{"type": "FeatureCollection", "features": [{"id": "11585/996230", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:53Z", "type": "Journal Article", "created": "2023-10-10", "title": "Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities", "description": "The analysis of phospholipid fatty acids (PLFAs) is one of the most common methods used to quantify the abundance, and analyse the community structure, of soil microbes. The PLFA extraction method can yield two additional lipid fractions\u2014neutral lipids and glycolipids\u2014which potentially hold additional, valuable information on soil microbial communities. Yet its quantitative sensitivity on complete neutral lipid (NLFA) and glycolipid fatty acid (GLFA) profiles has never been validated. In this study we tested (i) if the high-throughput PLFA method can be expanded to concurrently extract complete NLFA and GLFA profiles, as well as sterols, (ii) whether taxonomic specificities of signature fatty acids are retained across the three lipid fractions in pure culture strains, and (iii) whether NLFAs and GLFAs allow soil-specific fingerprinting to the same extent as PLFA analysis. By adjusting the polarity of chloroform with 2% ethanol for solid phase extraction, pure lipid standards were fully fractionated into neutral lipids, glycolipids, and phospholipids. Sterols eluted in the neutral lipid fraction, and a betaine lipid co-eluted with phospholipids. We found consistent taxonomic specificities of fatty acid markers across the three lipid fractions by analysing pure culture extracts representative of soil microbes. Fatty acid profiles from soil extracts, however, showed stronger differences between PLFAs, NLFAs, and GLFAs than between soil types. This indicates that PLFAs and NLFAs signify different community properties (biomass vs. carbon storage, putatively), and that GLFAs are sensitive markers for community traits which behave differently than PLFAs. Although we consistently found high abundances of characteristic sterols in fungal extracts, the PLFA extraction method only yielded miniscule amounts of ergosterol from soil extracts. We argue that concomitant measurement of fatty acid profiles from all three lipid fractions is a low-effort and potentially information-rich addition to the PLFA method, and discuss its applicability for soil microbial community analyses.", "keywords": ["0301 basic medicine", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "15. Life on land", "Soil lipids", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "NLFA", "Ergosterol", "Ergosterol; GLFA; NLFA; Phospholipid fatty acids; Soil lipids", "Phospholipid fatty acid", "soil lipids", "Phospholipid fatty acids", "106022 Microbiology", "GLFA", "106026 Ecosystem research"]}, "links": [{"href": "https://doi.org/11585/996230"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11585/996230", "name": "item", "description": "11585/996230", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11585/996230"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "10.1016/j.geoderma.2023.116399", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:19Z", "type": "Journal Article", "created": "2023-02-27", "title": "One-time freeze-thawing or carbon input events have long-term legacies in soil microbial communities", "description": "Soil microbial communities are regularly exposed to sudden changes in environmental conditions, such as root exudation pulses or freeze-thaw events. As microbial communities have a high potential to adapt to changing conditions, they are expected to be resilient towards this kind of short-term perturbations and return to their pre-perturbed state quickly. Here, we conducted a lab incubation experiment to evaluate the resilience of soil microbial communities to single-pulse perturbations.<br/><br/>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.<br/><br/>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).<br/><br/>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": "10.1007/s10533-015-0082-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:14:36Z", "type": "Journal Article", "created": "2015-02-23", "title": "Deeper Snow Alters Soil Nutrient Availability And Leaf Nutrient Status In High Arctic Tundra", "description": "Nitrogen (N) mineralization, nutrient availability, and plant growth in the Arctic are often restricted by low temperatures. Predicted increases of cold-season temperatures may be important for plant nutrient availability and growth, given that N mineralization is also taking place during the cold season. Changing nutrient availability may be reflected in plant N and chlorophyll content and lead to increased photosynthetic capacity, plant growth, and ultimately carbon (C) assimilation by plants. In this study, we increased snow depth and thereby cold-season soil temperatures in high Arctic Svalbard in two vegetation types spanning three moisture regimes. We measured growing-season availability of ammonium (NH4 +), nitrate (NO3 \u2212), total dissolved organic carbon (DOC) and nitrogen (TON) in soil; C, N, \u03b415N and chlorophyll content in Salix polaris leaves; and leaf sizes of Salix, Bistorta vivipara, and Luzula arcuata at peak season. Nutrient availability was significantly higher with increased snow depth in the two mesic meadow vegetation types, but not in the drier heath vegetation. Nitrogen concentrations and \u03b415N values of Salix leaves were significantly higher in all vegetation types, but the leaf sizes were unchanged. Leaves of Bistorta and Luzula were significantly larger but only significantly so in one moist vegetation type. Increased N and chlorophyll concentrations in leaves indicate a potential for increased growth (C uptake), supported by large leaf sizes for some species. Responses to cold-season soil warming are vegetation type- and species-specific, with potentially stronger responses in moister vegetation types. This study therefore highlights the contrasting effect of snow in a tundra landscape and has important implications for projections of whole tundra responses to climate change", "keywords": ["winter processes", "Mineralization", "Winter processes", "4. Education", "plant growth", "04 agricultural and veterinary sciences", "15. Life on land", "01 natural sciences", "Svalbard", "Arctic", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "SDG 13 - Climate Action", "0401 agriculture", " forestry", " and fisheries", "mineralization", "106026 Ecosystem research", "Plant growth", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1007/s10533-015-0082-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biogeochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10533-015-0082-7", "name": "item", "description": "10.1007/s10533-015-0082-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10533-015-0082-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-02-24T00:00:00Z"}}, {"id": "10.1007/s11104-022-05508-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:14:53Z", "type": "Journal Article", "created": "2022-06-22", "title": "Harnessing belowground processes for sustainable intensification of agricultural systems", "description": "Abstract <p>Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.</p", "keywords": ["0301 basic medicine", "BIOLOGICAL NITRIFICATION INHIBITION", "PHOSPHATE SOLUBILIZING BACTERIA", "Plant-plant interaction", "Rhizobiome", "MEDIATED PH CHANGES", "Review Article", "Plant health", "MEMBRANE H+-ATPASE", "12. Responsible consumption", "03 medical and health sciences", "Soil health", "Soil structure", "C sequestration", "SDG 13 - Climate Action", "SDG 2 \u2013 Kein Hunger", "106026 Ecosystem research", "Plant nutrition", "SDG 2 - Zero Hunger", "2. Zero hunger", "0303 health sciences", "Water availability", "Root exudation", "JASMONIC ACID", "15. Life on land", "Microbes", "Intercropping", "106026 \u00d6kosystemforschung", "PLANT-GROWTH", "13. Climate action", "ROOT BORDER CELLS", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "C cycling", "INNATE IMMUNITY", "NITROGEN-FIXATION", "ORGANIC-ACIDS"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s11104-022-05508-z.pdf"}, {"href": "https://doi.org/10.1007/s11104-022-05508-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-022-05508-z", "name": "item", "description": "10.1007/s11104-022-05508-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-022-05508-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-06-22T00:00:00Z"}}, {"id": "10.1007/s11104-023-05991-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:14:54Z", "type": "Journal Article", "created": "2023-05-10", "title": "Tree stem and soil methane and nitrous oxide fluxes, but not carbon dioxide fluxes, switch sign along a topographic gradient in a tropical forest", "description": "Purpose<br/>Tropical forests exchange large amounts of greenhouse gases (GHGs: carbon dioxide, CO2; methane, CH4; and nitrous oxide, N2O) with the atmosphere. Forest soils and stems can be either sources or sinks for CH4 and N2O, but little is known about what determines the sign and magnitude of these fluxes. Here, we aimed to study how stem and soil GHG fluxes vary along a topographic gradient in a tropical forest.<br/><br/>Methods<br/>Fluxes of GHG from 56 individual tree stems and adjacent soils were measured with manual static chambers. The topographic gradient was characterized by a soil moisture gradient, with one end in a wetland area (\u201cseasonally flooded\u201d; SF), the other end in an upland area (\u201cterra firme\u201d; TF) and in between a transitional area on the slope (SL).<br/><br/>Results<br/>Tree stems and soils were always sources of CO2 with higher fluxes in SF compared to TF and SL. Fluxes of CH4 and N2O were more variable, even within one habitat. Results showed that, in TF, soils acted as sinks for N2O whereas, in SF and SL, they acted as sources. In contrast, tree stems which were predominantly sources of N2O in SF and TF, were sinks in SL. In the soil, N2O fluxes were significantly influenced by both temperature and soil water content, whereas CH4 fluxes were only significantly correlated with soil water content.<br/><br/>Conclusion<br/>SF areas were major sources of the three gases, whereas SL and TF soils and tree stems acted as either sources or sinks for CH4 and N2O. Our results indicate that tree stems represent overlooked sources of CH4 and N2O in tropical forests that need to be further studied to refine GHG budgets.", "keywords": ["[SDV.SA.AGRO] Life Sciences [q-bio]/Agricultural sciences/Agronomy", "106022 Mikrobiologie", "550", "source", "Spatial variation", "Sink", "[SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy", "spatial variation", "Source", "15. Life on land", "Stem", "630", "soil", "[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics", "Soil", "Greenhouse gas (GHG) exchange", "13. Climate action", "106026 \u00d6kosystemforschung", "[SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics", "106022 Microbiology", "stem", "sink", "106026 Ecosystem research", "Biology", "greenhouse gas (GHG) exchange"]}, "links": [{"href": "https://doi.org/10.1007/s11104-023-05991-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-023-05991-y", "name": "item", "description": "10.1007/s11104-023-05991-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-023-05991-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-05-09T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2016.03.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:56Z", "type": "Journal Article", "created": "2016-03-26", "title": "Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland", "description": "<p>Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of <sup>18</sup>O from labeled water into microbial DNA. Microbial respiration was 28-37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland. </p>", "keywords": ["FUNGAL", "2. Zero hunger", "106022 Mikrobiologie", "Nitrogen addition", "BACTERIAL", "NITROGEN DEPOSITION", "GROWTH EFFICIENCY", "FOREST FLOOR", "Nutrients", "04 agricultural and veterinary sciences", "15. Life on land", "Stoichiometry", "ORGANIC-MATTER", "RESPIRATION", "106026 \u00d6kosystemforschung", "13. Climate action", "Nutrient limitation", "Microbial growth yield", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Mean residence time", "STOICHIOMETRIC CONTROLS", "ENZYME-ACTIVITY", "106026 Ecosystem research", "COMMUNITY STRUCTURE"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2016.03.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2016.03.008", "name": "item", "description": "10.1016/j.soilbio.2016.03.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2016.03.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2019.03.028", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:57Z", "type": "Journal Article", "created": "2019-04-01", "title": "Coupled carbon and nitrogen losses in response to seven years of chronic warming in subarctic soils", "description": "Increasing temperatures may alter the stoichiometric demands of soil microbes and impair their capacity to stabilize carbon (C) and retain nitrogen (N), with critical consequences for the soil C and N storage at high latitude soils. Geothermally active areas in Iceland provided wide, continuous and stable gradients of\u00a0soil temperatures\u00a0to test this hypothesis. In order to characterize the stoichiometric demands of microbes from these subarctic soils, we incubated soils from ambient temperatures after the factorial addition of C, N and P substrates separately and in combination. In a second experiment, soils that had been exposed to different\u00a0in situ\u00a0warming intensities (+0, +0.5, +1.8, +3.4, +8.7, +15.9\u00a0\u00b0C above ambient) for seven years were incubated after the combined addition of C, N and P to evaluate the capacity of soil microbes to store and immobilize C and N at the different warming scenarios. The seven years of chronic soil warming triggered large and proportional soil C and N losses (4.1\u00a0\u00b1\u00a00.5% \u00b0C\u22121\u00a0of the stocks in unwarmed soils) from the upper 10\u202fcm of soil, with a predominant depletion of the physically accessible organic substrates that were weakly sorbed in\u00a0soil minerals\u00a0up to 8.7\u202f\u00b0C warming. Soil microbes met the increasing respiratory demands under conditions of low C accessibility at the expenses of a reduction of the standing biomass in warmer soils. This together with the strict microbial C:N stoichiometric demands also constrained their capacity of N retention, and increased the vulnerability of soil to N losses. Our findings suggest a strong control of\u00a0microbial physiology and C:N stoichiometric needs on the retention of soil N and on the resilience of soil C stocks from high-latitudes to warming, particularly during periods of vegetation dormancy and low C inputs.", "keywords": ["0301 basic medicine", "Microbial carbon and nutrients limitation", "Microbial biomass", "TERM", "03 medical and health sciences", "FOREST SOIL", "Temperature increase", "ORGANIC-CARBON", "Substrate induced respiration", "SDG 13 - Climate Action", "TEMPERATURE SENSITIVITY", "CYCLE", "106026 Ecosystem research", "METAANALYSIS", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "CLIMATE-CHANGE", "Nitrogen loss", "AVAILABILITY", "15. Life on land", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "FEEDBACKS", "Nitrogen immobilization", "106022 Microbiology", "PLANT BIOMASS"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2019.03.028"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2019.03.028", "name": "item", "description": "10.1016/j.soilbio.2019.03.028", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2019.03.028"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-07-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2021.108357", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:58Z", "type": "Journal Article", "created": "2021-07-10", "title": "A critical perspective on interpreting amplicon sequencing data in soil ecological research", "description": "Abstract   Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation, and availability to improve the rigor of future studies.", "keywords": ["2. Zero hunger", "0301 basic medicine", "Soil microbial diversity", "0303 health sciences", "Soil metabarcoding", "DIVERSITY", "Ecology; Soil microbes; Amplicon sequencing", "Compositional data", "SCALE SPATIAL HETEROGENEITY", "15. Life on land", "BIOMASS", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "Soil complexity", "CARBON-USE EFFICIENCY", "BACTERIA", "DNA EXTRACTION", "MICROORGANISMS", "MICROBIAL COMMUNITIES", "106026 Ecosystem research", "RIBOSOMAL-RNA", "Amplicon sequencing", "Soil microorganisms", "GENERATION"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2021.108357"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2021.108357", "name": "item", "description": "10.1016/j.soilbio.2021.108357", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2021.108357"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2022.108604", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:58Z", "type": "Journal Article", "created": "2022-03-18", "title": "From diversity to complexity: Microbial networks in soils", "description": "ABSTRACT<p>Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.</p", "keywords": ["2. Zero hunger", "0301 basic medicine", "106022 Mikrobiologie", "0303 health sciences", "Microbial community structure", "Perspectives Paper", "15. Life on land", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "13. Climate action", "Ecological networks", "Soil microbial ecology", "Microbial network analysis", "106022 Microbiology", "106026 Ecosystem research", "Co-occurrence networks"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2022.108604"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2022.108604", "name": "item", "description": "10.1016/j.soilbio.2022.108604", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2022.108604"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-16T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2023.109205", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:58Z", "type": "Journal Article", "created": "2023-10-10", "title": "Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities", "description": "The analysis of phospholipid fatty acids (PLFAs) is one of the most common methods used to quantify the abundance, and analyse the community structure, of soil microbes. The PLFA extraction method can yield two additional lipid fractions\u2014neutral lipids and glycolipids\u2014which potentially hold additional, valuable information on soil microbial communities. Yet its quantitative sensitivity on complete neutral lipid (NLFA) and glycolipid fatty acid (GLFA) profiles has never been validated. In this study we tested (i) if the high-throughput PLFA method can be expanded to concurrently extract complete NLFA and GLFA profiles, as well as sterols, (ii) whether taxonomic specificities of signature fatty acids are retained across the three lipid fractions in pure culture strains, and (iii) whether NLFAs and GLFAs allow soil-specific fingerprinting to the same extent as PLFA analysis. By adjusting the polarity of chloroform with 2% ethanol for solid phase extraction, pure lipid standards were fully fractionated into neutral lipids, glycolipids, and phospholipids. Sterols eluted in the neutral lipid fraction, and a betaine lipid co-eluted with phospholipids. We found consistent taxonomic specificities of fatty acid markers across the three lipid fractions by analysing pure culture extracts representative of soil microbes. Fatty acid profiles from soil extracts, however, showed stronger differences between PLFAs, NLFAs, and GLFAs than between soil types. This indicates that PLFAs and NLFAs signify different community properties (biomass vs. carbon storage, putatively), and that GLFAs are sensitive markers for community traits which behave differently than PLFAs. Although we consistently found high abundances of characteristic sterols in fungal extracts, the PLFA extraction method only yielded miniscule amounts of ergosterol from soil extracts. We argue that concomitant measurement of fatty acid profiles from all three lipid fractions is a low-effort and potentially information-rich addition to the PLFA method, and discuss its applicability for soil microbial community analyses.", "keywords": ["0301 basic medicine", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "15. Life on land", "Soil lipids", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "NLFA", "Ergosterol", "Ergosterol; GLFA; NLFA; Phospholipid fatty acids; Soil lipids", "Phospholipid fatty acid", "soil lipids", "Phospholipid fatty acids", "106022 Microbiology", "GLFA", "106026 Ecosystem research"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2023.109205"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2023.109205", "name": "item", "description": "10.1016/j.soilbio.2023.109205", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2023.109205"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2023.109259", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:58Z", "type": "Journal Article", "created": "2023-12-01", "title": "A pulse of simulated root exudation alters the composition and temporal dynamics of microbial metabolites in its immediate vicinity", "description": "Root exudation increases the concentration of readily available carbon (C) compounds in its immediate environment. This creates \u2018hotspots\u2019 of microbial activity characterized by accelerated soil organic matter turnover with direct implications for nutrient availability for plants. However, our knowledge of the microbial metabolic processes occurring in the immediate vicinity of roots during and after a root exudation event is still limited.<br/><br/>Using reverse microdialysis, we simulated root exudation by releasing a13C-labelled mix of low-molecular-weight organic C compounds at mm-sized locations in undisturbed soil. Combined with stable isotope tracing, we investigated the fine-scale temporal and spatial response of microbial metabolism, soil chemistry, and traced microbial respiration and uptake of exuded compounds.<br/><br/>Our results show that a 9-h simulated root exudation pulse leads to i) a large local respiration event and ii) alteration of the temporal dynamics of soil metabolites over the following 12\u202fday\u202fat the exudation spot. Notably, we observed a threefold increase in ammonium concentrations at 12\u202fh and increased nitrate concentrations five days after the pulse. Moreover, various short-chain fatty acids (acetate, propionate, formate) increased over the following days, indicating altered microbial metabolic pathways and activity. Phospholipid and neutral lipid fatty acids (PLFAs, NLFAs) of all major microbial groups were significantly 13C-enriched within a 5\u202fmm radius around the microdialysis probes, but not beyond. The highest relative 13C enrichment was observed in fungal NLFAs, indicating that a significant proportion of the exuded compounds had been incorporated into fungal storage compounds.<br/><br/>Our findings indicate that the punctual release of low-molecular-weight organic C compounds into intact soil significantly changes microbial metabolism and activity in its immediate surroundings, enhancing mineralization of native organic nitrogen. This highlights the versatility of microbial metabolic pathways in response to rapidly changing C availability and their effectiveness in increasing nutrient availability near plant roots.", "keywords": ["Oxygen depletion", "2. Zero hunger", "570", "106022 Mikrobiologie", "Root exudation", "short-chain fatty acids", "Reverse microdialysis", "reverse microdialysis", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "15. Life on land", "root exudation", "6. Clean water", "Short-chain fatty acids", "Sugar metabolism", "106026 \u00d6kosystemforschung", "thizosphere priming effect", "crabtree effect", "sugar metabolism", "106022 Microbiology", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "106026 Ecosystem research", "Rhizosphere priming effect"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2023.109259"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2023.109259", "name": "item", "description": "10.1016/j.soilbio.2023.109259", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2023.109259"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-01T00:00:00Z"}}, {"id": "10.1038/s41396-020-00750-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:37Z", "type": "Journal Article", "created": "2020-10-06", "title": "Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils", "description": "Abstract                <p>Significant rates of atmospheric dihydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.</p", "keywords": ["0301 basic medicine", "Bacterial physiology", "Article", "HIGH-AFFINITY", "MULTIPLE SEQUENCE ALIGNMENT", "Soil", "03 medical and health sciences", "Hydrogenase", "106026 Ecosystem research", "Soil Microbiology", "H-2", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "Biodiversity", "PHYLUM ACIDOBACTERIA", "15. Life on land", "FOREST", "16. Peace & justice", "ENERGY-SOURCE", "Acidobacteria", "Soil microbiology", "106026 \u00d6kosystemforschung", "13. Climate action", "MOLECULAR-HYDROGEN", "BACTERIA", "106022 Microbiology", "SP-NOV.", "GEN. NOV.", "Oxidation-Reduction", "Hydrogen"]}, "links": [{"href": "https://www.nature.com/articles/s41396-020-00750-8.pdf"}, {"href": "https://doi.org/10.1038/s41396-020-00750-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41396-020-00750-8", "name": "item", "description": "10.1038/s41396-020-00750-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41396-020-00750-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-06T00:00:00Z"}}, {"id": "10.1038/s41467-024-46920-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:39Z", "type": "Journal Article", "created": "2024-04-17", "title": "Survival and rapid resuscitation permit limited productivity in desert microbial communities", "description": "Abstract<p>Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.</p", "keywords": ["0301 basic medicine", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "105904 Environmental research", "Science", "Microbiota", "Rain", "Q", "15. Life on land", "microbial ecology", "Article", "Microbial ecology", "Soil", "03 medical and health sciences", "Soil microbiology", "106026 \u00d6kosystemforschung", "106022 Microbiology", "Desert Climate", "106026 Ecosystem research", "105904 Umweltforschung", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/s41467-024-46920-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-024-46920-6", "name": "item", "description": "10.1038/s41467-024-46920-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-024-46920-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-17T00:00:00Z"}}, {"id": "10.1038/s41467-019-11993-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:38Z", "type": "Journal Article", "created": "2019-09-04", "title": "Plant roots increase both decomposition and stable organic matter formation in boreal forest soil", "description": "Abstract<p>Boreal forests are ecosystems with low nitrogen (N) availability that store globally significant amounts of carbon (C), mainly in plant biomass and soil organic matter (SOM). Although crucial for future climate change predictions, the mechanisms controlling boreal C and N pools are not well understood. Here, using a three-year field experiment, we compare SOM decomposition and stabilization in the presence of roots, with exclusion of roots but presence of fungal hyphae and with exclusion of both roots and fungal hyphae. Roots accelerate SOM decomposition compared to the root exclusion treatments, but also promote a different soil N economy with higher concentrations of organic soil N compared to inorganic soil N accompanied with the build-up of stable SOM-N. In contrast, root exclusion leads to an inorganic soil N economy (i.e., high level of inorganic N) with reduced stable SOM-N build-up. Based on our findings, we provide a framework on how plant roots affect SOM decomposition and stabilization.</p>", "keywords": ["roots", "0106 biological sciences", "330", "Nitrogen", "Science", "ta1171", "Hyphae", "Models", " Biological", "Plant Roots", "01 natural sciences", "Article", "LITTER DECOMPOSITION", "Soil", "POLYPHENOLS", "CARBON SEQUESTRATION", "soil organic matter", "Taiga", "SDG 13 - Climate Action", "SUGAR MAPLE", "Biomass", "Organic Chemicals", "forest ecology", "106026 Ecosystem research", "Ecosystem", "Soil Microbiology", "TANNINS", "2. Zero hunger", "106022 Mikrobiologie", "ECTOMYCORRHIZAL FUNGI", "MYCORRHIZA", "Q", "ta1182", "Forestry", "04 agricultural and veterinary sciences", "Plants", "15. Life on land", "Carbon", "Environmental sciences", "NITROGEN", "Boreal forests", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "106022 Microbiology", "ta1181", "0401 agriculture", " forestry", " and fisheries", "COMMUNITIES", "STORAGE"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-11993-1.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-11993-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-11993-1", "name": "item", "description": "10.1038/s41467-019-11993-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-11993-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-09-04T00:00:00Z"}}, {"id": "10.1038/s41559-019-1055-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:40Z", "type": "Journal Article", "created": "2019-12-09", "title": "A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem", "description": "Temperature governs most biotic processes, yet we know little about how warming affects whole ecosystems. Here we examined the responses of 128\u2009components of a subarctic grassland to either 5-8 or >50\u2009years of soil warming. Warming of >50\u2009years drove the ecosystem to a new steady state possessing a distinct biotic composition and reduced species richness, biomass and soil organic matter. However, the warmed state was preceded by an overreaction to warming, which was related to organism physiology and was evident after 5-8\u2009years. Ignoring this overreaction yielded errors of >100% for 83\u2009variables when predicting their responses to a realistic warming scenario of 1\u2009\u00b0C over 50\u2009years, although some, including soil carbon content, remained stable after 5-8\u2009years. This study challenges long-term ecosystem predictions made from short-term observations, and provides a framework for characterization of ecosystem responses to sustained climate change.", "keywords": ["0301 basic medicine", "570", "Environmental management", "INCREASES", "Ecosystem ecology", "Climate Change", "Evolutionary biology", "TERM", "630", "Article", "Carbon Cycle", "Soil", "03 medical and health sciences", "SDG 13 - Climate Action", "106026 Ecosystem research", "Life Below Water", "Ecosystem", "106022 Mikrobiologie", "0303 health sciences", "Ecology", "Climate-change ecology", "SHIFTS", "Biological Sciences", "15. Life on land", "Grassland", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "FEEDBACKS", "106022 Microbiology", "VEGETATION", "SENSITIVITY", "Environmental Sciences", "SOIL RESPIRATION", "RESPONSES"]}, "links": [{"href": "https://escholarship.org/content/qt99v0g8pc/qt99v0g8pc.pdf"}, {"href": "https://doi.org/10.1038/s41559-019-1055-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Ecology%20%26amp%3B%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41559-019-1055-3", "name": "item", "description": "10.1038/s41559-019-1055-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41559-019-1055-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-09T00:00:00Z"}}, {"id": "10.1038/s41561-020-0612-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:40Z", "type": "Journal Article", "created": "2020-07-27", "title": "Persistence of soil organic carbon caused by functional complexity", "description": "Soil organic carbon management has the potential to aid climate change mitigation through drawdown of atmospheric carbon dioxide. To be effective, such management must account for processes influencing carbon storage and re-emission at different space and time scales. Achieving this requires a conceptual advance in our understanding to link carbon dynamics from the scales at which processes occur to the scales at which decisions are made. Here, we propose that soil carbon persistence can be understood through the lens of decomposers as a result of functional complexity derived from the interplay between spatial and temporal variation of molecular diversity and composition. For example, co-location alone can determine whether a molecule is decomposed, with rapid changes in moisture leading to transport of organic matter and constraining the fitness of the microbial community, while greater molecular diversity may increase the metabolic demand of, and thus potentially limit, decomposition. This conceptual shift accounts for emergent behaviour of the microbial community and would enable soil carbon changes to be predicted without invoking recalcitrant carbon forms that have not been observed experimentally. Functional complexity as a driver of soil carbon persistence suggests soil management should be based on constant care rather than one-time action to lock away carbon in soils.", "keywords": ["[SDE] Environmental Sciences", "DECOMPOSITION", "2. Zero hunger", "106022 Mikrobiologie", "[SDE.MCG]Environmental Sciences/Global Changes", "UNCERTAINTY", "04 agricultural and veterinary sciences", "INPUTS", "15. Life on land", "TRANSPORT", "MODEL", "[SDE.MCG] Environmental Sciences/Global Changes", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "[SDE]Environmental Sciences", "SDG 13 - Climate Action", "Meteorology & Atmospheric Sciences", "106022 Microbiology", "GROWTH", "0401 agriculture", " forestry", " and fisheries", "TURNOVER", "PLANT", "106026 Ecosystem research", "MATTER"]}, "links": [{"href": "http://www.nature.com/articles/s41561-020-0612-3.pdf"}, {"href": "https://escholarship.org/content/qt84n3398c/qt84n3398c.pdf"}, {"href": "https://doi.org/10.1038/s41561-020-0612-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Geoscience", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41561-020-0612-3", "name": "item", "description": "10.1038/s41561-020-0612-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41561-020-0612-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-07-27T00:00:00Z"}}, {"id": "10.1038/s42003-022-04178-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:43Z", "type": "Journal Article", "created": "2022-11-17", "title": "Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities", "description": "Abstract<p>Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.</p", "keywords": ["0301 basic medicine", "QH301-705.5", "Fungal ecology; Microbial ecology; Symbiosis", "microbial ecology", "Plant Roots", "Article", "Microbial ecology", "Soil", "03 medical and health sciences", "Mycorrhizae", "RNA", " Ribosomal", " 16S", "Fagus", "Biology (General)", "106026 Ecosystem research", "Fungal ecology", "Symbiosis", "Soil Microbiology", "106022 Mikrobiologie", "0303 health sciences", "Bacteria", "15. Life on land", "Archaea", "symbiosis", "106026 \u00d6kosystemforschung", "fungal ecology", "106022 Microbiology"]}, "links": [{"href": "https://www.nature.com/articles/s42003-022-04178-y.pdf"}, {"href": "https://doi.org/10.1038/s42003-022-04178-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Communications%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s42003-022-04178-y", "name": "item", "description": "10.1038/s42003-022-04178-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s42003-022-04178-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-17T00:00:00Z"}}, {"id": "10.1038/s43247-021-00192-w", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:44Z", "type": "Journal Article", "created": "2021-06-10", "title": "Carbon dioxide fluxes increase from day to night across European streams", "description": "Abstract<p>Globally, inland waters emit over 2 Pg of carbon per year as carbon dioxide, of which the majority originates from streams and rivers. Despite the global significance of fluvial carbon dioxide emissions, little is known about their diel dynamics. Here we present a large-scale assessment of day- and night-time carbon dioxide fluxes at the water-air interface across 34 European streams. We directly measured fluxes four times between October 2016 and July 2017 using drifting chambers. Median fluxes are 1.4 and 2.1\uffe2\uff80\uff89mmol\uffe2\uff80\uff89m\uffe2\uff88\uff922 h\uffe2\uff88\uff921 at midday and midnight, respectively, with night fluxes exceeding those during the day by 39%. We attribute diel carbon dioxide flux variability mainly to changes in the water partial pressure of carbon dioxide. However, no consistent drivers could be identified across sites. Our findings highlight widespread day-night changes in fluvial carbon dioxide fluxes and suggest that the time of day greatly influences measured carbon dioxide fluxes across European streams.</p", "keywords": ["DYNAMICS", "0106 biological sciences", "DIURNAL-VARIATION", "550", "Naturgeografi", "PCO(2)", "Geography & travel", "Oceanografi", " hydrologi och vattenresurser", "910", "01 natural sciences", "Oceanography", " Hydrology and Water Resources", "105205 Klimawandel", "Limnology", "105304 Hydrologie", "SDG 13 - Climate Action", "info:eu-repo/classification/ddc/910", "106026 Ecosystem research", "1ST-ORDER STREAM", "106020 Limnology", "105205 Climate change", "0105 earth and related environmental sciences", "[SDU.OCEAN]Sciences of the Universe [physics]/Ocean", "Atmosphere", "[SDU.OCEAN] Sciences of the Universe [physics]/Ocean", " Atmosphere", "EVASION", "Carbon cycle", "ddc:910", "106020 Limnologie", "Climate Science", "ECOSYSTEM METABOLISM", "WATER-AIR", "Physical Geography", "106026 \u00d6kosystemforschung", "CO2 EMISSIONS", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "Environmental chemistry", "DISSOLVED ORGANIC-MATTER", "Klimatvetenskap", "105304 Hydrology", "GAS-EXCHANGE"]}, "links": [{"href": "https://eprints.bournemouth.ac.uk/35763/1/s43247-021-00192-w.pdf"}, {"href": "https://iris.unito.it/bitstream/2318/1799544/1/106%20EURORUN.pdf"}, {"href": "https://www.nature.com/articles/s43247-021-00192-w.pdf"}, {"href": "https://doi.org/10.1038/s43247-021-00192-w"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Communications%20Earth%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s43247-021-00192-w", "name": "item", "description": "10.1038/s43247-021-00192-w", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s43247-021-00192-w"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-22T00:00:00Z"}}, {"id": "10.1093/femsec/fiae152", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:16Z", "type": "Journal Article", "created": "2024-11-19", "title": "A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum", "description": "Abstract                <p>Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations. The decrease from 10 to 0.1\uffc2\uffa0\uffc2\uffb5M oxygen (3.6 to 0.036 pO2% present atmospheric level, respectively) caused the upregulation of the transcription of genes involved in signal transduction mechanisms, energy production and conversion and secondary metabolites biosynthesis, transport, and catabolism based on clusters of orthologous group categories. Contrary to established observations for aerobic metabolism, key genes in oxidative stress response were significantly upregulated at lower oxygen concentrations, presumably due to an NADH/NAD+ redox ratio imbalance as the cells transitioned into nanoxia. Furthermore, A. capsulatum adapted to nanoxia by inducing a respiro-fermentative metabolism and rerouting fluxes of its central carbon and energy pathways to adapt to high NADH/NAD+ redox ratios. Our results reveal physiological features and metabolic capabilities that allowed A. capsulatum to adapt to oxygen-limited conditions, which could expand into other environmentally relevant soil strains.</p", "keywords": ["0301 basic medicine", "106022 Mikrobiologie", "0303 health sciences", "Acidobacteriota", "NADH imbalances", "microaerobic respiration", "Gene Expression Regulation", " Bacterial", "Adaptation", " Physiological", "oxygen limitation", "Acidobacteria", "Oxygen", "Oxidative Stress", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "Fermentation", "106022 Microbiology", "106026 Ecosystem research", "fermentation", "transcriptome", "Oxidation-Reduction", "Soil Microbiology", "Research Article"]}, "links": [{"href": "https://doi.org/10.1093/femsec/fiae152"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiae152", "name": "item", "description": "10.1093/femsec/fiae152", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiae152"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-11-18T00:00:00Z"}}, {"id": "10.1101/2023.10.03.560709", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:25Z", "type": "Journal Article", "created": "2023-10-04", "title": "Bacteria face trade-offs in the decomposition of complex biopolymers", "description": "Abstract<p>Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system\uffe2\uff80\uff99s complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low- or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.</p>Author summary<p>The decomposition of polysaccharides by microbes is a key process in the global carbon cycle. It requires the joint action of a variety of microbially-produced extracellular enzymes. They can be broadly classified into endo-enzymes, that act in the middle of polymers, and exo-enzymes, that cleave units from polymer ends. Little is known about the benefits for microbes producing a certain enzyme type and the interplay between enzyme producing strategies in mixed communities. This hampers our comprehensive understanding of decomposition in terrestrial and marine ecosystems and thus limits the prediction of decomposition processes, for example in a changing climate.</p><p>Based on theoretical modelling, we revealed a fundamental trade-off in the action of these enzymes. While exo-enzymes are more efficient at high substrate conditions, endo-enzymes perform better when substrate is low. Generalists producing both enzymes expand their ecological niche of substrate availability compared to specialists only producing one of the two types. Complementary specialists only co-exist in oligotrophic conditions. We conclude that producing enzymes for specific steps within polymer degradation represents relevant ecological strategies for microbes in decomposer communities.</p", "keywords": ["2. Zero hunger", "106022 Mikrobiologie", "decomposition", "Bacteria", "Polymers", "QH301-705.5", "complex biopolymers", "Monomers", "Computational Biology", "Chitin", "Models", " Biological", "Enzymes", "Biopolymers", "Consortia", "106026 \u00d6kosystemforschung", "Oligomers", "106022 Microbiology", "14. Life underwater", "Biology (General)", "106026 Ecosystem research", "bacteria", "Depolymerization", "Research Article"]}, "links": [{"href": "https://doi.org/10.1101/2023.10.03.560709"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20Computational%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2023.10.03.560709", "name": "item", "description": "10.1101/2023.10.03.560709", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2023.10.03.560709"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-03T00:00:00Z"}}, {"id": "10.1093/ismejo/wrae156", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:17Z", "type": "Journal Article", "created": "2024-08-06", "title": "Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates", "description": "Abstract                <p>Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3\uffe2\uff80\uff934 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%\uffe2\uff80\uff9330% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.</p", "keywords": ["0301 basic medicine", "millimetre-scale", "archaea", "Nitrogen", "bulk soil samples", "individual aggregates", "diversity", "soil", "Soil", "03 medical and health sciences", "106026 Ecosystem research", "bacteria", "Soil Microbiology", "106022 Mikrobiologie", "0303 health sciences", "Bacteria", "Microbiota", "Fungi", "Biodiversity", "15. Life on land", "Archaea", "Carbon", "106026 \u00d6kosystemforschung", "106022 Microbiology", "Original Article", "fungi", "community structure", "environment"]}, "links": [{"href": "https://doi.org/10.1093/ismejo/wrae156"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/ismejo/wrae156", "name": "item", "description": "10.1093/ismejo/wrae156", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/ismejo/wrae156"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "10.1111/nph.19112", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:02Z", "type": "Journal Article", "created": "2023-06-29", "title": "Gold\u2010FISH enables targeted NanoSIMS analysis of plant\u2010associated bacteria", "description": "Summary<p> <p>Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in\uffc2\uffa0situ evidence of bacterial activity.</p> <p>To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold\uffe2\uff80\uff90based in\uffc2\uffa0situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity.</p> <p>We incubated Kosakonia strain DS\uffe2\uff80\uff901\uffe2\uff80\uff90associated, gnotobiotically grown rice plants with 15N\uffe2\uff80\uff93N2 gas to detect in\uffc2\uffa0situ N2 fixation activity. Bacterial cells along the rhizoplane showed\uffc2\uffa0heterogeneous patterns of 15N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15N (average and median of 3.36 and 2.85 at% 15N, respectively, n\uffe2\uff80\uff89=\uffe2\uff80\uff89697 cells).</p> <p>The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant\uffe2\uff80\uff93microbe interactions. For example, it enables verification of the in\uffc2\uffa0situ metabolic activity of host\uffe2\uff80\uff90associated commercialized strains or plant growth\uffe2\uff80\uff90promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant\uffe2\uff80\uff93microbe combinations for improvement of crop management.</p> </p", "keywords": ["2. Zero hunger", "106022 Mikrobiologie", "rhizosphere bacteria", "Bacteria", "plant growth-promoting bacteria", "plant\u2013microbe interaction", "Research", "Oryza", "biological nitrogen fixation", "Plants", "microbial activity", "in\u00a0situ hybridization", "Plant Roots", "106026 \u00d6kosystemforschung", "Rhizosphere", "106022 Microbiology", "NanoSIMS", "in situ hybridization", "106026 Ecosystem research", "In situ hybridization", "In Situ Hybridization", "Soil Microbiology", "plant-microbe interaction"]}, "links": [{"href": "https://doi.org/10.1111/nph.19112"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.19112", "name": "item", "description": "10.1111/nph.19112", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.19112"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-28T00:00:00Z"}}, {"id": "10.1111/nph.20145", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:03Z", "type": "Journal Article", "created": "2024-10-01", "title": "What determines transfer of carbon from plants to mycorrhizal fungi?", "description": "Summary<p>Biological Market Models are common evolutionary frameworks to understand the maintenance of mutualism in mycorrhizas. \uffe2\uff80\uff98Surplus C\uffe2\uff80\uff99 hypotheses provide an alternative framework where stoichiometry and source\uffe2\uff80\uff93sink dynamics govern mycorrhizal function. A critical difference between these frameworks is whether carbon transfer from plants is regulated by nutrient transfer from fungi or through source\uffe2\uff80\uff93sink dynamics. In this review, we: provide a historical perspective; summarize studies that asked whether plants transfer more carbon to fungi that transfer more nutrients; conduct a meta\uffe2\uff80\uff90analysis to assess whether mycorrhizal plant growth suppressions are related to carbon transfer; and review literature on cellular mechanisms for carbon transfer. In sum, current knowledge does not indicate that carbon transfer from plants is directly regulated by nutrient delivery from fungi. Further, mycorrhizal plant growth responses were linked to nutrient uptake rather than carbon transfer. These findings are more consistent with \uffe2\uff80\uff98Surplus C\uffe2\uff80\uff99 hypotheses than Biological Market Models. However, we also identify research gaps, and future research may uncover a mechanism directly linking carbon and nutrient transfer. Until then, we urge caution when applying economic terminology to describe mycorrhizas. We present a synthesis of ideas, consider knowledge gaps, and suggest experiments to advance the field.</p", "keywords": ["106022 Mikrobiologie", "sanctions and rewards", "membrane transport", "comparative advantage", "Biological Transport", "mycorrhizas", "transporters", "Plants", "symbiosis", "Carbon", "106026 \u00d6kosystemforschung", "Mycorrhizae", "functional equilibrium", "106022 Microbiology", "106026 Ecosystem research", "Symbiosis", "shading"], "contacts": [{"organization": "Rebecca A. Bunn, Ana Corr\u00eaa, Jaya Joshi, Christina Kaiser, Ylva Lekberg, Cindy E. Prescott, Anna Sala, Justine Karst,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1111/nph.20145"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.20145", "name": "item", "description": "10.1111/nph.20145", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.20145"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-10-01T00:00:00Z"}}, {"id": "10.1128/msystems.00495-19", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:09Z", "type": "Journal Article", "created": "2020-04-13", "title": "Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation.</p></article>", "keywords": ["0301 basic medicine", "dormancy", "CYANOBACTERIAL EXOPOLYSACCHARIDES", "Trace gas", "Microbiology", "SOIL CRUSTS", "Energy reserve", "HIGH-AFFINITY", "03 medical and health sciences", "trace gas", "ATMOSPHERIC TRACE GASES", "Energetics", "energy reserve", "Dormancy", "SOR RONDANE MOUNTAINS", "Desert", "Photosynthesis", "106026 Ecosystem research", "CARBON-MONOXIDE", "desert", "ATACAMA DESERT", "energetics", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "photosynthesis", "COMMUNITY RESPONSE", "15. Life on land", "QR1-502", "106026 \u00d6kosystemforschung", "DRY SOIL", "13. Climate action", "MOLECULAR-HYDROGEN", "106022 Microbiology", "Minireview"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSystems.00495-19"}, {"href": "https://doi.org/10.1128/msystems.00495-19"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00495-19", "name": "item", "description": "10.1128/msystems.00495-19", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00495-19"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-28T00:00:00Z"}}, {"id": "10.3389/fpls.2021.682142", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:20:44Z", "type": "Journal Article", "created": "2021-07-21", "title": "Shifts in the Abundances of Saprotrophic and Ectomycorrhizal Fungi With Altered Leaf Litter Inputs", "description": "<p>Ectomycorrhizal (EcM) and saprotrophic fungi interact in the breakdown of organic matter, but the mechanisms underlying the EcM role on organic matter decomposition are not totally clear. We hypothesized that the ecological relations between EcM and saprotroph fungi are modulated by resources availability and accessibility, determining decomposition rates. We manipulated the amount of leaf litter inputs (No-Litter, Control Litter, Doubled Litter) on Trenched (root exclusion) and Non-Trenched plots (with roots) in a temperate deciduous forest of EcM-associated trees. Resultant shifts in soil fungal communities were determined by phospholipid fatty acids and DNA sequencing after 3 years, and CO2 fluxes were measured throughout this period. Different levels of leaf litter inputs generated a gradient of organic substrate availability and accessibility, altering the composition and ecological relations between EcM and saprotroph fungal communities. EcM fungi dominated at low levels of fresh organic substrates and lower organic matter quality, where short-distances exploration types seem to be better competitors, whereas saprotrophs and longer exploration types of EcM fungi tended to dominate at high levels of leaf litter inputs, where labile organic substrates were easily accessible. We were, however, not able to detect unequivocal signs of competition between these fungal groups for common resources. These results point to the relevance of substrate quality and availability as key factors determining the role of EcM and saprotroph fungi on litter and soil organic matter decay and represent a path forward on the capacity of organic matter decomposition of different exploration types of EcM fungi.</p", "keywords": ["Plant detritus", "0301 basic medicine", "570", "litter decomposition", "Plant Science", "630", "SB1-1110", "03 medical and health sciences", "environment/Symbiosis", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "plant detritus", "106026 Ecosystem research", "Biology", "soil fungal communities", "0303 health sciences", "Ectomycorrhiza fungal exploration types", "ectomycorrhiza fungal exploration types", "Litter decomposition", "Plant culture", "Soil fungal communities", "[SDV.EE.IEO] Life Sciences [q-bio]/Ecology", " environment/Symbiosis", "15. Life on land", "Gadgil effect", "CO2 fluxes", "106026 \u00d6kosystemforschung", "CO fluxes", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "[SDV.EE.IEO]Life Sciences [q-bio]/Ecology", "environment/Ecosystems"]}, "links": [{"href": "https://doi.org/10.3389/fpls.2021.682142"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fpls.2021.682142", "name": "item", "description": "10.3389/fpls.2021.682142", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2021.682142"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-07-21T00:00:00Z"}}, {"id": "10.5194/egusphere-egu22-5811", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:21:44Z", "type": "Journal Article", "created": "2022-03-27", "title": "Agricultural management affects active carbon and nitrogen mineralisation potential in soils", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>&amp;lt;p&amp;gt;Soil organic matter (SOM) is important for soil fertility and climate change mitigation. Agricultural management - including soil amendments - can improve soil fertility and contribute to climate change mitigation by stabilising carbon in soils. This calls for cost-effective parameters to assess&amp;amp;#160; the influence of management practices on SOM. The current study aimed at understanding how sensitive the parameters active/permanganate oxidisable carbon (AC) and nitrogen mineralisation potential (NMP) react to different agricultural management practices compared to total organic carbon (TOC) and total nitrogen (Nt). We aimed to gain a better understanding of SOM processes, mainly regarding depth distribution and seasonality of SOM dynamics using AC and NMP.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Data were obtained in five Austrian long-term field experiments (LTEs) testing four management practices: i) tillage, ii) compost application, iii) crop residue management, and iv) mineral fertilisation.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;AC was specifically sensitive in detecting the effect of tillage treatment at different soil depths. NMP differentiated between all different tillage treatments in the top soil layer, it showed the temporal dynamics between the years in the compost LTE, and it was identified as an early detection property in the crop residue LTE. Both AC and NMP detected short-term fluctuations better than TOC and Nt over the course of two years in the crop residue LTE. Thus, we suggest that AC and NMP are two valuable soil biochemical parameters providing more detailed information on C and N dynamics regarding depth distribution and seasonal dynamics and react more sensitively to different agricultural management practices compared to TOC and Nt. They should be integrated in monitoring agricultural LTEs and in field analyses conducted by farmers. However, when evaluating results of long-term carbon storage, their sensitivity towards annual fluctuations should be taken into account.&amp;lt;/p&amp;gt;</p></article>", "keywords": ["DYNAMICS", "agricultural long-term experiments", "N-MINERALIZATION", "climate change mitigation", "", "agricultural long-term experiments", "", "climate change mitigation", "ORGANIC-CARBON", "soil organic matter", "SDG 13 - Climate Action", "ENZYME-ACTIVITIES", "SDG 2 \u2013 Kein Hunger", "106026 Ecosystem research", "SDG 2 - Zero Hunger", "early parameters of change", "TILLAGE", "2. Zero hunger", "106022 Mikrobiologie", "MICROBIAL BIOMASS", "CROP", "04 agricultural and veterinary sciences", "15. Life on land", "PERMANGANATE-OXIDIZABLE CARBON", "6. Clean water", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "RESIDUE MANAGEMENT", "FRACTIONS"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/jpln.202100130"}, {"href": "https://doi.org/10.5194/egusphere-egu22-5811"}, {"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": "10.5194/egusphere-egu22-5811", "name": "item", "description": "10.5194/egusphere-egu22-5811", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5194/egusphere-egu22-5811"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-27T00:00:00Z"}}, {"id": "10.5281/zenodo.13791160", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:22:19Z", "type": "Journal Article", "created": "2022-03-27", "title": "Agricultural management affects active carbon and nitrogen mineralisation potential in soils", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>&amp;lt;p&amp;gt;Soil organic matter (SOM) is important for soil fertility and climate change mitigation. Agricultural management - including soil amendments - can improve soil fertility and contribute to climate change mitigation by stabilising carbon in soils. This calls for cost-effective parameters to assess&amp;amp;#160; the influence of management practices on SOM. The current study aimed at understanding how sensitive the parameters active/permanganate oxidisable carbon (AC) and nitrogen mineralisation potential (NMP) react to different agricultural management practices compared to total organic carbon (TOC) and total nitrogen (Nt). We aimed to gain a better understanding of SOM processes, mainly regarding depth distribution and seasonality of SOM dynamics using AC and NMP.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Data were obtained in five Austrian long-term field experiments (LTEs) testing four management practices: i) tillage, ii) compost application, iii) crop residue management, and iv) mineral fertilisation.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;AC was specifically sensitive in detecting the effect of tillage treatment at different soil depths. NMP differentiated between all different tillage treatments in the top soil layer, it showed the temporal dynamics between the years in the compost LTE, and it was identified as an early detection property in the crop residue LTE. Both AC and NMP detected short-term fluctuations better than TOC and Nt over the course of two years in the crop residue LTE. Thus, we suggest that AC and NMP are two valuable soil biochemical parameters providing more detailed information on C and N dynamics regarding depth distribution and seasonal dynamics and react more sensitively to different agricultural management practices compared to TOC and Nt. They should be integrated in monitoring agricultural LTEs and in field analyses conducted by farmers. However, when evaluating results of long-term carbon storage, their sensitivity towards annual fluctuations should be taken into account.&amp;lt;/p&amp;gt;</p></article>", "keywords": ["DYNAMICS", "agricultural long-term experiments", "N-MINERALIZATION", "climate change mitigation", "", "agricultural long-term experiments", "", "climate change mitigation", "ORGANIC-CARBON", "soil organic matter", "SDG 13 - Climate Action", "ENZYME-ACTIVITIES", "SDG 2 \u2013 Kein Hunger", "106026 Ecosystem research", "SDG 2 - Zero Hunger", "early parameters of change", "TILLAGE", "2. Zero hunger", "106022 Mikrobiologie", "MICROBIAL BIOMASS", "CROP", "04 agricultural and veterinary sciences", "15. Life on land", "PERMANGANATE-OXIDIZABLE CARBON", "6. Clean water", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "RESIDUE MANAGEMENT", "FRACTIONS"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/jpln.202100130"}, {"href": "https://doi.org/10.5281/zenodo.13791160"}, {"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": "10.5281/zenodo.13791160", "name": "item", "description": "10.5281/zenodo.13791160", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.13791160"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-27T00:00:00Z"}}, {"id": "11353/10.2114337", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:48Z", "type": "Journal Article", "created": "2024-08-05", "title": "Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates", "description": "Abstract                   <p>Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3\uffe2\uff80\uff934 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%\uffe2\uff80\uff9330% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.</p", "keywords": ["0301 basic medicine", "millimetre-scale", "archaea", "Nitrogen", "bulk soil samples", "individual aggregates", "diversity", "soil", "Soil", "03 medical and health sciences", "106026 Ecosystem research", "bacteria", "Soil Microbiology", "106022 Mikrobiologie", "0303 health sciences", "Bacteria", "Microbiota", "Fungi", "Biodiversity", "15. Life on land", "Archaea", "Carbon", "106026 \u00d6kosystemforschung", "106022 Microbiology", "Original Article", "fungi", "community structure", "environment"]}, "links": [{"href": "https://academic.oup.com/ismej/article-pdf/18/1/wrae156/58820679/wrae156.pdf"}, {"href": "https://doi.org/11353/10.2114337"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11353/10.2114337", "name": "item", "description": "11353/10.2114337", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11353/10.2114337"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "11353/10.2115948", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:48Z", "type": "Journal Article", "created": "2023-10-04", "title": "Bacteria face trade-offs in the decomposition of complex biopolymers", "description": "Abstract<p>Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system\uffe2\uff80\uff99s complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low- or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.</p>Author summary<p>The decomposition of polysaccharides by microbes is a key process in the global carbon cycle. It requires the joint action of a variety of microbially-produced extracellular enzymes. They can be broadly classified into endo-enzymes, that act in the middle of polymers, and exo-enzymes, that cleave units from polymer ends. Little is known about the benefits for microbes producing a certain enzyme type and the interplay between enzyme producing strategies in mixed communities. This hampers our comprehensive understanding of decomposition in terrestrial and marine ecosystems and thus limits the prediction of decomposition processes, for example in a changing climate.</p><p>Based on theoretical modelling, we revealed a fundamental trade-off in the action of these enzymes. While exo-enzymes are more efficient at high substrate conditions, endo-enzymes perform better when substrate is low. Generalists producing both enzymes expand their ecological niche of substrate availability compared to specialists only producing one of the two types. Complementary specialists only co-exist in oligotrophic conditions. We conclude that producing enzymes for specific steps within polymer degradation represents relevant ecological strategies for microbes in decomposer communities.</p", "keywords": ["2. Zero hunger", "106022 Mikrobiologie", "decomposition", "Bacteria", "Polymers", "QH301-705.5", "complex biopolymers", "Monomers", "Computational Biology", "Chitin", "Models", " Biological", "Enzymes", "Biopolymers", "Consortia", "106026 \u00d6kosystemforschung", "Oligomers", "106022 Microbiology", "14. Life underwater", "Biology (General)", "106026 Ecosystem research", "bacteria", "Depolymerization", "Research Article"]}, "links": [{"href": "https://doi.org/11353/10.2115948"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20Computational%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11353/10.2115948", "name": "item", "description": "11353/10.2115948", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11353/10.2115948"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-03T00:00:00Z"}}, {"id": "10.5281/zenodo.14790778", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:22:38Z", "type": "Journal Article", "created": "2019-04-01", "title": "Coupled carbon and nitrogen losses in response to seven years of chronic warming in subarctic soils", "description": "Increasing temperatures may alter the stoichiometric demands of soil microbes and impair their capacity to stabilize carbon (C) and retain nitrogen (N), with critical consequences for the soil C and N storage at high latitude soils. Geothermally active areas in Iceland provided wide, continuous and stable gradients of\u00a0soil temperatures\u00a0to test this hypothesis. In order to characterize the stoichiometric demands of microbes from these subarctic soils, we incubated soils from ambient temperatures after the factorial addition of C, N and P substrates separately and in combination. In a second experiment, soils that had been exposed to different\u00a0in situ\u00a0warming intensities (+0, +0.5, +1.8, +3.4, +8.7, +15.9\u00a0\u00b0C above ambient) for seven years were incubated after the combined addition of C, N and P to evaluate the capacity of soil microbes to store and immobilize C and N at the different warming scenarios. The seven years of chronic soil warming triggered large and proportional soil C and N losses (4.1\u00a0\u00b1\u00a00.5% \u00b0C\u22121\u00a0of the stocks in unwarmed soils) from the upper 10\u202fcm of soil, with a predominant depletion of the physically accessible organic substrates that were weakly sorbed in\u00a0soil minerals\u00a0up to 8.7\u202f\u00b0C warming. Soil microbes met the increasing respiratory demands under conditions of low C accessibility at the expenses of a reduction of the standing biomass in warmer soils. This together with the strict microbial C:N stoichiometric demands also constrained their capacity of N retention, and increased the vulnerability of soil to N losses. Our findings suggest a strong control of\u00a0microbial physiology and C:N stoichiometric needs on the retention of soil N and on the resilience of soil C stocks from high-latitudes to warming, particularly during periods of vegetation dormancy and low C inputs.", "keywords": ["0301 basic medicine", "Microbial carbon and nutrients limitation", "Microbial biomass", "TERM", "03 medical and health sciences", "Temperature increase", "FOREST SOIL", "Substrate induced respiration", "ORGANIC-CARBON", "SDG 13 - Climate Action", "TEMPERATURE SENSITIVITY", "CYCLE", "106026 Ecosystem research", "METAANALYSIS", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "Nitrogen loss", "CLIMATE-CHANGE", "AVAILABILITY", "15. Life on land", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "Nitrogen immobilization", "FEEDBACKS", "106022 Microbiology", "PLANT BIOMASS"]}, "links": [{"href": "https://doi.org/10.5281/zenodo.14790778"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.14790778", "name": "item", "description": "10.5281/zenodo.14790778", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.14790778"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-07-01T00:00:00Z"}}, {"id": "10067/1974270151162165141", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:24Z", "type": "Journal Article", "created": "2023-05-10", "title": "Tree stem and soil methane and nitrous oxide fluxes, but not carbon dioxide fluxes, switch sign along a topographic gradient in a tropical forest", "description": "Purpose<br/>Tropical forests exchange large amounts of greenhouse gases (GHGs: carbon dioxide, CO2; methane, CH4; and nitrous oxide, N2O) with the atmosphere. Forest soils and stems can be either sources or sinks for CH4 and N2O, but little is known about what determines the sign and magnitude of these fluxes. Here, we aimed to study how stem and soil GHG fluxes vary along a topographic gradient in a tropical forest.<br/><br/>Methods<br/>Fluxes of GHG from 56 individual tree stems and adjacent soils were measured with manual static chambers. The topographic gradient was characterized by a soil moisture gradient, with one end in a wetland area (\u201cseasonally flooded\u201d; SF), the other end in an upland area (\u201cterra firme\u201d; TF) and in between a transitional area on the slope (SL).<br/><br/>Results<br/>Tree stems and soils were always sources of CO2 with higher fluxes in SF compared to TF and SL. Fluxes of CH4 and N2O were more variable, even within one habitat. Results showed that, in TF, soils acted as sinks for N2O whereas, in SF and SL, they acted as sources. In contrast, tree stems which were predominantly sources of N2O in SF and TF, were sinks in SL. In the soil, N2O fluxes were significantly influenced by both temperature and soil water content, whereas CH4 fluxes were only significantly correlated with soil water content.<br/><br/>Conclusion<br/>SF areas were major sources of the three gases, whereas SL and TF soils and tree stems acted as either sources or sinks for CH4 and N2O. Our results indicate that tree stems represent overlooked sources of CH4 and N2O in tropical forests that need to be further studied to refine GHG budgets.", "keywords": ["[SDV.SA.AGRO] Life Sciences [q-bio]/Agricultural sciences/Agronomy", "106022 Mikrobiologie", "550", "source", "Spatial variation", "Sink", "[SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy", "spatial variation", "Source", "15. Life on land", "Stem", "630", "soil", "[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics", "Soil", "Greenhouse gas (GHG) exchange", "13. Climate action", "106026 \u00d6kosystemforschung", "[SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics", "106022 Microbiology", "stem", "sink", "106026 Ecosystem research", "Biology", "greenhouse gas (GHG) exchange"]}, "links": [{"href": "https://doi.org/10067/1974270151162165141"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10067/1974270151162165141", "name": "item", "description": "10067/1974270151162165141", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10067/1974270151162165141"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-05-09T00:00:00Z"}}, {"id": "2932651632", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:42Z", "type": "Journal Article", "created": "2019-04-01", "title": "Coupled carbon and nitrogen losses in response to seven years of chronic warming in subarctic soils", "description": "Increasing temperatures may alter the stoichiometric demands of soil microbes and impair their capacity to stabilize carbon (C) and retain nitrogen (N), with critical consequences for the soil C and N storage at high latitude soils. Geothermally active areas in Iceland provided wide, continuous and stable gradients of\u00a0soil temperatures\u00a0to test this hypothesis. In order to characterize the stoichiometric demands of microbes from these subarctic soils, we incubated soils from ambient temperatures after the factorial addition of C, N and P substrates separately and in combination. In a second experiment, soils that had been exposed to different\u00a0in situ\u00a0warming intensities (+0, +0.5, +1.8, +3.4, +8.7, +15.9\u00a0\u00b0C above ambient) for seven years were incubated after the combined addition of C, N and P to evaluate the capacity of soil microbes to store and immobilize C and N at the different warming scenarios. The seven years of chronic soil warming triggered large and proportional soil C and N losses (4.1\u00a0\u00b1\u00a00.5% \u00b0C\u22121\u00a0of the stocks in unwarmed soils) from the upper 10\u202fcm of soil, with a predominant depletion of the physically accessible organic substrates that were weakly sorbed in\u00a0soil minerals\u00a0up to 8.7\u202f\u00b0C warming. Soil microbes met the increasing respiratory demands under conditions of low C accessibility at the expenses of a reduction of the standing biomass in warmer soils. This together with the strict microbial C:N stoichiometric demands also constrained their capacity of N retention, and increased the vulnerability of soil to N losses. Our findings suggest a strong control of\u00a0microbial physiology and C:N stoichiometric needs on the retention of soil N and on the resilience of soil C stocks from high-latitudes to warming, particularly during periods of vegetation dormancy and low C inputs.", "keywords": ["0301 basic medicine", "Microbial carbon and nutrients limitation", "Microbial biomass", "TERM", "03 medical and health sciences", "FOREST SOIL", "Temperature increase", "ORGANIC-CARBON", "Substrate induced respiration", "SDG 13 - Climate Action", "TEMPERATURE SENSITIVITY", "CYCLE", "106026 Ecosystem research", "METAANALYSIS", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "CLIMATE-CHANGE", "Nitrogen loss", "AVAILABILITY", "15. Life on land", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "FEEDBACKS", "Nitrogen immobilization", "106022 Microbiology", "PLANT BIOMASS"]}, "links": [{"href": "https://doi.org/2932651632"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2932651632", "name": "item", "description": "2932651632", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2932651632"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-07-01T00:00:00Z"}}, {"id": "10067/1804720151162165141", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:24Z", "type": "Journal Article", "created": "2021-07-21", "title": "Shifts in the Abundances of Saprotrophic and Ectomycorrhizal Fungi With Altered Leaf Litter Inputs", "description": "<p>Ectomycorrhizal (EcM) and saprotrophic fungi interact in the breakdown of organic matter, but the mechanisms underlying the EcM role on organic matter decomposition are not totally clear. We hypothesized that the ecological relations between EcM and saprotroph fungi are modulated by resources availability and accessibility, determining decomposition rates. We manipulated the amount of leaf litter inputs (No-Litter, Control Litter, Doubled Litter) on Trenched (root exclusion) and Non-Trenched plots (with roots) in a temperate deciduous forest of EcM-associated trees. Resultant shifts in soil fungal communities were determined by phospholipid fatty acids and DNA sequencing after 3 years, and CO2 fluxes were measured throughout this period. Different levels of leaf litter inputs generated a gradient of organic substrate availability and accessibility, altering the composition and ecological relations between EcM and saprotroph fungal communities. EcM fungi dominated at low levels of fresh organic substrates and lower organic matter quality, where short-distances exploration types seem to be better competitors, whereas saprotrophs and longer exploration types of EcM fungi tended to dominate at high levels of leaf litter inputs, where labile organic substrates were easily accessible. We were, however, not able to detect unequivocal signs of competition between these fungal groups for common resources. These results point to the relevance of substrate quality and availability as key factors determining the role of EcM and saprotroph fungi on litter and soil organic matter decay and represent a path forward on the capacity of organic matter decomposition of different exploration types of EcM fungi.</p", "keywords": ["liti\u00e8re v\u00e9g\u00e9tale", "Plant detritus", "0301 basic medicine", "570", "Quercus petraea", "http://aims.fao.org/aos/agrovoc/c_24064", "Champignon", "http://aims.fao.org/aos/agrovoc/c_14083", "litter decomposition", "Plant Science", "630", "SB1-1110", "03 medical and health sciences", "Saprophyte", "http://aims.fao.org/aos/agrovoc/c_33550", "environment/Symbiosis", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "plant detritus", "106026 Ecosystem research", "http://aims.fao.org/aos/agrovoc/c_3047", "Biology", "http://aims.fao.org/aos/agrovoc/c_3145", "http://aims.fao.org/aos/agrovoc/c_5023", "http://aims.fao.org/aos/agrovoc/c_35657", "http://aims.fao.org/aos/agrovoc/c_5387", "soil fungal communities", "Mycorhiz\u00e9", "0303 health sciences", "liti\u00e8re foresti\u00e8re", "Ectomycorrhiza fungal exploration types", "ectomycorrhiza fungal exploration types", "http://aims.fao.org/aos/agrovoc/c_24692", "Litter decomposition", "Plant culture", "Soil fungal communities", "[SDV.EE.IEO] Life Sciences [q-bio]/Ecology", " environment/Symbiosis", "15. Life on land", "Gadgil effect", "http://aims.fao.org/aos/agrovoc/c_35482", "CO2 fluxes", "ectomycorhize", "106026 \u00d6kosystemforschung", "mati\u00e8re organique", "CO fluxes", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "[SDV.EE.IEO]Life Sciences [q-bio]/Ecology", "champignon du sol", "environment/Ecosystems", "mati\u00e8re organique du sol"]}, "links": [{"href": "https://doi.org/10067/1804720151162165141"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10067/1804720151162165141", "name": "item", "description": "10067/1804720151162165141", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10067/1804720151162165141"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-07-21T00:00:00Z"}}, {"id": "10261/284332", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:31Z", "type": "Journal Article", "created": "2022-03-17", "title": "From diversity to complexity: Microbial networks in soils", "description": "ABSTRACT<p>Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.</p", "keywords": ["0301 basic medicine", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "Microbial community structure", "Perspectives Paper", "15. Life on land", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "13. Climate action", "Ecological networks", "Soil microbial ecology", "Microbial network analysis", "106022 Microbiology", "106026 Ecosystem research", "Co-occurrence networks"]}, "links": [{"href": "https://doi.org/10261/284332"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10261/284332", "name": "item", "description": "10261/284332", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10261/284332"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-16T00:00:00Z"}}, {"id": "11353/10.2037573", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:48Z", "type": "Journal Article", "created": "2023-06-29", "title": "Gold\u2010FISH enables targeted NanoSIMS analysis of plant\u2010associated bacteria", "description": "Summary<p> <p>Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in\uffc2\uffa0situ evidence of bacterial activity.</p> <p>To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold\uffe2\uff80\uff90based in\uffc2\uffa0situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity.</p> <p>We incubated Kosakonia strain DS\uffe2\uff80\uff901\uffe2\uff80\uff90associated, gnotobiotically grown rice plants with 15N\uffe2\uff80\uff93N2 gas to detect in\uffc2\uffa0situ N2 fixation activity. Bacterial cells along the rhizoplane showed\uffc2\uffa0heterogeneous patterns of 15N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15N (average and median of 3.36 and 2.85 at% 15N, respectively, n\uffe2\uff80\uff89=\uffe2\uff80\uff89697 cells).</p> <p>The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant\uffe2\uff80\uff93microbe interactions. For example, it enables verification of the in\uffc2\uffa0situ metabolic activity of host\uffe2\uff80\uff90associated commercialized strains or plant growth\uffe2\uff80\uff90promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant\uffe2\uff80\uff93microbe combinations for improvement of crop management.</p> </p", "keywords": ["2. Zero hunger", "106022 Mikrobiologie", "rhizosphere bacteria", "Bacteria", "plant growth-promoting bacteria", "plant\u2013microbe interaction", "Research", "Oryza", "biological nitrogen fixation", "Plants", "microbial activity", "in\u00a0situ hybridization", "Plant Roots", "106026 \u00d6kosystemforschung", "Rhizosphere", "106022 Microbiology", "NanoSIMS", "in situ hybridization", "106026 Ecosystem research", "In situ hybridization", "In Situ Hybridization", "Soil Microbiology", "plant-microbe interaction"]}, "links": [{"href": "https://doi.org/11353/10.2037573"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11353/10.2037573", "name": "item", "description": "11353/10.2037573", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11353/10.2037573"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-28T00:00:00Z"}}, {"id": "11353/10.2067045", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:48Z", "type": "Journal Article", "created": "2024-04-17", "title": "Survival and rapid resuscitation permit limited productivity in desert microbial communities", "description": "Abstract<p>Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.</p", "keywords": ["2. Zero hunger", "0301 basic medicine", "106022 Mikrobiologie", "0303 health sciences", "105904 Environmental research", "Science", "Microbiota", "Rain", "Q", "15. Life on land", "microbial ecology", "Article", "Microbial ecology", "Soil", "03 medical and health sciences", "Soil microbiology", "106026 \u00d6kosystemforschung", "106022 Microbiology", "Desert Climate", "106026 Ecosystem research", "105904 Umweltforschung", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/11353/10.2067045"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11353/10.2067045", "name": "item", "description": "11353/10.2067045", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11353/10.2067045"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-17T00:00:00Z"}}, {"id": "11353/10.2110681", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:48Z", "type": "Journal Article", "created": "2024-11-19", "title": "A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum", "description": "Abstract                <p>Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations. The decrease from 10 to 0.1\uffc2\uffa0\uffc2\uffb5M oxygen (3.6 to 0.036 pO2% present atmospheric level, respectively) caused the upregulation of the transcription of genes involved in signal transduction mechanisms, energy production and conversion and secondary metabolites biosynthesis, transport, and catabolism based on clusters of orthologous group categories. Contrary to established observations for aerobic metabolism, key genes in oxidative stress response were significantly upregulated at lower oxygen concentrations, presumably due to an NADH/NAD+ redox ratio imbalance as the cells transitioned into nanoxia. Furthermore, A. capsulatum adapted to nanoxia by inducing a respiro-fermentative metabolism and rerouting fluxes of its central carbon and energy pathways to adapt to high NADH/NAD+ redox ratios. Our results reveal physiological features and metabolic capabilities that allowed A. capsulatum to adapt to oxygen-limited conditions, which could expand into other environmentally relevant soil strains.</p", "keywords": ["0301 basic medicine", "106022 Mikrobiologie", "0303 health sciences", "Acidobacteriota", "NADH imbalances", "microaerobic respiration", "Gene Expression Regulation", " Bacterial", "Adaptation", " Physiological", "oxygen limitation", "Acidobacteria", "Oxygen", "Oxidative Stress", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "Fermentation", "106022 Microbiology", "106026 Ecosystem research", "fermentation", "transcriptome", "Oxidation-Reduction", "Soil Microbiology", "Research Article"]}, "links": [{"href": "https://doi.org/11353/10.2110681"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11353/10.2110681", "name": "item", "description": "11353/10.2110681", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11353/10.2110681"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-11-18T00:00:00Z"}}, {"id": "11579/142540", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:52Z", "type": "Journal Article", "created": "2021-06-10", "title": "Carbon dioxide fluxes increase from day to night across European streams", "description": "Abstract<p>Globally, inland waters emit over 2 Pg of carbon per year as carbon dioxide, of which the majority originates from streams and rivers. Despite the global significance of fluvial carbon dioxide emissions, little is known about their diel dynamics. Here we present a large-scale assessment of day- and night-time carbon dioxide fluxes at the water-air interface across 34 European streams. We directly measured fluxes four times between October 2016 and July 2017 using drifting chambers. Median fluxes are 1.4 and 2.1\uffe2\uff80\uff89mmol\uffe2\uff80\uff89m\uffe2\uff88\uff922 h\uffe2\uff88\uff921 at midday and midnight, respectively, with night fluxes exceeding those during the day by 39%. We attribute diel carbon dioxide flux variability mainly to changes in the water partial pressure of carbon dioxide. However, no consistent drivers could be identified across sites. Our findings highlight widespread day-night changes in fluvial carbon dioxide fluxes and suggest that the time of day greatly influences measured carbon dioxide fluxes across European streams.</p", "keywords": ["DYNAMICS", "0106 biological sciences", "DIURNAL-VARIATION", "550", "Naturgeografi", "PCO(2)", "Geography & travel", "Oceanografi", " hydrologi och vattenresurser", "910", "01 natural sciences", "Oceanography", " Hydrology and Water Resources", "105205 Klimawandel", "Limnology", "105304 Hydrologie", "SDG 13 - Climate Action", "info:eu-repo/classification/ddc/910", "106026 Ecosystem research", "1ST-ORDER STREAM", "106020 Limnology", "105205 Climate change", "0105 earth and related environmental sciences", "[SDU.OCEAN]Sciences of the Universe [physics]/Ocean", "Atmosphere", "[SDU.OCEAN] Sciences of the Universe [physics]/Ocean", " Atmosphere", "EVASION", "Carbon cycle", "ddc:910", "106020 Limnologie", "Climate Science", "ECOSYSTEM METABOLISM", "WATER-AIR", "Physical Geography", "106026 \u00d6kosystemforschung", "CO2 EMISSIONS", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "Environmental chemistry", "DISSOLVED ORGANIC-MATTER", "Klimatvetenskap", "105304 Hydrology", "GAS-EXCHANGE"]}, "links": [{"href": "https://eprints.bournemouth.ac.uk/35763/1/s43247-021-00192-w.pdf"}, {"href": "https://repositorio.ulisboa.pt/bitstream/10451/49425/1/s43247-021-00192-w.pdf"}, {"href": "https://iris.unito.it/bitstream/2318/1799544/1/106%20EURORUN.pdf"}, {"href": "https://www.nature.com/articles/s43247-021-00192-w.pdf"}, {"href": "https://doi.org/11579/142540"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Communications%20Earth%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11579/142540", "name": "item", "description": "11579/142540", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11579/142540"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-22T00:00:00Z"}}, {"id": "11585/996222", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:53Z", "type": "Journal Article", "created": "2021-07-10", "title": "A critical perspective on interpreting amplicon sequencing data in soil ecological research", "description": "Abstract   Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation, and availability to improve the rigor of future studies.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Soil microbial diversity", "0303 health sciences", "Soil metabarcoding", "DIVERSITY", "Ecology; Soil microbes; Amplicon sequencing", "Compositional data", "SCALE SPATIAL HETEROGENEITY", "15. Life on land", "BIOMASS", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "Soil complexity", "CARBON-USE EFFICIENCY", "BACTERIA", "DNA EXTRACTION", "MICROORGANISMS", "MICROBIAL COMMUNITIES", "106026 Ecosystem research", "RIBOSOMAL-RNA", "Amplicon sequencing", "Soil microorganisms", "GENERATION"]}, "links": [{"href": "https://doi.org/11585/996222"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11585/996222", "name": "item", "description": "11585/996222", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11585/996222"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-01T00:00:00Z"}}, {"id": "1871.1/3309bf72-4ad9-4331-981a-6fc05d319188", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:02Z", "type": "Journal Article", "created": "2019-12-09", "title": "A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem", "description": "Temperature governs most biotic processes, yet we know little about how warming affects whole ecosystems. Here we examined the responses of 128\u2009components of a subarctic grassland to either 5-8 or >50\u2009years of soil warming. Warming of >50\u2009years drove the ecosystem to a new steady state possessing a distinct biotic composition and reduced species richness, biomass and soil organic matter. However, the warmed state was preceded by an overreaction to warming, which was related to organism physiology and was evident after 5-8\u2009years. Ignoring this overreaction yielded errors of >100% for 83\u2009variables when predicting their responses to a realistic warming scenario of 1\u2009\u00b0C over 50\u2009years, although some, including soil carbon content, remained stable after 5-8\u2009years. This study challenges long-term ecosystem predictions made from short-term observations, and provides a framework for characterization of ecosystem responses to sustained climate change.", "keywords": ["0301 basic medicine", "570", "Environmental management", "INCREASES", "Ecosystem ecology", "Climate Change", "Evolutionary biology", "TERM", "630", "Article", "Carbon Cycle", "3103 Ecology (for-2020)", "Soil (mesh)", "Soil", "03 medical and health sciences", "14 Life Below Water (sdg)", "SDG 13 - Climate Action", "106026 Ecosystem research", "Life Below Water", "Ecosystem", "106022 Mikrobiologie", "0303 health sciences", "31 Biological Sciences (for-2020)", "41 Environmental Sciences (for-2020)", "Ecology", "Grassland (mesh)", "Climate-change ecology", "Ecosystem (mesh)", "SHIFTS", "3104 Evolutionary biology (for-2020)", "Biological Sciences", "15. Life on land", "4104 Environmental management (for-2020)", "Grassland", "Carbon Cycle (mesh)", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "FEEDBACKS", "Climate Change (mesh)", "106022 Microbiology", "VEGETATION", "SENSITIVITY", "Environmental Sciences", "SOIL RESPIRATION", "RESPONSES"]}, "links": [{"href": "https://escholarship.org/content/qt99v0g8pc/qt99v0g8pc.pdf"}, {"href": "https://doi.org/1871.1/3309bf72-4ad9-4331-981a-6fc05d319188"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Ecology%20%26amp%3B%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1871.1/3309bf72-4ad9-4331-981a-6fc05d319188", "name": "item", "description": "1871.1/3309bf72-4ad9-4331-981a-6fc05d319188", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1871.1/3309bf72-4ad9-4331-981a-6fc05d319188"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-09T00:00:00Z"}}, {"id": "20.500.11850/583232", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:15Z", "type": "Journal Article", "created": "2022-11-17", "title": "Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities", "description": "Abstract<p>Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.</p", "keywords": ["0301 basic medicine", "QH301-705.5", "Fungal ecology; Microbial ecology; Symbiosis", "microbial ecology", "Plant Roots", "Article", "Microbial ecology", "Soil", "03 medical and health sciences", "Mycorrhizae", "RNA", " Ribosomal", " 16S", "Fagus", "Biology (General)", "106026 Ecosystem research", "Fungal ecology", "Symbiosis", "Soil Microbiology", "106022 Mikrobiologie", "0303 health sciences", "Bacteria", "15. Life on land", "Archaea", "symbiosis", "106026 \u00d6kosystemforschung", "fungal ecology", "106022 Microbiology"]}, "links": [{"href": "https://www.nature.com/articles/s42003-022-04178-y.pdf"}, {"href": "https://doi.org/20.500.11850/583232"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Communications%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.11850/583232", "name": "item", "description": "20.500.11850/583232", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.11850/583232"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-17T00:00:00Z"}}, {"id": "2263/74486", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:28Z", "type": "Journal Article", "created": "2020-04-13", "title": "Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation.</p></article>", "keywords": ["0301 basic medicine", "dormancy", "CYANOBACTERIAL EXOPOLYSACCHARIDES", "Trace gas", "Microbiology", "SOIL CRUSTS", "Energy reserve", "HIGH-AFFINITY", "03 medical and health sciences", "trace gas", "ATMOSPHERIC TRACE GASES", "Energetics", "energy reserve", "Dormancy", "SOR RONDANE MOUNTAINS", "Desert", "Photosynthesis", "106026 Ecosystem research", "CARBON-MONOXIDE", "desert", "ATACAMA DESERT", "energetics", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "photosynthesis", "COMMUNITY RESPONSE", "15. Life on land", "QR1-502", "106026 \u00d6kosystemforschung", "DRY SOIL", "13. Climate action", "MOLECULAR-HYDROGEN", "106022 Microbiology", "Minireview"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSystems.00495-19"}, {"href": "https://doi.org/2263/74486"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2263/74486", "name": "item", "description": "2263/74486", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2263/74486"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-28T00:00:00Z"}}, {"id": "2309129852", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:30Z", "type": "Journal Article", "created": "2016-03-26", "title": "Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland", "description": "<p>Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of <sup>18</sup>O from labeled water into microbial DNA. Microbial respiration was 28-37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland. </p>", "keywords": ["FUNGAL", "2. Zero hunger", "106022 Mikrobiologie", "Nitrogen addition", "BACTERIAL", "NITROGEN DEPOSITION", "GROWTH EFFICIENCY", "FOREST FLOOR", "Nutrients", "04 agricultural and veterinary sciences", "15. Life on land", "Stoichiometry", "ORGANIC-MATTER", "RESPIRATION", "106026 \u00d6kosystemforschung", "13. Climate action", "Nutrient limitation", "Microbial growth yield", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Mean residence time", "STOICHIOMETRIC CONTROLS", "ENZYME-ACTIVITY", "106026 Ecosystem research", "COMMUNITY STRUCTURE"]}, "links": [{"href": "https://doi.org/2309129852"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2309129852", "name": "item", "description": "2309129852", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2309129852"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "21.11116/0000-0006-C73B-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:22Z", "type": "Journal Article", "created": "2020-07-27", "title": "Persistence of soil organic carbon caused by functional complexity", "description": "Soil organic carbon management has the potential to aid climate change mitigation through drawdown of atmospheric carbon dioxide. To be effective, such management must account for processes influencing carbon storage and re-emission at different space and time scales. Achieving this requires a conceptual advance in our understanding to link carbon dynamics from the scales at which processes occur to the scales at which decisions are made. Here, we propose that soil carbon persistence can be understood through the lens of decomposers as a result of functional complexity derived from the interplay between spatial and temporal variation of molecular diversity and composition. For example, co-location alone can determine whether a molecule is decomposed, with rapid changes in moisture leading to transport of organic matter and constraining the fitness of the microbial community, while greater molecular diversity may increase the metabolic demand of, and thus potentially limit, decomposition. This conceptual shift accounts for emergent behaviour of the microbial community and would enable soil carbon changes to be predicted without invoking recalcitrant carbon forms that have not been observed experimentally. Functional complexity as a driver of soil carbon persistence suggests soil management should be based on constant care rather than one-time action to lock away carbon in soils.", "keywords": ["[SDE] Environmental Sciences", "DECOMPOSITION", "2. Zero hunger", "106022 Mikrobiologie", "[SDE.MCG]Environmental Sciences/Global Changes", "UNCERTAINTY", "04 agricultural and veterinary sciences", "INPUTS", "15. Life on land", "TRANSPORT", "MODEL", "[SDE.MCG] Environmental Sciences/Global Changes", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "[SDE]Environmental Sciences", "SDG 13 - Climate Action", "Meteorology & Atmospheric Sciences", "106022 Microbiology", "GROWTH", "0401 agriculture", " forestry", " and fisheries", "TURNOVER", "PLANT", "106026 Ecosystem research", "MATTER"]}, "links": [{"href": "http://www.nature.com/articles/s41561-020-0612-3.pdf"}, {"href": "https://escholarship.org/content/qt84n3398c/qt84n3398c.pdf"}, {"href": "https://doi.org/21.11116/0000-0006-C73B-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Geoscience", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "21.11116/0000-0006-C73B-8", "name": "item", "description": "21.11116/0000-0006-C73B-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/21.11116/0000-0006-C73B-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-07-27T00:00:00Z"}}, {"id": "2994175618", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:46Z", "type": "Journal Article", "created": "2019-12-09", "title": "A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem", "description": "Temperature governs most biotic processes, yet we know little about how warming affects whole ecosystems. Here we examined the responses of 128\u2009components of a subarctic grassland to either 5-8 or >50\u2009years of soil warming. Warming of >50\u2009years drove the ecosystem to a new steady state possessing a distinct biotic composition and reduced species richness, biomass and soil organic matter. However, the warmed state was preceded by an overreaction to warming, which was related to organism physiology and was evident after 5-8\u2009years. Ignoring this overreaction yielded errors of >100% for 83\u2009variables when predicting their responses to a realistic warming scenario of 1\u2009\u00b0C over 50\u2009years, although some, including soil carbon content, remained stable after 5-8\u2009years. This study challenges long-term ecosystem predictions made from short-term observations, and provides a framework for characterization of ecosystem responses to sustained climate change.", "keywords": ["0301 basic medicine", "570", "Environmental management", "INCREASES", "Ecosystem ecology", "Climate Change", "Evolutionary biology", "TERM", "630", "Article", "Carbon Cycle", "Soil", "03 medical and health sciences", "SDG 13 - Climate Action", "106026 Ecosystem research", "Life Below Water", "Ecosystem", "106022 Mikrobiologie", "0303 health sciences", "Ecology", "Climate-change ecology", "SHIFTS", "Biological Sciences", "15. Life on land", "Grassland", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "FEEDBACKS", "106022 Microbiology", "VEGETATION", "SENSITIVITY", "Environmental Sciences", "SOIL RESPIRATION", "RESPONSES"]}, "links": [{"href": "https://escholarship.org/content/qt99v0g8pc/qt99v0g8pc.pdf"}, {"href": "https://doi.org/2994175618"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Ecology%20%26amp%3B%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2994175618", "name": "item", "description": "2994175618", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2994175618"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-09T00:00:00Z"}}, {"id": "3045287773", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:53Z", "type": "Journal Article", "created": "2020-07-27", "title": "Persistence of soil organic carbon caused by functional complexity", "description": "Soil organic carbon management has the potential to aid climate change mitigation through drawdown of atmospheric carbon dioxide. To be effective, such management must account for processes influencing carbon storage and re-emission at different space and time scales. Achieving this requires a conceptual advance in our understanding to link carbon dynamics from the scales at which processes occur to the scales at which decisions are made. Here, we propose that soil carbon persistence can be understood through the lens of decomposers as a result of functional complexity derived from the interplay between spatial and temporal variation of molecular diversity and composition. For example, co-location alone can determine whether a molecule is decomposed, with rapid changes in moisture leading to transport of organic matter and constraining the fitness of the microbial community, while greater molecular diversity may increase the metabolic demand of, and thus potentially limit, decomposition. This conceptual shift accounts for emergent behaviour of the microbial community and would enable soil carbon changes to be predicted without invoking recalcitrant carbon forms that have not been observed experimentally. Functional complexity as a driver of soil carbon persistence suggests soil management should be based on constant care rather than one-time action to lock away carbon in soils.", "keywords": ["[SDE] Environmental Sciences", "DECOMPOSITION", "2. Zero hunger", "106022 Mikrobiologie", "[SDE.MCG]Environmental Sciences/Global Changes", "UNCERTAINTY", "04 agricultural and veterinary sciences", "INPUTS", "15. Life on land", "TRANSPORT", "MODEL", "[SDE.MCG] Environmental Sciences/Global Changes", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "[SDE]Environmental Sciences", "SDG 13 - Climate Action", "Meteorology & Atmospheric Sciences", "106022 Microbiology", "GROWTH", "0401 agriculture", " forestry", " and fisheries", "TURNOVER", "PLANT", "106026 Ecosystem research", "MATTER"]}, "links": [{"href": "http://www.nature.com/articles/s41561-020-0612-3.pdf"}, {"href": "https://escholarship.org/content/qt84n3398c/qt84n3398c.pdf"}, {"href": "https://doi.org/3045287773"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Geoscience", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3045287773", "name": "item", "description": "3045287773", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3045287773"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-07-27T00:00:00Z"}}, {"id": "3091797412", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:55Z", "type": "Journal Article", "created": "2020-10-06", "title": "Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils", "description": "Abstract                <p>Significant rates of atmospheric dihydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.</p", "keywords": ["0301 basic medicine", "Bacterial physiology", "Article", "HIGH-AFFINITY", "MULTIPLE SEQUENCE ALIGNMENT", "Soil", "03 medical and health sciences", "Hydrogenase", "106026 Ecosystem research", "Soil Microbiology", "H-2", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "Biodiversity", "PHYLUM ACIDOBACTERIA", "15. Life on land", "FOREST", "16. Peace & justice", "ENERGY-SOURCE", "Acidobacteria", "Soil microbiology", "106026 \u00d6kosystemforschung", "13. Climate action", "MOLECULAR-HYDROGEN", "BACTERIA", "106022 Microbiology", "SP-NOV.", "GEN. NOV.", "Oxidation-Reduction", "Hydrogen"]}, "links": [{"href": "https://www.nature.com/articles/s41396-020-00750-8.pdf"}, {"href": "https://doi.org/3091797412"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3091797412", "name": "item", "description": "3091797412", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3091797412"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-06T00:00:00Z"}}, {"id": "39352455", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:26:18Z", "type": "Journal Article", "created": "2024-10-01", "title": "What determines transfer of carbon from plants to mycorrhizal fungi?", "description": "Summary<p>Biological Market Models are common evolutionary frameworks to understand the maintenance of mutualism in mycorrhizas. \uffe2\uff80\uff98Surplus C\uffe2\uff80\uff99 hypotheses provide an alternative framework where stoichiometry and source\uffe2\uff80\uff93sink dynamics govern mycorrhizal function. A critical difference between these frameworks is whether carbon transfer from plants is regulated by nutrient transfer from fungi or through source\uffe2\uff80\uff93sink dynamics. In this review, we: provide a historical perspective; summarize studies that asked whether plants transfer more carbon to fungi that transfer more nutrients; conduct a meta\uffe2\uff80\uff90analysis to assess whether mycorrhizal plant growth suppressions are related to carbon transfer; and review literature on cellular mechanisms for carbon transfer. In sum, current knowledge does not indicate that carbon transfer from plants is directly regulated by nutrient delivery from fungi. Further, mycorrhizal plant growth responses were linked to nutrient uptake rather than carbon transfer. These findings are more consistent with \uffe2\uff80\uff98Surplus C\uffe2\uff80\uff99 hypotheses than Biological Market Models. However, we also identify research gaps, and future research may uncover a mechanism directly linking carbon and nutrient transfer. Until then, we urge caution when applying economic terminology to describe mycorrhizas. We present a synthesis of ideas, consider knowledge gaps, and suggest experiments to advance the field.</p", "keywords": ["106022 Mikrobiologie", "sanctions and rewards", "membrane transport", "comparative advantage", "Biological Transport", "mycorrhizas", "transporters", "Plants", "symbiosis", "Carbon", "106026 \u00d6kosystemforschung", "Mycorrhizae", "functional equilibrium", "106022 Microbiology", "106026 Ecosystem research", "Symbiosis", "shading"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20145"}, {"href": "https://doi.org/39352455"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "39352455", "name": "item", "description": "39352455", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/39352455"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-10-01T00:00:00Z"}}, {"id": "PMC9579094", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:08Z", "type": "Journal Article", "created": "2022-06-22", "title": "Harnessing belowground processes for sustainable intensification of agricultural systems", "description": "Abstract <p>Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.</p", "keywords": ["0301 basic medicine", "BIOLOGICAL NITRIFICATION INHIBITION", "PHOSPHATE SOLUBILIZING BACTERIA", "Plant-plant interaction", "Rhizobiome", "MEDIATED PH CHANGES", "Review Article", "Plant health", "MEMBRANE H+-ATPASE", "12. Responsible consumption", "03 medical and health sciences", "Soil health", "Soil structure", "C sequestration", "SDG 13 - Climate Action", "SDG 2 \u2013 Kein Hunger", "106026 Ecosystem research", "Plant nutrition", "SDG 2 - Zero Hunger", "2. Zero hunger", "0303 health sciences", "Water availability", "Root exudation", "JASMONIC ACID", "15. Life on land", "Microbes", "Intercropping", "106026 \u00d6kosystemforschung", "PLANT-GROWTH", "13. Climate action", "ROOT BORDER CELLS", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "C cycling", "INNATE IMMUNITY", "NITROGEN-FIXATION", "ORGANIC-ACIDS"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s11104-022-05508-z.pdf"}, {"href": "https://doi.org/PMC9579094"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC9579094", "name": "item", "description": "PMC9579094", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC9579094"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-06-22T00:00:00Z"}}, {"id": "PMC8027828", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:05Z", "type": "Journal Article", "created": "2020-10-06", "title": "Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils", "description": "Abstract                <p>Significant rates of atmospheric dihydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.</p", "keywords": ["0301 basic medicine", "Bacterial physiology", "Article", "HIGH-AFFINITY", "MULTIPLE SEQUENCE ALIGNMENT", "Soil", "03 medical and health sciences", "Hydrogenase", "106026 Ecosystem research", "Soil Microbiology", "H-2", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "Biodiversity", "PHYLUM ACIDOBACTERIA", "15. Life on land", "FOREST", "16. Peace & justice", "ENERGY-SOURCE", "Acidobacteria", "Soil microbiology", "106026 \u00d6kosystemforschung", "13. Climate action", "MOLECULAR-HYDROGEN", "BACTERIA", "106022 Microbiology", "SP-NOV.", "GEN. 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