate field measurements to regional or national scales, to simulate emissions over long time periods, or to run scenarios to compare mitigation practices. Process\uffe2\uff80\uff90based models can also be used as an aid to understanding the underlying processes, as they can simulate feedbacks and interactions that can be difficult to distinguish in the field. However, when applying models, it is important to understand the conceptual process differences in models, how conceptual understanding changed over time in various models, and the model requirements and limitations to ensure that the model is well suited to the purpose of the investigation and the type of system being simulated. The aim of this paper is to give the reader a high\uffe2\uff80\uff90level overview of some of the important issues that should be considered when modeling. This includes conceptual understanding of widely used models, common modeling techniques such as calibration and validation, assessing model fit, sensitivity analysis, and uncertainty assessment. We also review examples of N2O modeling for different purposes and describe three commonly used process\uffe2\uff80\uff90based N2O models (APSIM, DayCent, and DNDC).The relationship between the spatial variability of soil multifunctionality (i.e., the capacity of soils to conduct multiple functions; SVM) and major climatic drivers, such as temperature and aridity, has never been assessed globally in terrestrial ecosystems. We surveyed 236 dryland ecosystems from six continents to evaluate the relative importance of aridity and mean annual temperature, and of other abiotic (e.g., texture) and biotic (e.g., plant cover) variables as drivers of SVM, calculated as the averaged coefficient of variation for multiple soil variables linked to nutrient stocks and cycling. We found that increases in temperature and aridity were globally correlated to increases in SVM. Some of these climatic effects on SVM were direct, but others were indirectly driven through reductions in the number of vegetation patches and increases in soil sand content. The predictive capacity of our structural equation\uffc2\uffa0modelling was clearly higher for the spatial variability of N\uffe2\uff80\uff90 than for C\uffe2\uff80\uff90 and P\uffe2\uff80\uff90related soil variables. In the case of N cycling, the effects of temperature and aridity were both direct and indirect via changes in soil properties. For C and P, the effect of climate was mainly indirect via changes in plant attributes. These results suggest that future changes in climate may decouple the spatial availability of these elements for plants and microbes in dryland soils. Our findings significantly advance our understanding of the patterns and mechanisms driving SVM in drylands across the globe, which is critical for predicting changes in ecosystem functioning in response to climate change.Recent studies have shown that invasive earthworms can dramatically reduce native biodiversity, both above and below the ground. However, we still lack a synthetic understanding of the underlying mechanisms behind these changes, such as whether earthworm effects on soil chemical properties drive such relationships. Here, we investigated the effects of invasive earthworms on soil chemical properties (pH, water content, and the stocks and fluxes of carbon, nitrogen, and phosphorus) by conducting a meta\uffe2\uff80\uff90analysis. Invasive earthworms generally increased soil pH, indicating that the removal of organic layers and the upward transport of more base\uffe2\uff80\uff90rich mineral soil caused a shift in soil pH. Moreover, earthworms significantly decreased soil water content, suggesting that the burrowing activities of earthworms may have increased water infiltration of and/or increased evapotranspiration from soil. Notably, invasive earthworms had opposing effects on organic and mineral soil for carbon and nitrogen stocks, with decreases in organic, and increases in mineral soil. Nitrogen fluxes were higher in mineral soil, whereas fluxes in organic soil were not significantly affected by the presence of invasive earthworms, indicating that earthworms mobilize and redistribute nutrients among soil layers and increase overall nitrogen loss from the soil. Invasive earthworm effects on element stocks increased with ecological group richness only in organic soil. Earthworms further decreased ammonium stocks with negligible effects on nitrate stocks in organic soil, whereas they increased nitrate stocks but not ammonium stocks in mineral soil. Notably, all of these results were consistent across forest and grassland ecosystems underlining the generality of our findings. However, we found some significant differences between studies that were conducted in the field (observational and experimental settings) and in the lab, such as that the effects on soil pH decreased from field to lab settings, calling for a careful interpretation of lab findings. Our meta\uffe2\uff80\uff90analysis provides strong empirical evidence that earthworm invasion may lead to substantial changes in soil chemical properties and element cycling in soil. Furthermore, our results can help explain the dramatic effects of invasive earthworms on native biodiversity, for example, shifts towards the dominance of grass species over herbaceous ones, as shown by recent meta\uffe2\uff80\uff90analyses.
", "keywords": ["Element flux", "Nitrogen", "Earthworm ecological group", "Forests", "Nitrate", "exotic earthworms", "Nutrient cycling", "nitrogen", "Article", "earthworm ecological group", "Soil", "nitrate", "Animals", "phosphorus", "soil carbon", "Oligochaeta", "Ecosystem", "Soil Microbiology", "water content", "Exotic earthworms", "2. Zero hunger", "Water content", "Plan_S-Compliant-TA", "pH", "nutrient cycling", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Nitrification", "Soil carbon", "nitrification", "ammonium", "13. Climate action", "international", "0401 agriculture", " forestry", " and fisheries", "element flux", "Ammonium"]}, "links": [{"href": "https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2936"}, {"href": "https://doi.org/10.1002/ecy.2936"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ecy.2936", "name": "item", "description": "10.1002/ecy.2936", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecy.2936"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-08T00:00:00Z"}}, {"id": "10.1002/biot.202000165", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-09-20T16:14:03Z", "type": "Journal Article", "created": "2020-10-21", "title": "Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates", "description": "AbstractGrowing environmental concern sparks renewed interest in the sustainable production of (bio)materials that can replace oil\uffe2\uff80\uff90derived goods. Polyhydroxyalkanoates (PHAs) are isotactic polymers that play a critical role in the central metabolism of producer bacteria, as they act as dynamic reservoirs of carbon and reducing equivalents. PHAs continue to attract industrial attention as a starting point toward renewable, biodegradable, biocompatible, and versatile thermoplastic and elastomeric materials. Pseudomonas species have been known for long as efficient biopolymer producers, especially for medium\uffe2\uff80\uff90chain\uffe2\uff80\uff90length PHAs. The surge of synthetic biology and metabolic engineering approaches in recent years offers the possibility of exploiting the untapped potential of Pseudomonas cell factories for the production of tailored PHAs. In this article, an overview of the metabolic and regulatory circuits that rule PHA accumulation in Pseudomonas putida is provided, and approaches leading to the biosynthesis of novel polymers (e.g., PHAs including nonbiological chemical elements in their structures) are discussed. The potential of novel PHAs to disrupt existing and future market segments is closer to realization than ever before. The review is concluded by pinpointing challenges that currently hinder the wide adoption of bio\uffe2\uff80\uff90based PHAs, and strategies toward programmable polymer biosynthesis from alternative substrates in engineered P. putida strains are proposed.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Biopolymer", "PHA", "Pseudomonas putida", "Polyhydroxyalkanoates", "Carbon", "12. Responsible consumption", "03 medical and health sciences", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "Metabolic Engineering", "Pseudomonas", "Pathway engineering", "Metabolic engineering", "Synthetic biology"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/biot.202000165"}, {"href": "https://doi.org/10.1002/biot.202000165"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biotechnology%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/biot.202000165", "name": "item", "description": "10.1002/biot.202000165", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/biot.202000165"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-09T00:00:00Z"}}, {"id": "10.1002/eap.1648", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:03Z", "type": "Journal Article", "created": "2017-11-07", "title": "Crop rotations for increased soil carbon: perenniality as a guiding principle", "description": "AbstractMore diverse crop rotations have been promoted for their potential to remediate the range of ecosystem services compromised by biologically simplified grain\uffe2\uff80\uff90based agroecosystems, including increasing soil organic carbon (SOC). We hypothesized that functional diversity offers a more predictive means of characterizing the impact of crop rotations on SOC concentrations than species diversity per se. Furthermore, we hypothesized that functional diversity can either increase or decrease SOC depending on its associated carbon (C) input to soil. We compiled a database of 27 cropping system sites and 169 cropping systems, recorded the species and functional diversity of crop rotations, SOC concentrations (g C kg/soil), nitrogen (N) fertilizer applications (kg\uffc2\uffa0N\uffc2\uffb7ha\uffe2\uff88\uff921\uffc2\uffb7yr\uffe2\uff88\uff921), and estimated C input to soil (Mg\uffc2\uffa0C\uffc2\uffb7ha\uffe2\uff88\uff921\uffc2\uffb7yr\uffe2\uff88\uff921). We categorized crop rotations into three broad categories: grain\uffe2\uff80\uff90only rotations, grain rotations with cover crops, and grain rotations with perennial crops. We divided the grain\uffe2\uff80\uff90only rotations into two sub\uffe2\uff80\uff90categories: cereal\uffe2\uff80\uff90only rotations and those that included both cereals and a legume grain. We compared changes in SOC and C input using mean effect sizes and 95% bootstrapped confidence intervals. Cover cropped and perennial cropped rotations, relative to grain\uffe2\uff80\uff90only rotations, increased C input by 42% and 23% and SOC concentrations by 6.3% and 12.5%, respectively. Within grain\uffe2\uff80\uff90only rotations, cereal\uffc2\uffa0+\uffc2\uffa0legume grain rotations decreased total C input (\uffe2\uff88\uff9216%), root C input (\uffe2\uff88\uff9212%), and SOC (\uffe2\uff88\uff925.3%) relative to cereal\uffe2\uff80\uff90only rotations. We found no effect of species diversity on SOC within grain\uffe2\uff80\uff90only rotations. N fertilizer rates mediated the effect of functional diversity on SOC within grain\uffe2\uff80\uff90only crop rotations: at low N fertilizer rates (\uffe2\uff89\uffa475\uffc2\uffa0kg N\uffc2\uffb7ha\uffe2\uff88\uff921\uffc2\uffb7yr\uffe2\uff88\uff921), the decrease in SOC with cereal\uffc2\uffa0+\uffc2\uffa0legume grain rotations was less than at high N fertilizer rates. Our results show that increasing the functional diversity of crop rotations is more likely to increase SOC concentrations if it is accompanied by an increase in C input. Functionally diverse perennial and cover cropped rotations increased both C input and SOC concentrations, potentially by exploiting niches in time that would otherwise be unproductive, that is, increasing the \uffe2\uff80\uff9cperenniality\uffe2\uff80\uff9d of crop rotations.
", "keywords": ["Crops", " Agricultural", "2. Zero hunger", "Science", "Ecology and Evolutionary Biology", "Agriculture", "Fabaceae", "cropping systems", "04 agricultural and veterinary sciences", "15. Life on land", "functional diversity", "Poaceae", "sustainable agriculture", "Soil", "meta\u2010analysis", "soil organic matter", "0401 agriculture", " forestry", " and fisheries", "cover crops", "soil carbon", "Organic Chemicals", "perennials", "Fertilizers", "nitrogen fertilizer", "biodiversity"]}, "links": [{"href": "https://doi.org/10.1002/eap.1648"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecological%20Applications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/eap.1648", "name": "item", "description": "10.1002/eap.1648", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/eap.1648"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-12-27T00:00:00Z"}}, {"id": "10.1002/ecs2.2645", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:04Z", "type": "Journal Article", "created": "2019-03-19", "title": "Uneven global distribution of food web studies under climate change", "description": "AbstractTrophic interactions within food webs affect species distributions, coexistence, and provision of ecosystem services but can be strongly impacted by climatic changes. Understanding these impacts is therefore essential for managing ecosystems and sustaining human well\uffe2\uff80\uff90being. Here, we conducted a global synthesis of terrestrial, marine, and freshwater studies to identify key gaps in our knowledge of climate change impacts on food webs and determine whether the areas currently studied are those most likely to be impacted by climate change. We found research suffers from a strong geographic bias, with only 3.5% of studies occurring in the tropics. Importantly, the distribution of sites sampled under projected climate changes was biased\uffe2\uff80\uff94areas with decreases or large increases in precipitation and areas with low magnitudes of temperature change were under\uffe2\uff80\uff90represented. Our results suggest that understanding of climate change impacts on food webs could be broadened by considering more than two trophic levels, responses in addition to species abundance and biomass, impacts of a wider suite of climatic variables, and tropical ecosystems. Most importantly, to enable better forecasts of biodiversity responses to climate change, we identify critically under\uffe2\uff80\uff90represented geographic regions and climatic conditions which should be prioritized in future research.Changes in substrate quality driven by climate, land use, or other forms of global change may represent a strong selective force on microbial communities. Invasion of new taxa into a community through dispersal, evolution, or recolonization could impact the outcome of this environmental selection. Here, we simulated substrate change with a trait\uffe2\uff80\uff90based model of microbial litter decomposition (DEMENTpy) to assess the legacy effects of past substrate quality and the impact of selection by a new substrate on community decomposition activity. Simulations were run with different levels of invasion, including invasion from communities long\uffe2\uff80\uff90adapted to the new substrate. Legacy effects were evident with substrate change for native communities differing in composition. Protein was the only substrate that exerted a strong enough selective force to affect community composition. Legacy effects disappeared when invaders came from substrates similar to the new substrate. Together, our simulations demonstrate that substrate quality changes associated with global change can lead to legacy effects on substrate degradation. In decomposing plant litter, such legacy effects can occur if substrate inputs shift to higher protein content and if invasion is low.The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co\uffe2\uff80\uff90occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co\uffe2\uff80\uff90occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.BACKGROUND: Microbial activities involved in the dynamics of organic matter determine the potential for organic carbon (C) accumulation in soil. To understand this for paddy soil, an incubation experiment (25 \uffc2\uffb0C, 45% water\uffe2\uff80\uff90holding capacity) was established using 14C\uffe2\uff80\uff90labelled glucose and rice straw (500 \uffc2\uffb5g C g\uffe2\uff88\uff921 soil) as substrates; an adjacent upland soil was used for comparison.
RESULTS: The amount of microbial biomass in the paddy soil was approximately 6 times larger and its turnover rate was 1.5\uffe2\uff80\uff933 times faster than in the upland soil. These proportions of 14C\uffe2\uff80\uff90labelled glucose and rice straw mineralized in the paddy soil were about 3% smaller (P < 0.01) than those in the upland soil. Also, there was no significant priming effect of fresh substrate additions on the mineralization of native organic C in the paddy soil, while the priming effect was significant in the upland soil.
CONCLUSION: Although the paddy soil contains a large amount of microbial biomass, which is also very active, the mineralization of fresh substrates is significantly restricted in this soil, along with a small priming effect. This favours the accumulation of organic C in paddy soils. Copyright \uffc2\uffa9 2011 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "Minerals", "Tropical Climate", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "Carbon", "Carbon Cycle", "Soil", "Glucose", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Ecosystem", "Soil Microbiology"], "contacts": [{"organization": "Ping Zhou, John Keith Syers, Hongzhao Yuan, Yirong Su, Ling Li, Jinshui Wu,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1002/jsfa.4645"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.4645", "name": "item", "description": "10.1002/jsfa.4645", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.4645"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-10-12T00:00:00Z"}}, {"id": "10.1002/jsfa.4647", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:07Z", "type": "Journal Article", "created": "2011-09-27", "title": "Response Of Soil Organic Carbon Mineralization In Typical Karst Soils Following The Addition Of 14c-Labeled Rice Straw And Caco3", "description": "AbstractBACKGROUND: Organic substrates and calcium are important factors controlling organic matter turnover in Karst soils. To understand their effects on soil organic carbon (SOC) mineralization, an incubation experiment was conducted involving a control treatment (CK), the addition of a 14C\uffe2\uff80\uff90labeled rice straw (T1), CaCO3 (T2), and both 14C\uffe2\uff80\uff90labeled rice straw and CaCO3 (T3) to two types of Karst soils (terra fusca and rendzina) and a red soil from southwestern China.
RESULTS: Cumulative mineralization of the rice straw over 100 days in rendzina (22.96 mg kg\uffe2\uff88\uff921) and terra fusca (23.19 mg kg\uffe2\uff88\uff921) was higher than in the red soil (15.48 mg kg\uffe2\uff88\uff921; P < 0.05). Cumulative mineralization of native SOC decreased following addition of 14C\uffe2\uff80\uff90labeled rice straw in the rendzina and terra fusca but increased in the red soil (negative and positive priming effects on native SOC). The turnover times of 14C\uffe2\uff80\uff90labeled microbial biomass C (MBC) in the red soil, terra fusca and rendzina were 71 \uffc2\uffb1 2, 243 \uffc2\uffb1 20 and 254 \uffc2\uffb1 45 days, respectively. By adding CaCO3, the accumulation of SOC was greater in the Karst soils than in the red soil.
CONCLUSION: Although the interactions between rice straw decomposition and priming effects on native SOC are not yet understood, there was considerable variation between Karst and red soils. Soil calcium was a positive factor in maintaining SOC stability. MBC from rice straws was stable in terra fusca and rendzina, whereas it was active in the red soil. The Karst soils (terra fusca and rendzina) used in this study benefited SOC accumulation. Copyright \uffc2\uffa9 2011 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "Carbon Isotopes", "Soil", "0401 agriculture", " forestry", " and fisheries", "Calcium", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "Carbon", "Soil Microbiology", "6. Clean water", "Calcium Carbonate", "Carbon Cycle"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.4647"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.4647", "name": "item", "description": "10.1002/jsfa.4647", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.4647"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-09-23T00:00:00Z"}}, {"id": "10.1002/jsfa.4533", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:07Z", "type": "Journal Article", "created": "2011-07-27", "title": "Influence Of Fertilisation Regimes On A Nosz-Containing Denitrifying Community In A Rice Paddy Soil", "description": "AbstractBACKGROUND: Denitrification is a microbial process that has received considerable attention during the past decade since it can result in losses of added nitrogen fertilisers from agricultural soils. Paddy soil has been known to have strong denitrifying activity, but the denitrifying microorganisms responsible for fertilisers in paddy soil are not well known. The objective of this study was to explore the impacts of 17\uffe2\uff80\uff90year application of inorganic and organic fertiliser (rice straw) on the abundance and composition of a nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Soil samples were collected from CK plots (no fertiliser), N (nitrogen fertiliser), NPK (nitrogen, phosphorus and potassium fertilisers) and NPK + OM (NPK plus organic matter). The nitrous oxide reductase gene (nosZ) community composition was analysed using terminal restriction fragment length polymorphism, and the abundance was determined by quantitative PCR.
RESULTS: Both the largest abundance of nosZ\uffe2\uff80\uff90denitrifier and the highest potential denitrifying activity (PDA) occurred in the NPK + OM treatment with about four times higher than that in the CK and two times higher than that in the N and NPK treatments (no significant difference). Denitrifying community composition differed significantly among fertilisation treatments except for the comparison between CK and N treatments. Of the measured abiotic factors, total organic carbon was significantly correlated with the observed differences in community composition and abundance (P < 0.01 by Monte Carlo permutation).
CONCLUSION: This study shows that the addition of different fertilisers affects the size and composition of the nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Copyright \uffc2\uffa9 2011 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Nitrogen", "0402 animal and dairy science", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Carbon", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "Denitrification", "0405 other agricultural sciences", "Fertilizers", "Oxidoreductases", "Monte Carlo Method", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.4533"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.4533", "name": "item", "description": "10.1002/jsfa.4533", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.4533"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-27T00:00:00Z"}}, {"id": "10.1002/jsfa.5550", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:07Z", "type": "Journal Article", "created": "2012-01-06", "title": "The Effect Of Rice Straw Incorporation Into Paddy Soil On Carbon Sequestration And Emissions In The Double Cropping Rice System", "description": "AbstractBACKGROUND: Soil organic carbon (SOC) sequestration, methane emission, and the net carbon sink represented by rice straw incorporated into soil (RIS) were studied using long\uffe2\uff80\uff90term experimentation with rice straw incorporated into soil (LRIS) and short\uffe2\uff80\uff90term experimentation with different patterns of rice straw incorporated into soil (SPRIS).
RESULTS: Soil organic carbon could be improved by RIS combined with soil ploughing. The increased rate of SOC deposition per cultivated layer was 0.10 t C ha\uffe2\uff88\uff921 for 2.625 t ha\uffe2\uff88\uff921 straw incorporated each season in LRIS and 0.36 t C ha\uffe2\uff88\uff921 for 4.5 t straw ha\uffe2\uff88\uff921 season\uffe2\uff88\uff921 incorporated in SPRIS; the apparent SOC conversion by rice straw (stubble) was reduced as the amount of incorporated straw increased. However, RIS methane emission from paddy fields also significantly exacerbated the CH4 emission flux observed during the early and late rice growing seasons, which was increased by 75.0% (P < 0.01) and 251.5% (P < 0.01), respectively, compared with combined application of nitrogen, phosphorus and potassium fertiliser (NPK). The apparent methane conversion of straw was almost uniform with a similar rice yield and soil cultivating mode. Among the patterns of RIS, methane emission was significantly reduced under straw covering untilled land, and this property led to the lowest apparent methane conversion.
CONCLUSION: RIS with ploughing and tilling resulted in negative carbon sequestration because of increased methane emissions. A combined NPK application with only rice stubble incorporation may be sustainable for a higher rice yield, but this approach has a reduced rate of negative carbon sequestration in the paddy field. Straw covering with no tillage was the best measure to realise high yield and low carbon emission for RIS. Copyright \uffc2\uffa9 2012 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "Carbon", "6. Clean water", "Soil", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Fertilizers", "Methane", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.5550"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.5550", "name": "item", "description": "10.1002/jsfa.5550", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.5550"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-01-06T00:00:00Z"}}, {"id": "10.1002/jsfa.6206", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:07Z", "type": "Journal Article", "created": "2013-05-01", "title": "Effect Of Organic, Conventional And Mixed Cultivation Practices On Soil Microbial Community Structure And Nematode Abundance In A Cultivated Onion Crop", "description": "AbstractBACKGROUNDResponses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long\uffe2\uff80\uff90term field experiment which divides conventional and organic agriculture into component pest\uffe2\uff80\uff90control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles, microbial and nematode counts, and denaturing gradient gel electrophoresis (DGGE) to characterise soil microbial communities in plots used for onion (Allium cepa L.) cultivation.
RESULTSMicrobial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest\uffe2\uff80\uff90control treatment plots.
CONCLUSIONOrganic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. \uffc2\uffa9 2013 Society of Chemical Industry
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Microbial diversity", "Nematoda", "Soil", "03 medical and health sciences", "Onions", "Animals", "DNA", " Fungal", "Ecosystem", "Soil Microbiology", "2. Zero hunger", "Organic Agriculture", "0303 health sciences", "Bacteria", "Denaturing Gradient Gel Electrophoresis", "0402 animal and dairy science", "Fungi", "Denaturing gradient gel electrophoresis", "Agriculture", "Biolog Eco-plates", "04 agricultural and veterinary sciences", "15. Life on land", "Community level physiological profile", "Organic agriculture", "0405 other agricultural sciences"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.6206"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.6206", "name": "item", "description": "10.1002/jsfa.6206", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.6206"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-06-07T00:00:00Z"}}, {"id": "10.1002/jsfa.8606", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:07Z", "type": "Journal Article", "created": "2017-07-31", "title": "How Are Arbuscular Mycorrhizal Associations Related To Maize Growth Performance During Short-Term Cover Crop Rotation?", "description": "AbstractBACKGROUNDBetter cover crop management options aiming to maximize the benefits of arbuscular mycorrhizal fungi (AMF) to subsequent crops are largely unknown. We investigated the impact of cover crop management methods on maize growth performance and assemblages of AMF colonizing maize roots in a field trial. The cover crop treatments comprised Italian ryegrass, wheat, brown mustard and fallow in rotation with maize.
RESULTSThe diversity of AMF communities among cover crops used for maize management was significantly influenced by the cover crop and time course. Cover crops did not affect grain yield and aboveground biomass of subsequent maize but affected early growth. A structural equation model indicated that the root colonization, AMF diversity and maize phosphorus uptake had direct strong positive effects on yield performance.
CONCLUSIONAMF variables and maize performance were related directly or indirectly to maize grain yield, whereas root colonization had a positive effect on maize performance. AMF may be an essential factor that determines the success of cover crop rotational systems. Encouraging AMF associations can potentially benefit cover cropping systems. Therefore, it is imperative to consider AMF associations and crop phenology when making management decisions. \uffc2\uffa9 2017 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "0402 animal and dairy science", "Agriculture", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Plant Roots", "Zea mays", "Crop Production", "03 medical and health sciences", "Mycorrhizae", "Lolium", "0405 other agricultural sciences", "Soil Microbiology", "Triticum", "Mustard Plant"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.8606"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.8606", "name": "item", "description": "10.1002/jsfa.8606", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.8606"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-09-11T00:00:00Z"}}, {"id": "10.1002/lom3.10364", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:09Z", "type": "Journal Article", "created": "2020-06-05", "title": "An international laboratory comparison of dissolved organic matter composition by high resolution mass spectrometry: Are we getting the same answer?", "description": "AbstractHigh\uffe2\uff80\uff90resolution mass spectrometry (HRMS) has become a vital tool for dissolved organic matter (DOM) characterization. The upward trend in HRMS analysis of DOM presents challenges in data comparison and interpretation among laboratories operating instruments with differing performance and user operating conditions. It is therefore essential that the community establishes metric ranges and compositional trends for data comparison with reference samples so that data can be robustly compared among research groups. To this end, four identically prepared DOM samples were each measured by 16 laboratories, using 17 commercially purchased instruments, using positive\uffe2\uff80\uff90ion and negative\uffe2\uff80\uff90ion mode electrospray ionization (ESI) HRMS analyses. The instruments identified ~1000 common ions in both negative\uffe2\uff80\uff90 and positive\uffe2\uff80\uff90ion modes over a wide range of m/z values and chemical space, as determined by van Krevelen diagrams. Calculated metrics of abundance\uffe2\uff80\uff90weighted average indices (H/C, O/C, aromaticity, and m/z) of the commonly detected ions showed that hydrogen saturation and aromaticity were consistent for each reference sample across the instruments, while average mass and oxygenation were more affected by differences in instrument type and settings. In this paper we present 32 metric values for future benchmarking. The metric values were obtained for the four different parameters from four samples in two ionization modes and can be used in future work to evaluate the performance of HRMS instruments.Global change is affecting soil biodiversity and functioning across all terrestrial ecosystems. Still, much is unknown about how soil biodiversity and function will change in the future in response to simultaneous alterations in climate and land use, as well as other environmental drivers. It is crucial to understand the direct, indirect\uffc2\uffa0and interactive effects of global change drivers on soil communities and ecosystems across environmental contexts, not only today but also in the near future. This is particularly relevant for international efforts to tackle climate change like the Paris Agreement, and considering the failure to achieve the 2020 biodiversity targets, especially the target of halting soil degradation. Here, we outline the main frontiers related to soil ecology that were presented and discussed at the thematic sessions of the World Biodiversity Forum 2022 in Davos, Switzerland. We highlight multiple frontiers of knowledge associated with data integration, causal inference, soil biodiversity and function scenarios, critical soil biodiversity facets, underrepresented drivers, global collaboration, knowledge application and transdisciplinarity, as well as policy and public communication. These identified research priorities are not only of immediate interest to the scientific community but may also be considered in research priority programmes and calls for funding.BACKGROUND: In spite of increasing knowledge of allelopathic rice as an efficient component involved in paddy weed management, relatively little is known about its reproduction in response to competing weeds. Reproduction allocation of individual allelopathic rice plants in relation to monoculture and mixed culture with competing barnyardgrass in a paddy field was studied, along with analyses of soil nutrients and microbial communities to understand the potential mechanism.
RESULTS: At a 1:1 barnyardgrass and rice mixture proportion identified from a replacement series study, biomass, grain yield and major parameters of individual allelopathic rice plants at the mature stage were increased by competing barnyardgrass. There was no difference in allelopathic rice root\uffe2\uff80\uff90zone soil ammonium N and Olsen P between monoculture and mixed culture. However, mixed culture altered soil microbial biomass C and communities. When mixed with barnyardgrass, allelopathic rice root zone had an 87% increase in soil microbial biomass C. Phospholipid fatty acid (PLFA) profiling indicated that the signature lipid biomarkers of bacteria, actinobacteria and fungi were affected by mixed culture. Principal component analysis clearly identified differences in the composition of PLFA in different soil samples.
CONCLUSION: Allelopathic rice specific changes in soil microbial communities may generate a positive feedback on its own growth and reproduction in the presence of competing barnyardgrass in a given paddy system. Copyright \uffc2\uffa9 2012 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "0106 biological sciences", "China", "Reproduction", "Population Dynamics", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "01 natural sciences", "Pheromones", "Soil", "Echinochloa", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Soil Microbiology"], "contacts": [{"organization": "Chui-Hua Kong, Peng Wang, Xiang-Rui Meng, Hanwen Ni, Ming-Li Wang,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1002/ps.3380"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Pest%20Management%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ps.3380", "name": "item", "description": "10.1002/ps.3380", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ps.3380"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-08-07T00:00:00Z"}}, {"id": "10.1002/ps.7961", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:09Z", "type": "Journal Article", "created": "2024-01-20", "title": "The effect of natural products used as pesticides on the soil microbiota: OECD 216 nitrogen transformation test fails to identify effects that were detected viaq\u2010PCR microbial abundance measurement", "description": "AbstractBACKGROUNDNatural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off\uffe2\uff80\uff90target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co\uffe2\uff80\uff90operation and Development, which is a key international standard\uffe2\uff80\uff90setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5\uffe2\uff80\uff90dichloraniline). We determined the following in three different soils: (i) ammonium (NH4+) and nitrate (NO3\uffe2\uff88\uff92) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q\uffe2\uff80\uff90PCR).
RESULTSAll pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose\uffe2\uff80\uff90dependent effects on NH4+ and NO3\uffe2\uff88\uff92 levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q\uffe2\uff80\uff90PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5\uffe2\uff80\uff90dichloraniline.
CONCLUSIONOur findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well\uffe2\uff80\uff90standardized tools. \uffc2\uffa9 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.