{"type": "FeatureCollection", "features": [{"id": "10.1016/j.biocontrol.2022.104890", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-06-24T16:16:27Z", "type": "Journal Article", "created": "2022-03-14", "title": "Exploring microbiomes for plant disease management", "description": "Microbiome science is revolutionizing many concepts of plant biology, ecology, and evolution. Understanding plant microbiomes is key to developing solutions that protect crop health without impacting the environment. In this perspective article, we highlight the importance of both the structure and functions of plant-associated microbial communities in protecting their host from pathogens. These new findings have a high potential to aid biocontrol programs and to replace traditional chemical products, guiding the transition towards a sustainable production.", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "ddc:570", "15. Life on land", "Institut f\u00fcr Biochemie und Biologie"]}, "links": [{"href": "https://doi.org/10.1016/j.biocontrol.2022.104890"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biological%20Control", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biocontrol.2022.104890", "name": "item", "description": "10.1016/j.biocontrol.2022.104890", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biocontrol.2022.104890"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-06-01T00:00:00Z"}}, {"id": "10.1007/s10980-020-00984-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:15:41Z", "type": "Journal Article", "created": "2020-03-10", "title": "Global vulnerability of soil ecosystems to erosion", "description": "Abstract Context

Soil erosion is one of the main threats driving soil degradation across the globe with important impacts on crop yields, soil biota, biogeochemical cycles, and ultimately human nutrition.

Objectives

Here, using an empirical model, we present a global and temporally explicit assessment of soil erosion risk according to recent (2001\uffe2\uff80\uff932013) dynamics of rainfall and vegetation cover change to identify vulnerable areas for soils and soil biodiversity.

Methods

We used an adaptation of the Universal Soil Loss Equation together with state of the art remote sensing models to create a spatially and temporally explicit global model of soil erosion and soil protection. Finally, we overlaid global maps of soil biodiversity to assess the potential vulnerability of these soil communities to soil erosion.

Results

We show a consistent decline in soil erosion protection over time across terrestrial biomes, which resulted in a global increase of 11.7% in soil erosion rates. Notably, soil erosion risk systematically increased between 2006 and 2013 in relation to the baseline year (2001). Although vegetation cover is central to soil protection, this increase was mostly driven by changes in rainfall erosivity. Globally, soil erosion is expected not only to have an impact on the vulnerability of soil conditions but also on soil biodiversity with 6.4% (for soil macrofauna) and 7.6% (for soil fungi) of these vulnerable areas coinciding with regions with high soil biodiversity.

Conclusions

Our results indicate that an increasing proportion of soils are degraded globally, affecting not only livelihoods but also potentially degrading local and regional landscapes. Similarly, many degraded regions coincide with and may have impacted high levels of soil biodiversity.Soil microbes are essential for maintenance of life\uffe2\uff80\uff90supporting ecosystem services, but projections of how these microbes will be affected by global change scenarios are lacking. Therefore, our aim was to provide projections of future soil microbial distribution using several scenarios of global change.

Location

Global.

Time period

1950\uffe2\uff80\uff932090.

Major taxa studied

Bacteria and fungi.

Methods

We used a global database of soil microbial communities across six continents to estimate past and future trends of the soil microbiome. To do so, we used structural equation models to include the direct and indirect effects of changes in climate and land use in our predictions, using current climate (temperature and precipitation) and land\uffe2\uff80\uff90use projections between 1950 and 2090.

Results

Local bacterial richness will increase in all scenarios of change in climate and land use considered, although this increase will be followed by a generalized community homogenization process affecting >\uffc2\uffa085% of terrestrial ecosystems. Changes in the relative abundance of functional genes associated with the increases in bacterial richness are also expected. Based on an ecological cluster analysis, our results suggest that phylotypes such asGeodermatophilusspp. (typical desert bacteria),Mycobacteriumsp. (which are known to include important human pathogens),Streptomyces mirabilis(major producers of antibiotic resistance genes) or potential fungal soil\uffe2\uff80\uff90borne plant pathogens belonging to Ascomycota fungi (Venturiaspp.,Devriesiaspp.) will become more abundant in their communities.

Main conclusions

Our results provide evidence that climate change has a stronger influence on soil microbial communities than change in land use (often including deforestation and agricultural expansion), although most of the effects of climate are indirect, through other environmental variables (e.g., changes in soil pH). The same was found for microbial functions such as the prevalence of phosphate transport genes. We provide reliable predictions about the changes in the global distribution of microbial communities, showing an increase in alpha diversity and a homogenization of soil microbial communities in the Anthropocene.Diphthamide, a post-translationally modified histidine residue of eukaryotic TRANSLATION ELONGATION FACTOR2 (eEF2), is the human host cell-sensitizing target of diphtheria toxin. Diphthamide biosynthesis depends on the 4Fe-4S-cluster protein Dph1 catalyzing the first committed step, as well as Dph2 to Dph7, in yeast and mammals. Here we show that diphthamide modification of eEF2 is conserved inArabidopsis thalianaand requires AtDPH1. Ribosomal \uffe2\uff88\uff921 frameshifting-error rates are increased in Arabidopsisdph1mutants, similar to yeast and mice. Compared to the wild type, shorter roots and smaller rosettes ofdph1mutants result from fewer formed cells. TARGET OF RAPAMYCIN (TOR) kinase activity is attenuated, and autophagy is activated, indph1mutants. Under abiotic stress diphthamide-unmodified eEF2 accumulates in wild-type seedlings, most strongly upon heavy metal excess, which is conserved in human cells. In summary, our results suggest that diphthamide contributes to the functionality of the translational machinery monitored by plants to regulate growth.

Microplastics in soils have become an important threat for terrestrial systems as they may potentially alter the geochemical/biophysical soil environment and can interact with drought. As microplastics may affect soil water content, this could exacerbate the well\uffe2\uff80\uff90known negative effects of drought on ecosystem functionality. Thus, functions including litter decomposition, soil aggregation or those related with nutrient cycling can be altered. Despite this potential interaction, we know relatively little about how microplastics, under different soil water conditions, affect ecosystem functions and multifunctionality.

To address this gap, we performed an experiment using grassland plant communities growing in microcosms. Microplastic fibres (absent, present) and soil water conditions (well\uffe2\uff80\uff90watered, drought) were applied in a fully factorial design. At harvest, we measured soil ecosystem functions related to nutrient cycling (\uffce\uffb2\uffe2\uff80\uff90glucosaminidase, \uffce\uffb2\uffe2\uff80\uff90D\uffe2\uff80\uff90cellobiosidase, phosphatase, \uffce\uffb2\uffe2\uff80\uff90glucosidase enzymes), respiration, nutrient retention, pH, litter decomposition and soil aggregation (water stable aggregates). As terrestrial systems provide these functions simultaneously, we also assessed ecosystem multifunctionality, an index that encompasses the array of ecosystem functions measured here.

We found that the interaction between microplastic fibres and drought affected ecosystem functions and multifunctionality. Drought had negatively affected nutrient cycling by decreasing enzymatic activities by up to ~39%, while microplastics increased soil aggregation by ~18%, soil pH by ~4% and nutrient retention by up to ~70% by diminishing nutrient leaching. Microplastic fibres also impacted soil enzymes, respiration and ecosystem multifunctionality, but importantly, the direction of these effects depended on soil water status. That is, under well\uffe2\uff80\uff90watered conditions, these functions decreased with microplastic fibres by up to ~34% while under drought they had similar values irrespective of the microplastic presence, or tended to increase with microplastics. Litter decomposition had a contrary pattern increasing with microplastics by ~6% under well\uffe2\uff80\uff90watered conditions while decreasing to a similar percentage under drought.

Synthesis and applications. Single ecosystem functions can be positively or negatively affected by microplastics fibres depending on soil water status. However, our results suggest that microplastic fibres may cause negative effects on ecosystem soil multifunctionality of a similar magnitude as drought. Thus, strategies to counteract this new global change factor are necessary.

", "keywords": ["2. Zero hunger", "570", "ddc:630", "nutrient cycling", "litter decomposition", "500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie", "04 agricultural and veterinary sciences", "15. Life on land", "soil respiration", "01 natural sciences", "6. Clean water", "soil aggregation", "soil pH", "grasslands ecosystem", "13. Climate action", "nutrient leaching", "0401 agriculture", " forestry", " and fisheries", "ddc:570", "Institut f\u00fcr Biochemie und Biologie", "enzymatic activities", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2664.13839"}, {"href": "https://doi.org/10.1111/1365-2664.13839"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Applied%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1365-2664.13839", "name": "item", "description": "10.1111/1365-2664.13839", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1365-2664.13839"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-10T00:00:00Z"}}, {"id": "10.1111/ecog.05308", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:17Z", "type": "Journal Article", "created": "2021-01-19", "title": "Evaluating predictive performance of statistical models explaining wild bee abundance in a mass\u2010flowering crop", "description": "

Wild bee populations are threatened by current agricultural practices in many parts of the world, which may put pollination services and crop yields at risk. Loss of pollination services can potentially be predicted by models that link bee abundances with landscape\uffe2\uff80\uff90scale land\uffe2\uff80\uff90use, but there is little knowledge on the degree to which these statistical models are transferable across time and space. This study assesses the transferability of models for wild bee abundance in a mass\uffe2\uff80\uff90flowering crop across space (from one region to another) and across time (from one year to another). The models used existing data on bumblebee and solitary bee abundance in winter oilseed rape fields, together with high\uffe2\uff80\uff90resolution land\uffe2\uff80\uff90use crop\uffe2\uff80\uff90cover and semi\uffe2\uff80\uff90natural habitats data, from studies conducted in five different regions located in four countries (Sweden, Germany, Netherlands and the UK), in three different years (2011, 2012, 2013). We developed a hierarchical model combining all studies and evaluated the transferability using cross\uffe2\uff80\uff90validation. We found that both the landscape\uffe2\uff80\uff90scale cover of mass\uffe2\uff80\uff90flowering crops and permanent semi\uffe2\uff80\uff90natural habitats, including grasslands and forests, are important drivers of wild bee abundance in all regions. However, while the negative effect of increasing mass\uffe2\uff80\uff90flowering crops on the density of the pollinators is consistent between studies, the direction of the effect of semi\uffe2\uff80\uff90natural habitat is variable between studies. The transferability of these statistical models is limited, especially across regions, but also across time. Our study demonstrates the limits of using statistical models in conjunction with widely available land\uffe2\uff80\uff90use crop\uffe2\uff80\uff90cover classes for extrapolating pollinator density across years and regions, likely in part because input variables such as cover of semi\uffe2\uff80\uff90natural habitats poorly capture variability in pollinator resources between regions and years.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Model predictions", "Transferability in ecology", "Brassica napus", "wild pollinators", "mass flowering crops", "15. Life on land", "Mass flowering crops", "", "transferability in ecology", "03 medical and health sciences", "Permanent seminatural habitats", "model predictions", "ddc:570", "permanent semi-natural habitats", "Wild pollinators"]}, "links": [{"href": "https://centaur.reading.ac.uk/95616/1/ecog.05308.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.05308"}, {"href": "https://doi.org/10.1111/ecog.05308"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecography", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/ecog.05308", "name": "item", "description": "10.1111/ecog.05308", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/ecog.05308"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-19T00:00:00Z"}}, {"id": "10.1126/science.abq4062", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:49Z", "type": "Journal Article", "created": "2022-11-24", "title": "Grazing and ecosystem service delivery in global drylands", "description": "

Grazing represents the most extensive use of land worldwide. Yet its impacts on ecosystem services remain uncertain because pervasive interactions between grazing pressure, climate, soil properties, and biodiversity may occur but have never been addressed simultaneously. Using a standardized survey at 98 sites across six continents, we show that interactions between grazing pressure, climate, soil, and biodiversity are critical to explain the delivery of fundamental ecosystem services across drylands worldwide. Increasing grazing pressure reduced ecosystem service delivery in warmer and species-poor drylands, whereas positive effects of grazing were observed in colder and species-rich areas. Considering interactions between grazing and local abiotic and biotic factors is key for understanding the fate of dryland ecosystems under climate change and increasing human pressure.

", "keywords": ["[SDE] Environmental Sciences", "570", "Ecosystem services (ES)", "Livestock", "Climate", "Climate Change", "Wild", "630", "Dryland", "Soil", "SDG-02: Zero hunger", "XXXXXX - Unknown", "Climate change", "Humans", "Ecosystem services", "grazing", "Herbivory", "14. Life underwater", "climate", "Institut f\u00fcr Biochemie und Biologie", "Ecosystem", "biodiversity", "SDG-15: Life on land", "2. Zero hunger", "Systems", "Drylands", "Qu\u00edmica", "Biodiversity", "15. Life on land", "Grazing", "13. Climate action", "[SDE]Environmental Sciences", "ddc:570", "ecosystem services", "Rangeland"]}, "links": [{"href": "https://doi.org/10.1126/science.abq4062"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1126/science.abq4062", "name": "item", "description": "10.1126/science.abq4062", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1126/science.abq4062"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-25T00:00:00Z"}}, {"id": "10.14279/depositonce-15380", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:20:11Z", "type": "Journal Article", "created": "2022-02-24", "title": "Decoupling between ecosystem photosynthesis and transpiration: a last resort against overheating", "description": "Abstract

Ecosystems are projected to face extreme high temperatures more frequently in the near future. Various biotic coping strategies exist to prevent heat stress. Controlled experiments have recently provided evidence for continued transpiration in woody plants during high air temperatures, even when photosynthesis is inhibited. Such a decoupling of photosynthesis and transpiration would represent an effective strategy (\uffe2\uff80\uff98known as leaf or canopy cooling\uffe2\uff80\uff99) to prevent lethal leaf temperatures. At the ecosystem scale, continued transpiration might dampen the development and propagation of heat extremes despite further desiccating soils. However, at the ecosystem scale, evidence for the occurrence of this decoupling is still limited. Here, we aim to investigate this mechanism using eddy-covariance data of thirteen woody ecosystems located in Australia and a causal graph discovery algorithm. Working at half-hourly time resolution, we find evidence for a decoupling of photosynthesis and transpiration in four ecosystems which can be classified as Mediterranean woodlands. The decoupling occurred at air temperatures above 35 \uffe2\uff88\uff98C. At the nine other investigated woody sites, we found that vegetation CO2 exchange remained coupled to transpiration at the observed high air temperatures. Ecosystem characteristics suggest that the canopy energy balance plays a crucial role in determining the occurrence of a decoupling. Our results highlight the value of causal-inference approaches for the analysis of complex physiological processes. With regard to projected increasing temperatures and especially extreme events in future climates, further vegetation types might be pushed to threatening canopy temperatures. Our findings suggest that the coupling of leaf-level photosynthesis and stomatal conductance, common in land surface schemes, may need be re-examined when applied to high-temperature events.

", "keywords": ["heat wave", "570", "AUSTRALIA", "Science", "QC1-999", "UNCERTAINTY", "Environmental technology. Sanitary engineering", "01 natural sciences", "transpiration", "FLUX TOWER", "ddc:570", "GE1-350", "TOLERANCE", "TEMPERATURE", "TD1-1066", "0105 earth and related environmental sciences", "photosynthesis", "CONDUCTANCE", "Physics", "Q", "04 agricultural and veterinary sciences", "15. Life on land", "WATER-USE", "MODEL", "Environmental sciences", "13. Climate action", "Earth and Environmental Sciences", "ecosystem functioning", "PINUS-TAEDA", "0401 agriculture", " forestry", " and fisheries", "ELEVATED CO2", "570 Biowissenschaften; Biologie"]}, "links": [{"href": "https://doi.org/10.14279/depositonce-15380"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Research%20Letters", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.14279/depositonce-15380", "name": "item", "description": "10.14279/depositonce-15380", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.14279/depositonce-15380"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-14T00:00:00Z"}}, {"id": "10.3390/microorganisms8122024", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:21:40Z", "type": "Journal Article", "created": "2020-12-17", "title": "The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses", "description": "

Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.

", "keywords": ["Bioconversion", "anaerobic digestion", "0301 basic medicine", "2. Zero hunger", "bioconversion", "Biomethanation", "QH301-705.5", "570 Biologie", "polysaccharide utilization loci", "metabolic pathway reconstruction", "16. Peace & justice", "7. Clean energy", "Article", "660.6", "biomethanation", "03 medical and health sciences", "Metabolic pathway reconstruction", "Polysaccharide utilization loci", "carbohydrate-active enzymes; polysaccharide utilization loci; anaerobic digestion; biomethanation; metabolic pathway reconstruction; bioconversion", "Anaerobic digestion", "carbohydrate-active enzymes", "Carbohydrate-active enzymes", "ddc:570", "Biology (General)"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/12/2024/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/12/2024/pdf"}, {"href": "https://doi.org/10.3390/microorganisms8122024"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms8122024", "name": "item", "description": "10.3390/microorganisms8122024", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms8122024"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-17T00:00:00Z"}}, {"id": "21.11116/0000-0007-B312-A", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:26:30Z", "type": "Journal Article", "created": "2020-12-17", "title": "The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses", "description": "

Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.

", "keywords": ["Bioconversion", "anaerobic digestion", "0301 basic medicine", "2. Zero hunger", "bioconversion", "Biomethanation", "QH301-705.5", "570 Biologie", "polysaccharide utilization loci", "metabolic pathway reconstruction", "16. Peace & justice", "7. Clean energy", "Article", "660.6", "biomethanation", "03 medical and health sciences", "Metabolic pathway reconstruction", "Polysaccharide utilization loci", "Anaerobic digestion", "carbohydrate-active enzymes", "Carbohydrate-active enzymes", "ddc:570", "Biology (General)"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/12/2024/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/12/2024/pdf"}, {"href": "https://doi.org/21.11116/0000-0007-B312-A"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "21.11116/0000-0007-B312-A", "name": "item", "description": "21.11116/0000-0007-B312-A", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/21.11116/0000-0007-B312-A"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-17T00:00:00Z"}}, {"id": "10.3389/fmicb.2022.1032515", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:21:26Z", "type": "Journal Article", "created": "2022-11-09", "title": "The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses", "description": "

Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process and the corresponding microbiome composition in order to optimize the performance of the process and the biogas output. Previously,Lachnospiraceaespecies were frequently detected in mesophilic to moderately thermophilic biogas reactors. To analyze adaptive genome features of a representativeLachnospiraceaestrain,Anaeropeptidivorans aminofermentansM3/9Twas isolated from a mesophilic laboratory-scale biogas plant and its genome was sequenced and analyzed in detail. Strain M3/9Tpossesses a number of genes encoding enzymes for degradation of proteins, oligo- and dipeptides. Moreover, genes encoding enzymes participating in fermentation of amino acids released from peptide hydrolysis were also identified. Based on further findings obtained from metabolic pathway reconstruction, M3/9Twas predicted to participate in acidogenesis within the AD process. To understand the genomic diversity between the biogas isolate M3/9Tand closely relatedAnaerotignumtype strains, genome sequence comparisons were performed. M3/9Tharbors 1,693 strain-specific genes among others encoding different peptidases, a phosphotransferase system (PTS) for sugar uptake, but also proteins involved in extracellular solute binding and import, sporulation and flagellar biosynthesis. In order to determine the occurrence of M3/9Tin other environments, large-scale fragment recruitments with the M3/9Tgenome as a template and publicly available metagenomes representing different environments was performed. The strain was detected in the intestine of mammals, being most abundant in goat feces, occasionally used as a substrate for biogas production.Abstract. The LPJ-GUESS dynamic vegetation model uniquely combines an individual- and patch-based representation of vegetation dynamics with ecosystem biogeochemical cycling from regional to global scales. We present an updated version that includes plant and soil N dynamics, analysing the implications of accounting for C\uffe2\uff80\uff93N interactions on predictions and performance of the model. Stand structural dynamics and allometric scaling of tree growth suggested by global databases of forest stand structure and development were well reproduced by the model in comparison to an earlier multi-model study. Accounting for N cycle dynamics improved the goodness of fit for broadleaved forests. N limitation associated with low N-mineralisation rates reduces productivity of cold-climate and dry-climate ecosystems relative to mesic temperate and tropical ecosystems. In a model experiment emulating free-air CO2 enrichment (FACE) treatment for forests globally, N limitation associated with low N-mineralisation rates of colder soils reduces CO2 enhancement of net primary production (NPP) for boreal forests, while some temperate and tropical forests exhibit increased NPP enhancement. Under a business-as-usual future climate and emissions scenario, ecosystem C storage globally was projected to increase by ca. 10%; additional N requirements to match this increasing ecosystem C were within the high N supply limit estimated on stoichiometric grounds in an earlier study. Our results highlight the importance of accounting for C\uffe2\uff80\uff93N interactions in studies of global terrestrial N cycling, and as a basis for understanding mechanisms on local scales and in different regional contexts.

", "keywords": ["570", "QE1-996.5", "info:eu-repo/classification/ddc/550", "550", "Ecology", "ddc:550", "Geology", "15. Life on land", "551", "01 natural sciences", "Earth sciences", "Life", "13. Climate action", "ddc:570", "QH501-531", "616", "XXXXXX - Unknown", "nitrogen cycle", "carbon cycle (biogeochemistry)", "ecosystems", "QH540-549.5", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.5194/bg-11-2027-2014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biogeosciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.5194/bg-11-2027-2014", "name": "item", "description": "10.5194/bg-11-2027-2014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5194/bg-11-2027-2014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-28T00:00:00Z"}}, {"id": "10072/411486", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:25:25Z", "type": "Journal Article", "created": "2021-11-25", "title": "Cross-continental importance of CH4 emissions from dry inland-waters", "description": "Despite substantial advances in quantifying greenhouse gas (GHG) emissions from dry inland waters, existing estimates mainly consist of carbon dioxide (CO2) emissions. However, methane (CH4) may also be relevant due to its higher Global Warming Potential (GWP). We report CH4 emissions from dry inland water sediments to i) provide a cross-continental estimate of such emissions for different types of aquatic systems (i.e., lakes, ponds, reservoirs, and streams) and climate zones (i.e., tropical, continental, and temperate); and ii) determine the environmental factors that control these emissions. CH4 emissions from dry inland waters were consistently higher than emissions observed in adjacent uphill soils, across climate zones and in all aquatic systems except for streams. However, the CH4 contribution (normalized to CO2 equivalents; CO2-eq) to the total GHG emissions of dry inland waters was similar for all types of aquatic systems and varied from 10 to 21%. Although we discuss multiple controlling factors, dry inland water CH4 emissions were most strongly related to sediment organic matter content and moisture. Summing CO2 and CH4 emissions revealed a cross-continental average emission of 9.6\u00a0\u00b1\u00a017.4\u00a0g\u00a0CO2-eq\u00a0m-2\u00a0d-1 from dry inland waters. We argue that increasing droughts likely expand the worldwide surface area of atmosphere-exposed aquatic sediments, thereby increasing global dry inland water CH4 emissions. Hence, CH4 cannot be ignored if we want to fully understand the carbon (C) cycle of dry sediments.", "keywords": ["0106 biological sciences", "550", "Nitrous Oxide", "Aquatic Ecology", "Carbon Dioxide", "15. Life on land", "01 natural sciences", "6. Clean water", "[SDU] Sciences of the Universe [physics]", "Greenhouse Gases", "Lakes", "Rivers", "[SDU]Sciences of the Universe [physics]", "13. Climate action", "Ecological Microbiology", "11. Sustainability", "ddc:570", "Methane", "Institut f\u00fcr Biochemie und Biologie", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10072/411486"}, {"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": "10072/411486", "name": "item", "description": "10072/411486", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10072/411486"}, {"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": "10115/29781", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-24T16:25:26Z", "type": "Journal Article", "created": "2022-07-11", "title": "Translational fidelity and growth of Arabidopsis require stress-sensitive diphthamide biosynthesis", "description": "Abstract

Diphthamide, a post-translationally modified histidine residue of eukaryotic TRANSLATION ELONGATION FACTOR2 (eEF2), is the human host cell-sensitizing target of diphtheria toxin. Diphthamide biosynthesis depends on the 4Fe-4S-cluster protein Dph1 catalyzing the first committed step, as well as Dph2 to Dph7, in yeast and mammals. Here we show that diphthamide modification of eEF2 is conserved inArabidopsis thalianaand requires AtDPH1. Ribosomal \uffe2\uff88\uff921 frameshifting-error rates are increased in Arabidopsisdph1mutants, similar to yeast and mice. Compared to the wild type, shorter roots and smaller rosettes ofdph1mutants result from fewer formed cells. TARGET OF RAPAMYCIN (TOR) kinase activity is attenuated, and autophagy is activated, indph1mutants. Under abiotic stress diphthamide-unmodified eEF2 accumulates in wild-type seedlings, most strongly upon heavy metal excess, which is conserved in human cells. In summary, our results suggest that diphthamide contributes to the functionality of the translational machinery monitored by plants to regulate growth.Soil microbes are essential for maintenance of life\uffe2\uff80\uff90supporting ecosystem services, but projections of how these microbes will be affected by global change scenarios are lacking. Therefore, our aim was to provide projections of future soil microbial distribution using several scenarios of global change.

Location

Global.

Time period

1950\uffe2\uff80\uff932090.

Major taxa studied

Bacteria and fungi.

Methods

We used a global database of soil microbial communities across six continents to estimate past and future trends of the soil microbiome. To do so, we used structural equation models to include the direct and indirect effects of changes in climate and land use in our predictions, using current climate (temperature and precipitation) and land\uffe2\uff80\uff90use projections between 1950 and 2090.

Results

Local bacterial richness will increase in all scenarios of change in climate and land use considered, although this increase will be followed by a generalized community homogenization process affecting >\uffc2\uffa085% of terrestrial ecosystems. Changes in the relative abundance of functional genes associated with the increases in bacterial richness are also expected. Based on an ecological cluster analysis, our results suggest that phylotypes such asGeodermatophilusspp. (typical desert bacteria),Mycobacteriumsp. (which are known to include important human pathogens),Streptomyces mirabilis(major producers of antibiotic resistance genes) or potential fungal soil\uffe2\uff80\uff90borne plant pathogens belonging to Ascomycota fungi (Venturiaspp.,Devriesiaspp.) will become more abundant in their communities.

Main conclusions

Our results provide evidence that climate change has a stronger influence on soil microbial communities than change in land use (often including deforestation and agricultural expansion), although most of the effects of climate are indirect, through other environmental variables (e.g., changes in soil pH). The same was found for microbial functions such as the prevalence of phosphate transport genes. We provide reliable predictions about the changes in the global distribution of microbial communities, showing an increase in alpha diversity and a homogenization of soil microbial communities in the Anthropocene.Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.Enhancing the reliability of literature reviews and evidence synthesis is crucial for advancing the transformation of agriculture and food (agri-food) systems as well as for informed decisions and policy making. In this perspective, we argue that evidence syntheses in the field of agri-food systems research often suffer from a suite of methodological limitations that substantially increase the risk of bias, i.e., publication and selection bias, resulting in unreliable and potentially flawed conclusions and, consequently, poor decisions (e.g., policy direction, investment, research foci). We assessed 926 articles from the Collaboration for Environmental Evidence Database of Evidence Reviews (CEEDER) and recent examples from agri-food systems research to support our reasoning. The analysis of articles from CEEDER (n\uffe2\uff80\uff89=\uffe2\uff80\uff89926) specifically indicates poor quality (Red) in measures to minimize subjectivity during critical appraisal (98% of all reviews), application of the eligibility criteria (97%), cross-checking of extracted data by more than one reviewer (97%), critical appraisal of studies (88%), establishment of an a priori method/protocol (86%), and transparent reporting of eligibility decisions (65%). Additionally, deficiencies (Amber) were found in most articles (>50%) regarding the investigation and discussion of variability in study findings (89%), comprehensiveness of the search (78%), definition of eligibility criteria (72%), search approach (64%), reporting of extracted data for each study (59%), consideration and discussion of the limitations of the synthesis (56%), documentation of data extraction (54%) and regarding the statistical approach (52%). To enhance the quality of evidence synthesis in agri-food science, review authors should use tried-and-tested methodologies and publish peer-reviewed a priori protocols. Training in evidence synthesis methods should be scaled, with universities playing a crucial role. It is the shared duty of research authors, training providers, supervisors, reviewers, and editors to ensure that rigorous and robust evidence syntheses are made available to decision-makers. We argue that all these actors should be cognizant of these common mistakes to avoid publishing unreliable syntheses. Only by thinking as a community can we ensure that reliable evidence is provided to support appropriate decision-making in agri-food systems science.Simulation models represent soil organic carbon (SOC) dynamics in global carbon (C) cycle scenarios to support climate\uffe2\uff80\uff90change studies. It is imperative to increase confidence in long\uffe2\uff80\uff90term predictions of SOC dynamics by reducing the uncertainty in model estimates. We evaluated SOC simulated from an ensemble of 26 process\uffe2\uff80\uff90based C models by comparing simulations to experimental data from seven long\uffe2\uff80\uff90term bare\uffe2\uff80\uff90fallow (vegetation\uffe2\uff80\uff90free) plots at six sites: Denmark (two sites), France, Russia, Sweden and the United Kingdom. The decay of SOC in these plots has been monitored for decades since the last inputs of plant material, providing the opportunity to test decomposition without the continuous input of new organic material. The models were run independently over multi\uffe2\uff80\uff90year simulation periods (from 28 to 80\uffc2\uffa0years) in a blind test with no calibration (Bln) and with the following three calibration scenarios, each providing different levels of information and/or allowing different levels of model fitting: (a) calibrating decomposition parameters separately at each experimental site (Spe); (b) using a generic, knowledge\uffe2\uff80\uff90based, parameterization applicable in the Central European region (Gen); and (c) using a combination of both (a) and (b) strategies (Mix). We addressed uncertainties from different modelling approaches with or without spin\uffe2\uff80\uff90up initialization of SOC. Changes in the multi\uffe2\uff80\uff90model median (MMM) of SOC were used as descriptors of the ensemble performance. On average across sites, Gen proved adequate in describing changes in SOC, with MMM equal to average SOC (and standard deviation) of 39.2 (\uffc2\uffb115.5)\uffc2\uffa0Mg\uffc2\uffa0C/ha compared to the observed mean of 36.0 (\uffc2\uffb119.7)\uffc2\uffa0Mg\uffc2\uffa0C/ha (last observed year), indicating sufficiently reliable SOC estimates. Moving to Mix (37.5\uffc2\uffa0\uffc2\uffb1\uffc2\uffa016.7\uffc2\uffa0Mg\uffc2\uffa0C/ha) and Spe (36.8\uffc2\uffa0\uffc2\uffb1\uffc2\uffa019.8\uffc2\uffa0Mg\uffc2\uffa0C/ha) provided only marginal gains in accuracy, but modellers would need to apply more knowledge and a greater calibration effort than in Gen, thereby limiting the wider applicability of models.

Grazing represents the most extensive use of land worldwide. Yet its impacts on ecosystem services remain uncertain because pervasive interactions between grazing pressure, climate, soil properties, and biodiversity may occur but have never been addressed simultaneously. Using a standardized survey at 98 sites across six continents, we show that interactions between grazing pressure, climate, soil, and biodiversity are critical to explain the delivery of fundamental ecosystem services across drylands worldwide. Increasing grazing pressure reduced ecosystem service delivery in warmer and species-poor drylands, whereas positive effects of grazing were observed in colder and species-rich areas. Considering interactions between grazing and local abiotic and biotic factors is key for understanding the fate of dryland ecosystems under climate change and increasing human pressure.

", "keywords": ["[SDE] Environmental Sciences", "Climate", "Edafolog\u00eda (Biolog\u00eda)", "630", "3104 Producci\u00f3n Animal", "Dryland", "Soil", "636", "2511.06 Conservaci\u00f3n de Suelos", "591.5", "Climate change", "3104.90 Sistemas de Producci\u00f3n Ganadera", "biodiversity", "2. Zero hunger", "2417.13 Ecolog\u00eda Vegetal", "Qu\u00edmica", "Biodiversity", "2502 Climatolog\u00eda", "Grazing", "2401.06 Ecolog\u00eda Animal", "[SDE]Environmental Sciences", "ddc:570", "Rangeland", "581.5", "Ecolog\u00eda (Biolog\u00eda)", "570", "632.11", "Ecosystem services (ES)", "Livestock", "Climate Change", "631.45", "Wild", "SDG-02: Zero hunger", "XXXXXX - Unknown", "Humans", "Ecosystem services", "grazing", "Herbivory", "14. Life underwater", "climate", "Institut f\u00fcr Biochemie und Biologie", "631.585", "Ecosystem", "551.583", "SDG-15: Life on land", "3103.10 Pastos", "Systems", "Drylands", "15. Life on land", "13. Climate action", "58.032.3", "Veterinaria", "ecosystem services"]}, "links": [{"href": "https://repositorio.ulisboa.pt/bitstream/10451/56169/1/abq4062_CombinedPDF_v4.pdf"}, {"href": "https://doi.org/2263/91312"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2263/91312", "name": "item", "description": "2263/91312", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2263/91312"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-25T00:00:00Z"}}, {"id": "PMC9682168", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:29:50Z", "type": "Journal Article", "created": "2022-11-09", "title": "The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses", "description": "

Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process and the corresponding microbiome composition in order to optimize the performance of the process and the biogas output. Previously,Lachnospiraceaespecies were frequently detected in mesophilic to moderately thermophilic biogas reactors. To analyze adaptive genome features of a representativeLachnospiraceaestrain,Anaeropeptidivorans aminofermentansM3/9Twas isolated from a mesophilic laboratory-scale biogas plant and its genome was sequenced and analyzed in detail. Strain M3/9Tpossesses a number of genes encoding enzymes for degradation of proteins, oligo- and dipeptides. Moreover, genes encoding enzymes participating in fermentation of amino acids released from peptide hydrolysis were also identified. Based on further findings obtained from metabolic pathway reconstruction, M3/9Twas predicted to participate in acidogenesis within the AD process. To understand the genomic diversity between the biogas isolate M3/9Tand closely relatedAnaerotignumtype strains, genome sequence comparisons were performed. M3/9Tharbors 1,693 strain-specific genes among others encoding different peptidases, a phosphotransferase system (PTS) for sugar uptake, but also proteins involved in extracellular solute binding and import, sporulation and flagellar biosynthesis. In order to determine the occurrence of M3/9Tin other environments, large-scale fragment recruitments with the M3/9Tgenome as a template and publicly available metagenomes representing different environments was performed. The strain was detected in the intestine of mammals, being most abundant in goat feces, occasionally used as a substrate for biogas production.Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches.

Results

Strawberry plants carried a highly diverse microbiome, therein the bacterial familiesSphingomonadaceae(25%),Pseudomonadaceae(17%), andBurkholderiaceae(11%); and the fungal familyMycosphaerella(45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (107\uffe2\uff80\uff931010marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples\uffc2\uffa0than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats\uffc2\uffa0and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves\uffc2\uffa0and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused byBotrytis cinereadecreased the\uffc2\uffa0diversity as well, and induced a reduction of potentially beneficial taxa.

Conclusion

Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe\uffc2\uffa0transfer during fruit development and storage with potential implications for food health and safety.