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": "11245.1/e982467a-6b87-4f88-8ac3-53d0fb37aeb2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:25:22Z", "type": "Journal Article", "created": "2024-05-01", "title": "Arabinosylation of cell wall extensin is required for the directional response to salinity in roots", "description": "AbstractSoil salinity is a major contributor to crop yield losses. To improve our understanding of root responses to salinity, we developed and exploited a real-time salt-induced tilting assay. This assay follows root growth upon both gravitropic and salt challenges, revealing that root bending upon tilting is modulated by Na+ ions, but not by osmotic stress. Next, we measured this salt-specific response in 345 natural Arabidopsis (Arabidopsis thaliana) accessions and discovered a genetic locus, encoding the cell wall-modifying enzyme EXTENSIN ARABINOSE DEFICIENT TRANSFERASE (ExAD) that is associated with root bending in the presence of NaCl (hereafter salt). Extensins are a class of structural cell wall glycoproteins known as hydroxyproline (Hyp)-rich glycoproteins, which are posttranslationally modified by O-glycosylation, mostly involving Hyp-arabinosylation. We show that salt-induced ExAD-dependent Hyp-arabinosylation influences root bending responses and cell wall thickness. Roots of exad1 mutant seedlings, which lack Hyp-arabinosylation of extensin, displayed increased thickness of root epidermal cell walls and greater cell wall porosity. They also showed altered gravitropic root bending in salt conditions and a reduced salt-avoidance response. Our results suggest that extensin modification via Hyp-arabinosylation is a unique salt-specific cellular process required for the directional response of roots exposed to salinity.Drylands (hyperarid, arid, semiarid, and dry subhumid ecosystems) cover almost half of Earth\uffe2\uff80\uff99s land surface and are highly vulnerable to environmental pressures. Here we provide an inventory of soil properties including carbon (C), nitrogen (N), and phosphorus (P) stocks within the current boundaries of drylands, aimed at serving as a benchmark in the face of future challenges including increased population, food security, desertification, and climate change. Aridity limits plant production and results in poorly developed soils, with coarse texture, low C:N and C:P, scarce organic matter, and high vulnerability to erosion. Dryland soils store 646 Pg of organic C to 2\uffe2\uff80\uff89m, the equivalent of 32% of the global soil organic C pool. The magnitude of the historic loss of C from dryland soils due to human land use and cover change and their typically low C:N and C:P suggest high potential to build up soil organic matter, but coarse soil textures may limit protection and stabilization processes. Restoring, preserving, and increasing soil organic matter in drylands may help slow down rising levels of atmospheric carbon dioxide by sequestering C, and is strongly needed to enhance food security and reduce the risk of land degradation and desertification.Soil moisture is among the most important factors regulating soil biodiversity and functioning. Models forecast changes in the precipitation regime in many areas of the planet, but how these changes will influence soil functioning, and how biotic drivers modulate such effects, is far from being understood. We evaluated the responses of C and N fluxes, and soil microbial properties to different soil water regimes in soils from the main three ecotypes of the world's largest and most diverse tropical savanna. Further, we explored the direct and indirect effects of changes in the ecotype and soil water regimes on these key soil processes. Soils from the woodland savanna showed a better nutritional status than the other ecotypes, as well as higher potential N cycling rates, N2O emissions, and soil bacterial abundance but lower bacterial richness, whereas potential CO2 emissions and CH4 uptake peaked in the intermediate savanna. The ecotype also modulated the effects of changes in the soil water regime on nutrient cycling, greenhouse gas fluxes, and soil bacterial properties, with more intense responses in the intermediate savanna. Further, we highlight the existence of multiple contrasting direct and indirect (via soil microbes and abiotic properties) effects of an intensification of the precipitation regime on soil C- and N-related processes. Our results confirm that ecotype is a fundamental driver of soil properties and functioning in the Cerrado and that it can determine the responses of key soil processes to changes in the soil water regime.Theory suggests that the diversity of molecules in soil organic matter (SOM functional diversity) provides key insights on multiple ecosystem services. We aimed to investigate how and why SOM functional diversity and composition change as topsoils develop, and its implications for key soil functions (e.g., from nutrient pool to water regulation).
LocationWe reported data on 16 soil chronosequences globally distributed in nine countries from six continents.
Time Period2016\uffe2\uff80\uff932017.
Major Taxa StudiedSoil microbes (bacteria and fungi) and vascular plants.
MethodsSOM functional diversity and composition without mineral interference were measured using diffuse reflectance mid\uffe2\uff80\uff90infrared Fourier transform spectroscopy (DRIFT). We aimed to characterize the main environmental factors related to SOM functional diversity and composition. Also, we calculated the links among SOM functional diversity and key soil functions.
ResultsWe found that SOM functional diversity declines after millions of years of soil formation (pedogenesis). We further showed that increases in plant cover and productivity led to a higher ratio of reduced (e.g., alkanes) over oxidized carbon forms (i.e., C: O\uffe2\uff80\uff90functional groups ratio), which was positively correlated to SOM functional diversity as soils age. Our findings indicated that the plant footprint (i.e., the accumulation of plant\uffe2\uff80\uff90derived material promoting the C: O\uffe2\uff80\uff90functional group ratio) would explain the reduction of SOM functional diversity as ecosystems develop. Moreover, the dissimilarity in SOM composition consistently increased with soil age, with the soil development stage emerging as the main predictor of SOM dissimilarity across contrasting biomes.
Main ConclusionsOur global survey contextualized the natural history of SOM functional diversity and composition during long\uffe2\uff80\uff90term soil development. Together, we showed how plant footprint drives the losses of SOM functional diversity with increasing age, which might provide a novel mechanism to explain typically reported losses in ecosystem functions during ecosystem retrogression.Broadband topological metamaterials hold the key for designing the next generation of integrated photonic platforms and microwave devices given their protected back\uffe2\uff80\uff90scattering\uffe2\uff80\uff90free and unidirectional edge states, among other exotic properties. However, synthesizing such metamaterial has proven challenging. Here, a broadband bandgap (relative bandwidth of more than 43%) Valley\uffe2\uff80\uff90Hall topological metamaterial with deep subwavelength thickness is proposed. The present topological metamaterial is composed of three layers printed circuit boards whose total thickness is 1.524\uffc2\uffa0mm \uffe2\uff89\uff88 \uffce\uffbb/100. The topological phase transition is achieved by introducing an asymmetry parameter \uffce\uffb4r. Three mechanically reconfigurable edge states can be obtained by varying interlayer displacement. Their robust transmission is demonstrated through two kinds of waveguide domain walls with cavities and disorders. Exploiting the proposed topological metamaterial, a six\uffe2\uff80\uff90way power divider is constructed and measured as a proof\uffe2\uff80\uff90of\uffe2\uff80\uff90concept of the potential of the proposed technology for future electromagnetic devices.
We incubated temperate forest soil at constant temperature (20 \u00b0C) and water content, and exposed it to strong single-pulse perturbations, which nonetheless mimic common pulse-events in temperate soils (glucose addition at 4 mg g\u22121 soil, or freeze-thawing overnight at \u221220 \u00b0C). We subsequently measured microbial community composition and microbial storage compounds via phospho- and neutral lipid fatty acid (PLFA and NLFA) profiling, as well as C/N stoichiometry of microbial biomass and dissolved organic carbon and nitrogen in the soil solution shortly after (0.4, 1, 4, and 6 days) and after longer time periods (84 and 160 days) following the perturbations.
Transferring the soils from their natural environment to the laboratory and incubating them under controlled conditions led to a continuous change of microbial community structure over time, along with an increase in microbial biomass and dissolved N in both perturbed and control soils over the time of the experiment. Against the background of this \u2018press-disturbance\u2019, caused by the permanently changed conditions, we see immediate and long-lasting effects of the single pulse events on microbial community composition, C storage and C/N stoichiometry. Both perturbations significantly influenced the microbial community structure (based on PLFA profiles), microbial biomass N and dissolved N up to 160 days, as well as fungal and bacterial biomass and storage (based on absolute PLFA and NLFA concentrations) up to 84 days. Both perturbations increased microbial N (+59.6 \u00b5g g\u22121 dw) and decreased dissolved N (\u221240.3 \u00b5g g\u22121 dw) after 160 days, and significantly altered C/N ratios in microbial and dissolved pools (particularly in the first 6 days of the experiment).
Our results demonstrate that single-pulse perturbations can have long-term legacies in soil microbial ecosystems. In our experiment they led to alternative system states which differed from the unperturbed control in multiple parameters even after 160 days. This indicates that soil microbial communities exhibit a low resistance and resilience towards single-pulse perturbations, and may easily be pushed on alternative trajectories by short but strong environmental pulses.", "keywords": ["0301 basic medicine", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "Resilience", "04 agricultural and veterinary sciences", "15. Life on land", "Perturbations", "6. Clean water", "Transient state", "Pulse event", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "13. Climate action", "Soil microbial community", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "106026 Ecosystem research"]}, "links": [{"href": "https://doi.org/10.1016/j.geoderma.2023.116399"}, {"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": "10.1016/j.geoderma.2023.116399", "name": "item", "description": "10.1016/j.geoderma.2023.116399", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.geoderma.2023.116399"}, {"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.ijbiomac.2021.10.032", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:16:34Z", "type": "Journal Article", "created": "2021-10-14", "title": "Identification and molecular characterization of the high-affinity copper transporters family in Solanum lycopersicum.", "description": "Copper (Cu) plays a key role as cofactor in the plant proteins participating in essential cellular processes, such as electron transport and free radical scavenging. Despite high-affinity Cu transporters (COPTs) being key participants in Cu homeostasis maintenance, very little is known about COPTs in tomato (Solanum lycopersicum) even though it is the most consumed fruit worldwide and this crop is susceptible to suboptimal Cu conditions. In this study, a six-member family of COPT (SlCOPT1-6) was identified and characterized. SlCOPTs have a conserved architecture consisting of three transmembrane domains and \u03b2-strains. However, the presence of essential methionine residues, a methionine-enriched amino-terminal region, an Mx3Mx12Gx3G Cu-binding motif and a cysteine rich carboxy-terminal region, all required for their functionality, is more variable among members. Accordingly, functional complementation assays in yeast indicate that SlCOPT1 and SlCOPT2 are able to transport Cu inside the cell, while SlCOPT3 and SlCOPT5 are only partially functional. In addition, protein interaction network analyses reveal the connection between SlCOPTs and Cu PIB-type ATPases, other metal transporters, and proteins related to the peroxisome. Gene expression analyses uncover organ-dependency, fruit vasculature tissue specialization and ripening-dependent gene expression profiles, as well as different response to Cu deficiency or toxicity in an organ-dependent manner.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Biotecnologia agr\u00edcola", "Molecular Conformation", "COPT", "Gene Expression", "Tomato", "Structure-Activity Relationship", "03 medical and health sciences", "Copper Transport Proteins", "Solanum lycopersicum", "Multigene Family", "Tom\u00e0quets", "Amino Acid Sequence", "Heavy metal stress", "Conserved Sequence", "Copper", "Phylogeny", "Plant Proteins"]}, "links": [{"href": "https://doi.org/10.1016/j.ijbiomac.2021.10.032"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Biological%20Macromolecules", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ijbiomac.2021.10.032", "name": "item", "description": "10.1016/j.ijbiomac.2021.10.032", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ijbiomac.2021.10.032"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2018.12.079", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:16:54Z", "type": "Journal Article", "created": "2018-12-07", "title": "Vineyards in transition: A global assessment of the adaptation needs of grape producing regions under climate change", "description": "This paper suggests how climate change may transform vineyards. We consider changes in agro-climatic indicators derived from climatic variables as drivers for adaptation needs. We use two climate scenarios, GCM GFL-ESM2M and HadGEM2-ES, with 0.5\u00b0 spatial resolution and daily time step forced by two emission scenarios, RCP2.6 and 6.0, to estimate the transition of potential vineyards in the major grape production world areas by the late 21st century. We present and discuss changes in three impact indicators - one drought indicator and two temperature ones - aimed at exploring the benefits of transition-based policies. The drought indicator provides insights to prepare adaptation for extreme events in probabilistic terms. The temperature indicators offer information on the transition towards suitable zones of production. Future projections suggest a lack of water to maintain current levels of production in all regions of the world. Furthermore, thermal suitability of grapevine may be greatly affected in China and the Mediterranean region. Nevertheless, the possibility of quality wines is not altered within the regions with adequate suitability. Lastly, a portfolio of strategies to adapt to the future climate is presented.", "keywords": ["[SDE] Environmental Sciences", "2. Zero hunger", "0301 basic medicine", "China", "Models", " Statistical", "Mediterranean Region", "Climate Change", "Oceania", "Temperature", "Agriculture", "South America", "15. Life on land", "01 natural sciences", "Droughts", "South Africa", "03 medical and health sciences", "13. Climate action", "[SDE]Environmental Sciences", "North America", "Vitis", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2018.12.079"}, {"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.2018.12.079", "name": "item", "description": "10.1016/j.scitotenv.2018.12.079", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2018.12.079"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-01T00:00:00Z"}}, {"id": "10.1016/j.agrformet.2013.06.019", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:15:40Z", "type": "Journal Article", "created": "2013-08-03", "title": "Seasonal Dynamics Of Co2 Balance And Water Consumption Of C-3 And C-4-Type Cover Crops Compared To Bare Soil In A Suitability Study For Their Use In Vineyards In Germany And Argentina", "description": "Abstract Cover crops are used in vineyards to maintain soil structure, minimise soil erosion and optimise vineyard mechanisation, yet few data are available on water consumption and carbon dioxide assimilation (CO 2 ). Whereas cover crop use is common in the grape growing regions of Germany it is uncommon in Argentina. To obtain some information on the suitability of a selected number of species in terms of carbon gain and water expenditure under the climatic conditions of Germany and Argentina, we first quantified evapotranspiration (EvT), CO 2 assimilation and water use efficiency of Trifolium repens L. (white clover) (TR), Festuca arundinacea Schreb (tall fescue) (FE), Sorghum sudanense (Piper) Stapf (Sudan grass) (SO), and Digitaria californica (Benth) Henr. (Arizona cotton top) (DI) in a field trial in Geisenheim, Germany. We then compared the performance of TR, FE and DI together with Sorghum halepense L. (Johnson grass) (SH) in a pot experiment under the warmer climatic conditions of Mendoza, Argentina, where water supply could be controlled. In all cases bare soil served as a reference for soil water loss. Gas-exchange of plants and soil were measured with customised open system canopy chambers and an infrared gas analyser and water dynamics in the soil with soil moisture probes (field) or gravimetrically (pots). SO and TR were the two species that reached the highest degree of soil coverage in Germany and substantially reduced soil moisture in the first 0.40\u00a0m of depth. TR showed high EvT and CO 2 assimilation rates in both climates when water supply was sufficient and maintained relative high rates when water status was reduced under cool conditions in Germany, yet performed poorly when high temperatures occurred concomitant to low water supply in Argentina. DI, being a C 4 species from arid regions, had difficulties to get established in the cool conditions of Germany and there was no clear tendency for more efficient water use than the other cover crops. However under the warm condition of Argentina, especially when water supply was reduced, DI displayed higher WUE which was entirely related to the maintenance of higher assimilation rates at substantially reduced EvT. FE being common in German vineyards had low assimilation rates combined with high evapotranspiration rates under Argentinian conditions and was very sensitive to water deficit in combination with high temperature.", "keywords": ["0301 basic medicine", "2. Zero hunger", "03 medical and health sciences", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1016/j.agrformet.2013.06.019"}, {"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.2013.06.019", "name": "item", "description": "10.1016/j.agrformet.2013.06.019", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.agrformet.2013.06.019"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-01T00:00:00Z"}}, {"id": "PMC9846495", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:29:00Z", "type": "Journal Article", "created": "2023-01-04", "title": "A genome wide association study to dissect the genetic architecture of agronomic traits in Andean lupin (Lupinus mutabilis)", "description": "
Establishing Lupinus mutabilis as a protein and oil crop requires improved varieties adapted to EU climates. The genetic regulation of strategic breeding traits, including plant architecture, growing cycle length and yield, is unknown. This study aimed to identify associations between 16 669 single nucleotide polymorphisms (SNPs) and 9 agronomic traits on a panel of 223 L. mutabilis accessions, grown in four environments, by applying a genome wide association study (GWAS). Seven environment-specific QTLs linked to vegetative yield, plant height, pods number and flowering time, were identified as major effect QTLs, being able to capture 6 to 20% of the phenotypic variation observed in these traits. Furthermore, two QTLs across environments were identified for flowering time on chromosome 8. The genes FAF, GAMYB and LNK, regulating major pathways involved in flowering and growth habit, as well as GA30X1, BIM1, Dr1, HDA15, HAT3, interacting with these pathways in response to hormonal and environmental cues, were prosed as candidate genes. These results are pivotal to accelerate the development of L. mutabilis varieties adapted to European cropping conditions by using marker-assisted selection (MAS), as well as to provide a framework for further functional studies on plant development and phenology in this species.Approximately one\uffe2\uff80\uff90third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA\uffe2\uff80\uff90Stable Isotope Probing (DNA\uffe2\uff80\uff90SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia. Representative isolates, capable of growth on isoprene as sole carbon and energy source, were obtained from marine and estuarine locations, and isoprene\uffe2\uff80\uff90degrading strains of Gordonia and Mycobacterium were characterised physiologically and their genomes were sequenced. Genes predicted to be required for isoprene metabolism, including four\uffe2\uff80\uff90component isoprene monooxygenases (IsoMO), were identified and compared with previously characterised examples. Transcriptional and activity assays of strains growing on isoprene or alternative carbon sources showed that growth on isoprene is an inducible trait requiring a specific IsoMO. This study is the first to identify active isoprene degraders in estuarine and marine environments using DNA\uffe2\uff80\uff90SIP and to characterise marine isoprene\uffe2\uff80\uff90degrading bacteria at the physiological and molecular level.
", "keywords": ["0301 basic medicine", "570", "Volatile Organic Compounds", "0303 health sciences", "550", "Base Sequence", "610", "QR Microbiology", "Sequence Analysis", " DNA", "Environment", "6. Clean water", "Mixed Function Oxygenases", "Mycobacterium", "03 medical and health sciences", "Hemiterpenes", "13. Climate action", "Pentanes", "Butadienes", "Rhodococcus", "14. Life underwater", "Gordonia Bacterium", "Research Articles", "Genome", " Bacterial", "GE Environmental Sciences"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/63998/4/Published_manuscript.pdf"}, {"href": "http://onlinelibrary.wiley.com/wol1/doi/10.1111/1462-2920.13842/fullpdf"}, {"href": "https://doi.org/10.1111/1462-2920.13842"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.13842", "name": "item", "description": "10.1111/1462-2920.13842", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13842"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-21T00:00:00Z"}}, {"id": "10.1093/nar/gkz378", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:18:35Z", "type": "Journal Article", "created": "2019-05-06", "title": "Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport", "description": "AbstractCaver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels, and study of the ligands\uffe2\uff80\uff99 transport through these transport pathways. Caver Web is the first interactive tool allowing both the analyses within a single graphical user interface. The server is built on top of the abundantly used tunnel detection tool Caver 3.02 and CaverDock 1.0 enabling the study of the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for a tunnel identification and a list of ligands for the transport analysis. The automated guidance procedures assist the users to set up the calculation in a way to obtain biologically relevant results. The identified tunnels, their properties, energy profiles and trajectories for ligands\uffe2\uff80\uff99 passages can be calculated and visualized. The tool is very fast (2\uffe2\uff80\uff9320 min per job) and is applicable even for virtual screening purposes. Its simple setup and comprehensive graphical user interface make the tool accessible for a broad scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.
", "keywords": ["0301 basic medicine", "Internet", "0303 health sciences", "Binding Sites", "BINDING; STABILITY; MECHANISM; MYOGLOBIN; MIGRATION; DYNAMICS; KINETICS; PATHWAY; ENZYMES; SERVER", "Computational Biology", "Ligands", "Protein Structure", " Tertiary", "3. Good health", "Molecular Docking Simulation", "Benchmarking", "User-Computer Interface", "03 medical and health sciences", "Web Server Issue", "Animals", "Humans", "Protein Interaction Domains and Motifs", "Amino Acid Sequence", "Carrier Proteins", "Protein Structure", " Quaternary", "Algorithms", "Protein Binding"]}, "links": [{"href": "http://academic.oup.com/nar/article-pdf/47/W1/W414/28880050/gkz378.pdf"}, {"href": "https://doi.org/10.1093/nar/gkz378"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nucleic%20Acids%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/nar/gkz378", "name": "item", "description": "10.1093/nar/gkz378", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/nar/gkz378"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-22T00:00:00Z"}}, {"id": "10.1073/pnas.1913688117", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:18:17Z", "type": "Journal Article", "created": "2020-03-17", "title": "ENO regulates tomato fruit size through the floral meristem development network", "description": "A dramatic evolution of fruit size has accompanied the domestication and improvement of fruit-bearing crop species. In tomato (Solanum lycopersicum), naturally occurring cis-regulatory mutations in the genes of the CLAVATA-WUSCHEL signaling pathway have led to a significant increase in fruit size generating enlarged meristems that lead to flowers with extra organs and bigger fruits. In this work, by combining mapping-by-sequencing and CRISPR/Cas9 genome editing methods, we isolatedEXCESSIVE NUMBER OF FLORAL ORGANS(ENO), an AP2/ERF transcription factor which regulates floral meristem activity. Thus, theENOgene mutation gives rise to plants that yield larger multilocular fruits due to an increased size of the floral meristem. Genetic analyses indicate thatenoexhibits synergistic effects with mutations at theLOCULE NUMBER(encodingSlWUS) andFASCIATED(encodingSlCLV3) loci, two central players in the evolution of fruit size in the domestication of cultivated tomatoes. Our findings reveal that anenomutation causes a substantial expansion ofSlWUSexpression domains in a flower-specific manner. In vitro binding results show that ENO is able to interact with the GGC-box cis-regulatory element within theSlWUSpromoter region, suggesting that ENO directly regulatesSlWUSexpression domains to maintain floral stem-cell homeostasis. Furthermore, the study of natural allelic variation of theENOlocus proved that a cis-regulatory mutation in the promoter ofENOhad been targeted by positive selection during the domestication process, setting up the background for significant increases in fruit locule number and fruit size in modern tomatoes.
", "keywords": ["0301 basic medicine", "570", "Floral meristem", "[SPI] Engineering Sciences [physics]", "[SDV]Life Sciences [q-bio]", "Meristem", "Quantitative Trait Loci", "Genes", " Plant", "CLAVATA/WUSCHEL regulatory network", "Domestication", "[SPI]Engineering Sciences [physics]", "03 medical and health sciences", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "AP2/ERF transcription factor", "Promoter Regions", " Genetic", "Cell Proliferation", "Plant Proteins", "580", "Homeodomain Proteins", "2. Zero hunger", "Tomato (Solanum lycopersicum)", "0303 health sciences", "Stem Cells", "Biological Sciences", "15. Life on land", "fruit size", "Crop Production", "[SDV] Life Sciences [q-bio]", "CLAVATA-WUSCHEL regulatory network", "GENETICA", "Fruit", "Mutation", "Fruit size", "floral meristem", "Transcription Factors"]}, "links": [{"href": "https://pnas.org/doi/pdf/10.1073/pnas.1913688117"}, {"href": "https://doi.org/10.1073/pnas.1913688117"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.1913688117", "name": "item", "description": "10.1073/pnas.1913688117", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.1913688117"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-16T00:00:00Z"}}, {"id": "10.1016/j.jece.2020.104657", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:16:39Z", "type": "Journal Article", "created": "2020-10-24", "title": "Reductive/oxidative sequential bioelectrochemical process for Perchloroethylene (PCE) removal: effect of the applied reductive potential and microbial community characterization", "description": "Abstract In this paper, a bioelectrochemical process has been developed by the combination of two membrane-less reactors equipped with an internal graphite granules counterelectrode for the perchloroethylene (PCE) removal through a reductive/oxidative sequence. In the reductive reactor, the cathodic chamber supplied the reducing power to PCE dechlorinating biomass while a rutile electrode promoted the aerobic dechlorination of the less chlorinated PCE byproducts by oxygen in situ evolution. Two potentiostatic conditions, -350 and -550 mV vs SHE, were tested on the reductive reactor, which showed the capability to completely reduce the PCE into vinyl chloride (VC) and ethylene (Eth). These compounds were completely removed by the oxidative reactor with an average VC and Eth removal efficiency of 94 \u00b1 1% and 98 \u00b1 1%. The -350 mV vs SHE condition resulted in the higher coulombic efficiency for the reductive dechlorination which reached 22 \u00b1 7 % while by increasing the reductive potential to -550 mV the coulombic efficiency drop down to 6 \u00b1 1 % in favor of the methanogenesis reaction. Dehalococcoides mccartyi was found at high abundance in the reducing reactor while a heterogeneous bacterial consortium was observed in the oxidative reactor. Microbiome characterization of the reductive and oxidative reactors showed the concomitant presence of different redox niches in each compartment suggesting that the exchange of ionic species between the electrode and the counterelectrode allowed the co-existence of both reducing and oxidative reactions.", "keywords": ["0301 basic medicine", "0303 health sciences", "EC", "reductive dechlorination; oxidative dechlorination; bioremediation; bioelectrochemical systems; chlorinated aliphatic hydrocarbons; groundwater remediation", "Reductive dechlorination", "Process Chemistry and Technology", "H2020", "Pollution", "Horizon 2020 Framework Programme", "6. Clean water", "Research and Innovation action", "Bioelectrochemical systems", "03 medical and health sciences", "bioremediation", "Chemical Engineering (miscellaneous)", "European Commission", "Waste Management and Disposal"]}, "links": [{"href": "https://doi.org/10.1016/j.jece.2020.104657"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Environmental%20Chemical%20Engineering", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jece.2020.104657", "name": "item", "description": "10.1016/j.jece.2020.104657", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jece.2020.104657"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-01T00:00:00Z"}}, {"id": "10.1002/jpln.202000183", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:22Z", "type": "Journal Article", "created": "2020-10-09", "title": "Effects of water deficit and nitrogen application on leaf gas exchange, phytohormone signaling, biomass and water use efficiency of oat plants", "description": "AbstractBackground: Water and nitrogen (N) are essential resources influencing plant growth and yield. To improve their efficiencies in crop production is challenging because the physiological mechanisms of water and N coupling and their interactive effect on crop water use efficiency (WUE) are not well understood yet.
Aim: The aim of this study was to investigate the physiological responses and phytohormones signaling in oats in response to soil water status and N supply under fertigation, to explore the mechanisms regulating plant growth and WUE.
Methods: Oat plants were subjected to the factorial combination of three soil moisture regimes (50, 70, and 90% of soil water holding capacity, SWHC) and three N levels (fertilized with 74, 149, and 298 mg kg\uffe2\uff88\uff921).
Results: The stomatal conductance (gs) was significantly decreased by soil water deficit, and also by the highest N level, whereas photosynthesis rate (An) was unaffected by neither water nor N. Consequently, intrinsic WUE (WUEint, An/gs) was highest under reduced irrigation and high N fertilization. This effect at stomatal level was affirmed by responses in whole plant WUE (WUEb), which was positively correlated with shoot \uffce\uffb413C. A positive correlation between \uffce\uffb418O and \uffce\uffb413C in shoots further indicated that decreases of gs rather than changes in An contributed to the enhanced WUE.
Conclusion: Moderate soil water deficit and sufficient N supply is recommended for saving irrigation water and improving WUE on fertigated oat plants without compromising biomass accumulation to any large extent.Haloalkane dehalogenases (HLDs) are \uffce\uffb1/\uffce\uffb2\uffe2\uff80\uff90hydrolases that convert halogenated compounds to their corresponding alcohols. The overall kinetic mechanism proceeds via four steps: (i) binding of halogenated substrate, (ii) bimolecular nucleophilic substitution (SN2) leading to the cleavage of a carbon\uffe2\uff80\uff90halogen bond and the formation of an alkyl\uffe2\uff80\uff90enzyme intermediate, (iii) nucleophilic addition of a water molecule resulting in the hydrolysis of the intermediate to the corresponding alcohol and (iv) release of the reaction products \uffe2\uff80\uff93 an alcohol, a halide ion and a proton. Although, the overall reaction has been reported as irreversible, several kinetic evidences from previous studies suggest the reversibility of the first SN2 chemical step. To study this phenomenon, we have engineered HLDs to stop the catalytic cycle at the stage of the alkyl\uffe2\uff80\uff90enzyme intermediate. The ability of the intermediate to exchange halides was confirmed by a stopped\uffe2\uff80\uff90flow fluorescence binding analysis. Finally, the transhalogenation reaction was confirmed with several HLDs and 2,3\uffe2\uff80\uff90dichloropropene in the presence of a high concentration of iodide. The formation of the transhalogenation product 3\uffe2\uff80\uff90iodo\uffe2\uff80\uff902\uffe2\uff80\uff90chloropropene catalysed by five mutant HLDs was identified by gas chromatography coupled with mass spectrometry. Hereby we demonstrated the reversibility of the cleavage of the carbon\uffe2\uff80\uff90halogen bond by HLDs resulting in a transhalogenation. After optimization, the transhalogenation reaction can possibly find its use in biocatalytic applications. Enabling this reaction by strategically engineering the enzyme to stop at an intermediate in the catalytic cycle that is synthetically more useful than the product of the natural pathway is a novel concept.
magnified image
", "keywords": ["0301 basic medicine", "enzyme catalysis; halide exchange; haloalkane dehalogenase; nucleophilic substitution; redirection of reaction; transhalogenation", "0303 health sciences", "03 medical and health sciences"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/adsc.201900132"}, {"href": "https://doi.org/10.1002/adsc.201900132"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Advanced%20Synthesis%20%26amp%3B%20Catalysis", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/adsc.201900132", "name": "item", "description": "10.1002/adsc.201900132", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/adsc.201900132"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-17T00:00:00Z"}}, {"id": "10.1002/advs.201901408", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:16Z", "type": "Journal Article", "created": "2019-09-19", "title": "Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms", "description": "AbstractBiofouling proceeds in successive steps where the primary colonizers affect the phylogenetic and functional structure of a future microbial consortium. Using microbiologically influenced corrosion (MIC) as a study case, a novel approach for material surface protection is described, which does not prevent biofouling, but rather shapes the process of natural biofilm development to exclude MIC\uffe2\uff80\uff90related microorganisms. This approach interferes with the early steps of natural biofilm formation affecting how the community is finally developed. It is based on a multilayer artificial biofilm, composed of electrostatically modified bacterial cells, producing antimicrobial compounds, extracellular antimicrobial polyelectrolyte matrix, and a water\uffe2\uff80\uff90proof rubber elastomer barrier. The artificial biofilm is constructed layer\uffe2\uff80\uff90by\uffe2\uff80\uff90layer (LBL) by manipulating the electrostatic interactions between microbial cells and material surfaces. Field testing on standard steel coupons exposed in the sea for more than 30 days followed by laboratory analyses using molecular\uffe2\uff80\uff90biology tools demonstrate that the preapplied artificial biofilm affects the phylogenetic structure of the developing natural biofilm, reducing phylogenetic diversity and excluding MIC\uffe2\uff80\uff90related bacteria. This sustainable solution for material protection showcases the usefulness of artificially guiding microbial evolutionary processes via the electrostatic modification and controlled delivery of bacterial cells and extracellular matrix to the exposed material surfaces.Gypsum soils in the Mediterranean Basin house large numbers of edaphic specialists that are adapted to stressful environments. The evolutionary history and standing genetic variation of these taxa have been influenced by the geological and paleoclimatic complexity of this area and the long\uffe2\uff80\uff90standing effect of human activities. However, little is known about the origin of Mediterranean gypsophiles and the factors affecting their genetic diversity and population structure.
METHODSUsing phylogenetic and phylogeographic approaches based on microsatellites and sequence data from nuclear and chloroplast regions, we evaluated the divergence time, genetic diversity, and population structure of 27 different populations of the widespread Iberian gypsophile Lepidium subulatum throughout its entire geographic range.
RESULTSLepidium subulatum diverged from its nearest relatives ~3 million years ago, and ITS and psbA/matK trees supported the monophyly of the species. These results suggest that both geological and climatic changes in the region around the Plio\uffe2\uff80\uff90Pleistocene promoted its origin, compared to other evolutionary processes. We found high genetic diversity in both nuclear and chloroplast markers, but a greater population structure in the chloroplast data. These results suggest that while seed dispersal is limited, pollen flow may be favored by the presence of numerous habitat patches that enhance the movement of pollinators.
CONCLUSIONSDespite being an edaphic endemic, L. subulatum possesses high genetic diversity probably related to its relatively old age and high population sizes across its range. Our study highlights the value of using different markers to fully understand the phylogeographic history of plant species.There is an urgent need to develop viable, renewable, sustainable energy systems that can reduce global dependence on fossil fuel sources of energy. Biofuels such as ethanol are being utilized as blends in surface transportation fuels and have the potential to improve sustainability and reduce greenhouse gas emissions in the short term. Bioethanol, the most widely used liquid biofuel, is currently produced by converting sugars or starches from feed crops into ethanol. Use of this fuel source displaces and draws water consumption away from agricultural crops, increases soil erosion by shifting land from perennial grasses to annual crops, and increases use of fertilizers and insecticides. In contrast, bioethanol made from lignocellulosic biomass feedstocks does not have these limitations and in addition, offers a larger resource base: the amount of cellulosic material available for potential use vastly outweighs the amount of available starch\uffe2\uff80\uff90based feedstock. Therefore, bioethanol from lignocellulosic biomass has attracted considerable interest from biofuel developers. This review is an update of some developments to optimize cellulose extraction from feedstock crops and to improve crop yields and logistics. It concludes that agricultural and forestry systems that incorporate lignocellulosic biomass crops can be designed for improved ecological function and energy use efficiency. Development of crops that have both desirable cell\uffe2\uff80\uff90wall traits and high biomass productivity under sustainable low\uffe2\uff80\uff90input conditions can significantly enhance the economics and efficiency of the conversion process. Optimizing the logistics of moving feedstock from field or forest to bio\uffe2\uff80\uff90refinery can significantly reduce costs of using lignocellulosic feedstocks. \uffc2\uffa9 2013 Society of Chemical Industry and John Wiley & Sons, Ltd
", "keywords": ["0301 basic medicine", "2. Zero hunger", "03 medical and health sciences", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "7. Clean energy", "12. Responsible consumption"]}, "links": [{"href": "https://doi.org/10.1002/bbb.1418"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biofuels%2C%20Bioproducts%20and%20Biorefining", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/bbb.1418", "name": "item", "description": "10.1002/bbb.1418", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/bbb.1418"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-07-09T00:00:00Z"}}, {"id": "10.1002/bbb.325", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:17Z", "type": "Journal Article", "created": "2011-09-01", "title": "Biofuels: Ethics And Policy-Making", "description": "AbstractMandatory targets for biofuels have led to their rapid global adoption, but ethical problems with their large\uffe2\uff80\uff90scale production are widely reported. Research is underway to find new biofuel technologies that mitigate climate change and can be produced sustainably and economically. Following an 18\uffe2\uff80\uff90month inquiry, the Nuffield Council on Bioethics has developed an ethical framework for biofuels policy\uffe2\uff80\uff90making. Based on a number of widely held ethical values, six ethical principles are introduced that should be considered in biofuels policy\uffe2\uff80\uff90making. Many current biofuels policies fail this ethical \uffe2\uff80\uff98test\uffe2\uff80\uff99. An overarching ethical standard for biofuels is proposed that includes the protection of human rights and the environment, full life cycle assessment of greenhouse gas emissions, trade principles that are fair, access and benefit\uffe2\uff80\uff90sharing schemes to encourage equitable distribution of costs and benefits, and instruments to incentivize the development of promising new approaches. The Council goes on to make recommendations for changes to current policy. \uffc2\uffa9 2011 Society of Chemical Industry and John Wiley & Sons, Ltd
", "keywords": ["0301 basic medicine", "03 medical and health sciences", "13. Climate action", "01 natural sciences", "7. Clean energy", "0105 earth and related environmental sciences", "12. Responsible consumption", "3. Good health"], "contacts": [{"organization": "Joyce Tait, Alena Buyx,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1002/bbb.325"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biofuels%2C%20Bioproducts%20and%20Biorefining", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/bbb.325", "name": "item", "description": "10.1002/bbb.325", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/bbb.325"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-08-25T00:00:00Z"}}, {"id": "10.1002/biot.202000165", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:17Z", "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/cbic.202000051", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:17Z", "type": "Journal Article", "created": "2020-01-31", "title": "An Engineered E.\u2005coli Strain for Direct in Vivo Fluorination", "description": "AbstractSelectively fluorinated compounds are found frequently in pharmaceutical and agrochemical products where currently 25\uffe2\uff80\uff9330\uffe2\uff80\uff89% of optimised compounds emerge from development containing at least one fluorine atom. There are many methods for the site\uffe2\uff80\uff90specific introduction of fluorine, but all are chemical and they often use environmentally challenging reagents. Biochemical processes for C\uffe2\uff88\uff92F bond formation are attractive, but they are extremely rare. In this work, the fluorinase enzyme, originally identified from the actinomycete bacterium Streptomyces cattleya, is engineered into Escherichia coli in such a manner that the organism is able to produce 5\uffe2\uff80\uffb2\uffe2\uff80\uff90fluorodeoxyadenosine (5\uffe2\uff80\uffb2\uffe2\uff80\uff90FDA) from S\uffe2\uff80\uff90adenosyl\uffe2\uff80\uff90l\uffe2\uff80\uff90methionine (SAM) and fluoride in live E.\uffe2\uff80\uff85coli cells. Success required the introduction of a SAM transporter and deletion of the endogenous fluoride efflux capacity in order to generate an E.\uffe2\uff80\uff85coli host that has the potential for future engineering of more elaborate fluorometabolites.
", "keywords": ["SAM transporters", "0301 basic medicine", "570", "S-Adenosylmethionine", "0303 health sciences", "Deoxyadenosines", "Halogenation", "DAS", "Fluorine", "Halogenations", "540", "QD Chemistry", "Streptomyces", "3. Good health", "03 medical and health sciences", "Bacterial Proteins", "Isomerism", "Escherichia coli", "QD", "Fluoride channels", "Genetic Engineering", "Oxidoreductases", "Fluorinases"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/cbic.202000051"}, {"href": "https://doi.org/10.1002/cbic.202000051"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/ChemBioChem", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/cbic.202000051", "name": "item", "description": "10.1002/cbic.202000051", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/cbic.202000051"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-03T00:00:00Z"}}, {"id": "10.1002/ece3.1879", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:18Z", "type": "Journal Article", "created": "2016-01-22", "title": "Effects Of Fertilization On Microbial Abundance And Emissions Of Greenhouse Gases (Ch4 And N2o) In Rice Paddy Fields", "description": "AbstractThis study is to explore effects of nitrogen application and straw incorporation on abundance of relevant microbes and CH4 and N2O fluxes in a midseason aerated rice paddy field. Fluxes of CH4 and N2O were recorded, and abundance of relevant soil microbial functional genes was determined during rice\uffe2\uff80\uff90growing season in a 6\uffe2\uff80\uff90year\uffe2\uff80\uff90long fertilization experiment field in China. Results indicate that application of urea significantly changed the functional microbial composition, while the influence of straw incorporation was not significant. Application of urea significantly decreased the gene abundances of archaeal amoA and mcrA, but it significantly increased the gene abundances of bacterial amoA. CH4 emission was significantly increased by fresh straw incorporation. Incorporation of burnt straw tended to increase CH4 emission, while the urea application had no obvious effect on CH4 emission. N2O emission was significantly increased by urea application, while fresh or burnt straw incorporation tended to decrease N2O emission. The functional microbial composition did not change significantly over time, although the abundances of pmoA, archaeal amoA, nirS, and nosZ genes changed significantly. The change of CH4 emission showed an inverse trend with the one of the N2O emissions over time. To some extent, the abundance of some functional genes in this study can explain CH4 and N2O emissions. However, the correlation between CH4 and N2O emissions and the abundance of related functional genes was not significant. Environmental factors, such as soil Eh, may be more related to CH4 and N2O emissions.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "03 medical and health sciences", "13. Climate action", "15. Life on land", "Original Research"]}, "links": [{"href": "https://doi.org/10.1002/ece3.1879"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology%20and%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ece3.1879", "name": "item", "description": "10.1002/ece3.1879", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ece3.1879"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-01-22T00:00:00Z"}}, {"id": "10.1002/ecy.1513", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:18Z", "type": "Journal Article", "created": "2016-07-02", "title": "Land Use Intensification In The Humid Tropics Increased Both Alpha And Beta Diversity Of Soil Bacteria", "description": "AbstractAnthropogenic 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/ece3.5244", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:18Z", "type": "Journal Article", "created": "2019-06-10", "title": "Evolution of interdisciplinarity in biodiversity science", "description": "AbstractThe study of biodiversity has grown exponentially in the last thirty years in response to demands for greater understanding of the function and importance of Earth's biodiversity and finding solutions to conserve it. Here, we test the hypothesis that biodiversity science has become more interdisciplinary over time. To do so, we analyze 97,945 peer\uffe2\uff80\uff90reviewed articles over a twenty\uffe2\uff80\uff90two\uffe2\uff80\uff90year time period (1990\uffe2\uff80\uff932012) with a continuous time dynamic model, which classifies articles into concepts (i.e., topics and ideas) based on word co\uffe2\uff80\uff90occurrences. Using the model output, we then quantify different aspects of interdisciplinarity: concept diversity, that is, the diversity of topics and ideas across subdisciplines in biodiversity science, subdiscipline diversity, that is, the diversity of subdisciplines across concepts, and network structure, which captures interactions between concepts and subdisciplines. We found that, on average, concept and subdiscipline diversity in biodiversity science were either stable or declining, patterns which were driven by the persistence of rare concepts and subdisciplines and a decline in the diversity of common concepts and subdisciplines, respectively. Moreover, our results provide evidence that conceptual homogenization, that is, decreases in temporal \uffce\uffb2 concept diversity, underlies the observed trends in interdisciplinarity. Together, our results reveal that biodiversity science is undergoing a dynamic phase as a scientific discipline that is consolidating around a core set of concepts. Our results suggest that progress toward addressing the biodiversity crisis via greater interdisciplinarity during the study period may have been slowed by extrinsic factors, such as the failure to invest in research spanning across concepts and disciplines. However, recent initiatives such as the Intergovernmental Science\uffe2\uff80\uff90Policy Platform on Biodiversity and Ecosystem Services (IPBES) may attract broader support for biodiversity\uffe2\uff80\uff90related issues and hence interdisciplinary approaches to address scientific, political, and societal challenges in the coming years.
", "keywords": ["0301 basic medicine", "bibliographic analysis", "topic models", "0303 health sciences", "03 medical and health sciences", "conceptual homogenization", "interdisciplinarity", "Ecology", "13. Climate action", "15. Life on land", "Academic Practice in Ecology and Evolution", "QH540-549.5", "biodiversity"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.5244"}, {"href": "https://doi.org/10.1002/ece3.5244"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology%20and%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ece3.5244", "name": "item", "description": "10.1002/ece3.5244", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ece3.5244"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-01T00:00:00Z"}}, {"id": "10.1002/ece3.6547", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:18Z", "type": "Journal Article", "created": "2020-07-09", "title": "The distribution of herbivores between leaves matches their performance only in the absence of competitors", "description": "AbstractFew studies have tested how plant quality and the presence of competitors interact in determining how herbivores choose between different leaves within a plant. We investigated this in two herbivorous spider mites sharing tomato plants: Tetranychus urticae, which generally induces plant defenses, and Tetranychus evansi, which suppresses them, creating asymmetrical effects on coinfesting competitors. On uninfested plants, both herbivore species preferred young leaves, coinciding with increased mite performance. On plants with heterospecifics, the mites did not prefer leaves on which they had a better performance. In particular, T.\uffc2\uffa0urticae avoided leaves infested with T.\uffc2\uffa0evansi, which is in agreement with T.\uffc2\uffa0urticae being outcompeted by T.\uffc2\uffa0evansi. In contrast, T.\uffc2\uffa0evansi did not avoid leaves with the other species, but distributed itself evenly over plants infested with heterospecifics. We hypothesize that this behavior of T.\uffc2\uffa0evansi may prevent further spread of T.\uffc2\uffa0urticae over the shared plant. Our results indicate that leaf age determines within\uffe2\uff80\uff90plant distribution of herbivores only in absence of competitors. Moreover, they show that this distribution depends on the order of arrival of competitors and on their effects on each other, with herbivores showing differences in behavior within the plant as a possible response to the outcome of those interactions.Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500\uffc2\uffa0bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large\uffe2\uff80\uff90scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungs\uffc3\uffa4ngen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic\uffe2\uff80\uff90dry part that has a species rich grass\uffe2\uff80\uff90dominated plant community including a high frequency of F.\uffc2\uffa0meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%\uffe2\uff80\uff9340% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.
", "keywords": ["580", "species hypothesis", "Ekologi", "0301 basic medicine", "0303 health sciences", "Ecology", "rDNA", "Biological Systematics", "15. Life on land", "03 medical and health sciences", "14. Life underwater", "ITS", "Research Articles", "clustering"]}, "links": [{"href": "https://pub.epsilon.slu.se/27699/1/eshghi-sahraei-s-et-al-220505.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.8676"}, {"href": "https://doi.org/10.1002/ece3.8676"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology%20and%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ece3.8676", "name": "item", "description": "10.1002/ece3.8676", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ece3.8676"}, {"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": "10.1002/ecs2.2226", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:18Z", "type": "Journal Article", "created": "2018-05-31", "title": "Mycorrhiza in tree diversity-ecosystem function relationships: conceptual framework and experimental implementation", "description": "AbstractThe widely observed positive relationship between plant diversity and ecosystem functioning is thought to be substantially driven by complementary resource use of plant species. Recent work suggests that biotic interactions among plants and between plants and soil organisms drive key aspects of resource use complementarity. Here, we provide a conceptual framework for integrating positive biotic interactions across guilds of organisms, more specifically between plants and mycorrhizal types, to explain resource use complementarity in plants and its consequences for plant competition. Our overarching hypothesis is that ecosystem functioning increases when more plant species associate with functionally dissimilar mycorrhizal fungi because differing mycorrhizal types will increase coverage of habitat space for and reduce competition among plants. We introduce a recently established field experiment (MyDiv) that uses different pools of tree species that associate with either arbuscular or ectomycorrhizal fungi to create orthogonal experimental gradients in tree species richness and mycorrhizal associations and present initial results. Finally, we discuss options for future mechanistic studies on resource use complementarity within MyDiv. We show how mycorrhizal types and biotic interactions in MyDiv can be used in the future to test novel questions regarding the mechanisms underlying biodiversity\uffe2\uff80\uff93ecosystem function relationships.
", "keywords": ["0106 biological sciences", "0301 basic medicine", "2. Zero hunger", "biodiversity\u2013ecosystem functioning", "experimental design", "Ecology", "arbuscular mycorrhiza", "15. Life on land", "01 natural sciences", "ectomycorrhiza", "Article", "biotic interactions", "03 medical and health sciences", "biodiversity effects", "QH540-549.5"]}, "links": [{"href": "https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.2226"}, {"href": "https://doi.org/10.1002/ecs2.2226"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ecs2.2226", "name": "item", "description": "10.1002/ecs2.2226", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecs2.2226"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-05-01T00:00:00Z"}}, {"id": "10.1002/ecs2.2645", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:18Z", "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.
", "keywords": ["TERRESTRIAL", "0106 biological sciences", "0301 basic medicine", "extreme events", "SPECIES INTERACTIONS", "warming", "ecipitation", "precipitation", "01 natural sciences", "333", "03 medical and health sciences", "terrestrial", "14. Life underwater", "freshwater", "Food chains (Ecology)", "2. Zero hunger", "species interactions", "data gaps", "marine", "aquatic", "15. Life on land", "global", "Climate Science", "COMMUNITY", "climate change", "Ecology", " evolutionary biology", "13. Climate action", "food webs", "Climatic changes -- Research", "Klimatvetenskap"]}, "links": [{"href": "https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.2645"}, {"href": "https://doi.org/10.1002/ecs2.2645"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ecs2.2645", "name": "item", "description": "10.1002/ecs2.2645", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecs2.2645"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-01T00:00:00Z"}}, {"id": "10.1002/ecs2.4754", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:18Z", "type": "Journal Article", "created": "2024-01-15", "title": "Invasions eliminate the legacy effects of substrate history on microbial nitrogen cycling", "description": "AbstractChanges 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.
", "keywords": ["0301 basic medicine", "Terrestrial Ecosystems", "archaea", "Evolution", "Eukaryotes", "Antarctic Regions", "1105 Ecology", "Biodiversity; Terrestrial Ecosystems; Archaea; Bacteria; Eukaryotes; Australia; Antarctica.", "Terrestrial ecosystems", "Soil", "03 medical and health sciences", "eukaryotes", "Behavior and Systematics", "XXXXXX - Unknown", "14. Life underwater", "bacteria", "Phylogeny", "Soil Microbiology", "biodiversity", "2. Zero hunger", "0303 health sciences", "Bacteria", "Australia", "terrestrial ecosystems", "Biodiversity", "15. Life on land", "archaebacteria", "Archaea", "soil ecology", "13. Climate action", "eukaryotic cells", "Antarctica"]}, "links": [{"href": "https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2137"}, {"href": "https://doi.org/10.1002/ecy.2137"}, {"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.2137", "name": "item", "description": "10.1002/ecy.2137", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecy.2137"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-12T00:00:00Z"}}, {"id": "10.1002/jpln.200700186", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:21Z", "type": "Journal Article", "created": "2009-07-28", "title": "Abiotic Soil Properties And The Occurrence Of Rhizoctonia Crown And Root Rot In Sugar Beet", "description": "AbstractSince 1993, Rhizoctonia crown and root rot (Rhizoctonia solani AG 2\uffe2\uff80\uff932 IIIB) has represented an increasing problem for sugar beet production in Germany. Up to now, the outbreak of the infection and the spread of the disease within a field cannot be predicted and effective countermeasures are not available. Although little is known about the living conditions of R. solani in soils, abiotic soil properties are likely to influence the disease occurrence. Investigations were carried out based on 60 pairwise comparisons, each consisting of a disease\uffe2\uff80\uff90affected and an adjacent nonaffected patch on farmers' fields in 2002 and 2003. Soil samples from the top soil layer (0\uffe2\uff80\uff9330\uffe2\uff80\uff89cm) were collected before harvest, and eight of the most frequently mentioned soil properties potentially influencing Rhizoctonia crown and root rot infection were examined: bulk density, texture, carbonate carbon, potassium, phosphorus, organic carbon, total nitrogen, and pH. The occurrence of the disease was significantly related to the soil C : N ratio, indicating the influence of soil organic matter on the disease occurrence. Examinations of soil thin sections showed that organic\uffe2\uff80\uff90matter particles in the soil serve as a substrate for R. solani. All other soil physical and chemical properties examined did not differ between the disease\uffe2\uff80\uff90affected and nonaffected patches and seem to be of minor importance.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "03 medical and health sciences", "15. Life on land"]}, "links": [{"href": "https://doi.org/10.1002/jpln.200700186"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Plant%20Nutrition%20and%20Soil%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jpln.200700186", "name": "item", "description": "10.1002/jpln.200700186", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jpln.200700186"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-10-01T00:00:00Z"}}, {"id": "10.1002/jsfa.4207", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:23Z", "type": "Journal Article", "created": "2010-10-27", "title": "Algal Biorefinery-Based Industry: An Approach To Address Fuel And Food Insecurity For A Carbon-Smart World", "description": "Food and fuel production are intricately interconnected. In a carbon-smart society, it is imperative to produce both food and fuel sustainably. Integration of the emerging biorefinery concept with other industries can bring many environmental deliverables while mitigating several sustainability-related issues with respect to greenhouse gas emissions, fossil fuel usage, land use change for fuel production and future food insufficiency. A new biorefinery-based integrated industrial ecology encompasses the different value chain of products, coproducts, and services from the biorefinery industries. This paper discusses a framework to integrate the algal biofuel-based biorefinery, a booming biofuel sector, with other industries such as livestock, lignocellulosic and aquaculture. Using the USA as an example, this paper also illustrates the benefits associated with sustainable production of fuel and food. Policy and regulatory initiatives for synergistic development of the algal biofuel sector with other industries can bring many sustainable solutions for the future existence of mankind.", "keywords": ["2. Zero hunger", "0301 basic medicine", "Conservation of Natural Resources", "0303 health sciences", "9. Industry and infrastructure", "0402 animal and dairy science", "Agriculture", "04 agricultural and veterinary sciences", "Aquaculture", "15. Life on land", "7. Clean energy", "Food Supply", "12. Responsible consumption", "03 medical and health sciences", "Chlorophyta", "13. Climate action", "Biofuels", "11. Sustainability", "Animal Husbandry", "0405 other agricultural sciences"], "contacts": [{"organization": "Grinson-George, Bobban Subhadra,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1002/jsfa.4207"}, {"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.4207", "name": "item", "description": "10.1002/jsfa.4207", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.4207"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-10-27T00:00:00Z"}}, {"id": "10.1002/jsfa.4533", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:23Z", "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.5647", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:23Z", "type": "Journal Article", "created": "2012-03-19", "title": "Influence Of Rootstock On Drought Response In Young \u2018Gale Gala\u2019 Apple (Malus Domestica Borkh.) Trees", "description": "AbstractBACKGROUND: Drought is a major environmental stress limiting plant growth, productivity, and survival worldwide. Rootstocks are widely used to enhance plants resistance to drought stresses. This study determined influence of rootstock on drought responses in 1\uffe2\uff80\uff90year\uffe2\uff80\uff90old \uffe2\uff80\uff98Gale Gala\uffe2\uff80\uff99 apple trees grafted onto Malus sieversii or M. hupehensis.
RESULTS: Choice of rootstock resulted in differential response to drought stress. Specifically, M. sieversii caused less drought\uffe2\uff80\uff90induced reduction in relative growth rate, biomass accumulation, leaf area, leaf chlorophyll content, relative water content, photosynthesis rate and maximum chlorophyll fluorescence yield but greater increase in whole\uffe2\uff80\uff90plant water use efficiency compared to M. hupehensis. Secondly, compared with M. hupehensis, M. sieversii caused less drought\uffe2\uff80\uff90induced accumulation of reactive oxygen species but more increase in activities of antioxidant enzymes. In addition, xylem sap abscisic acid concentration was greater in trees grafted onto M. hupehensis than in those grafted onto M. sieversii under drought stress.
CONCLUSION: \uffe2\uff80\uff98Gale Gala\uffe2\uff80\uff99 trees' response to drought stress was associated with the rootstock's genotype onto which it was grafted. Trees with M. sieversii as rootstock are more drought resistant than trees with M. hupehensis as rootstock, which suggests that M. sieversii can be widely used as rootstock in arid and semi\uffe2\uff80\uff90arid regions. Copyright \uffc2\uffa9 2012 Society of Chemical Industry
", "keywords": ["Chlorophyll", "0301 basic medicine", "Plant Roots", "Antioxidants", "Fluorescence", "Trees", "03 medical and health sciences", "Species Specificity", "Stress", " Physiological", "Xylem", "Biomass", "Photosynthesis", "2. Zero hunger", "0402 animal and dairy science", "Water", "04 agricultural and veterinary sciences", "15. Life on land", "Adaptation", " Physiological", "6. Clean water", "Droughts", "Plant Leaves", "Malus", "0401 agriculture", " forestry", " and fisheries", "0405 other agricultural sciences", "Reactive Oxygen Species", "Abscisic Acid"], "contacts": [{"organization": "Binghua Liu, Fengwang Ma, Dong Liang, Yangjun Zou, Liang Cheng,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1002/jsfa.5647"}, {"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.5647", "name": "item", "description": "10.1002/jsfa.5647", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.5647"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-03-19T00:00:00Z"}}, {"id": "10.1002/jsfa.6206", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:23Z", "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": "2026-04-28T16:14:23Z", "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/ldr.3453", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-28T16:14:24Z", "type": "Journal Article", "created": "2019-10-15", "title": "Increases in aridity lead to drastic shifts in the assembly of dryland complex microbial networks", "description": "AbstractWe have little information on how and why soil microbial community assembly will respond to predicted increases in aridity by the end of this century. Here, we used correlation networks and structural equation modeling to assess the changes in the abundance of the ecological clusters including potential winner and loser microbial taxa associated with predicted increases in aridity. To do this, we conducted a field survey in an environmental gradient from eastern Australia and obtained information on bacterial and fungal community composition for 120 soil samples and multiple abiotic and biotic factors. Overall, our structural equation model explained 83% of the variance in the two mesic modules. Increases in aridity led to marked shifts in the abundance of the two major microbial modules found in our network, which accounted for >99% of all phylotypes. In particular, the relative abundance of one of these modules, the Mesic Module #1, which was positively related to multiple soil properties and plant productivity, declined strongly with aridity. Conversely, the relative abundance of a second dominant module (Xeric Module #2) was positively correlated with increases in aridity. Our study provides evidence that network analysis is a useful tool to identify microbial taxa that are either winners or losers under increasing aridity and therefore potentially under changing climates. Our work further suggests that climate change, and associated land degradation, could potentially lead to extensive microbial phylotypes exchange and local extinctions, as demonstrated by the reductions of up to 97% in the relative abundance of microbial taxa within Mesic Module #1.Dissolved organic matter (DOM) composition exerts a direct control on its degradation and subsequent persistence in aquatic ecosystems. Yet, under certain conditions, the degradation patterns of DOM cannot be solely explained by its composition, highlighting the relevance of environmental conditions for DOM degradation. Here, we experimentally assessed the relative influence of composition vs. environment on DOM degradation by performing degradation bioassays using three contrasting DOM sources inoculated with a standardized bacterial inoculum under five distinct environments. The DOM degradation kinetics modeled using reactivity continuum models showed that composition was more important than environment in determining the bulk DOM decay patterns. Changes in DOM composition resulted from the interaction between DOM source and environment. The role of environment was stronger on shaping the bacterial community composition, but the intrinsic nature of the DOM source exerted stronger control on the DOM degradation function.
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