{"type": "FeatureCollection", "features": [{"id": "10.1007/s11270-016-2884-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:16Z", "type": "Journal Article", "created": "2016-05-24", "title": "Root Production Of Fagus Crenata Blume Saplings Grown In Two Soils And Exposed To Elevated Co2 Concentration: An 11-Year Free-Air-Co2 Enrichment (Face) Experiment In Northern Japan", "description": "We examined the root production of a set of Fagus crenata (Siebold\u2019s beech) saplings grown in an infertile immature volcanic ash soil (VA) and another set in a fertile brown forest soil (BF) with both sets exposed to elevated CO2. After the saplings had been exposed to ambient (370\u2013390\u00a0\u03bcmol\u00a0mol\u22121) or elevated (500\u00a0\u03bcmol\u00a0mol\u22121) CO2, during the daytime, for 11 growing seasons, the root systems were excavated. Elevated CO2 boosted the total root production of saplings grown in VA and abolished the negative effect of VA under ambient CO2, but there was no significant effect of elevated CO2 on saplings grown in BF. These results indicate the projected elevated CO2 concentrations may have a different impact in regions with different soil fertility while in regions with VA, a higher net primary production is expected. In addition, we observed large elevated CO2-induced fine-root production and extensive foraging strategy of saplings in both soils, a phenomenon that may partly (a) adjust the biogeochemical cycles of ecosystems, (b) form their response to global change, and (c) increase the size and/or biodiversity of soil fauna. We recommend that future researches consider testing a soil with a higher degree of infertility than the one we tested.", "keywords": ["2. Zero hunger", "0106 biological sciences", "NPP", "Ecophysiology", "Air pollution", "Climate change", "Atmospheric environment", "15. Life on land", "Greenhouse gas", "01 natural sciences", "653"]}, "links": [{"href": "https://doi.org/10.1007/s11270-016-2884-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%2C%20Air%2C%20%26amp%3B%20Soil%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11270-016-2884-1", "name": "item", "description": "10.1007/s11270-016-2884-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11270-016-2884-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-05-23T00:00:00Z"}}, {"id": "10.1016/j.foreco.2008.02.005", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:30Z", "type": "Journal Article", "created": "2008-03-12", "title": "Why Does Rainfall Affect The Trend In Soil Carbon After Converting Pastures To Forests? A Possible Explanation Based On Nitrogen Dynamics", "description": "Abstract When trees are planted onto former pastures, soil carbon stocks typically either remain constant or decrease, with decreases more common in regions with higher rainfall. We conducted a modelling analysis to assess whether those changes in soil carbon, especially the interaction with rainfall, could be understood through consideration of nitrogen balances. The study was based on simulations with the whole-system ecophysiological model CenW which allowed explicit modelling of both carbon and nitrogen pools and their fluxes through plants and soil organic matter. We found that in a modelled coniferous forest without excess water input, total system nitrogen stocks remained similar to pre-forestation values because there were few pathways for nitrogen losses, and without biological nitrogen fixation or fertiliser inputs, gains were restricted to small inputs from atmospheric deposition. However, tree biomass and the litter layer accumulated considerable amounts of nitrogen. This accumulation of nitrogen came at the expense of depleting soil nitrogen stocks. With the change from input of grass litter that is low in lignin to forest litter with higher lignin concentration, organic-matter C:N ratios increased so that more carbon could be stored per unit of soil nitrogen which partly negated the effect of reduced nitrogen stocks. The increase in C:N ratios was initially confined to the surface litter layer because of slow transfer of material to the mineral soil. Over a period of decades, soil C:N ratios eventually increased in the soil as well. Simulations with different amounts of precipitation showed that greater amounts of nitrogen were leached from systems where water supply exceeded the plants\u2019 requirements. Reduced nitrogen stocks then caused a subsequent reduction in soil organic carbon stocks. These simulations thus provided a consistent explanation for the observation of greater losses of soil organic carbon in high-rainfall systems after converting pastures to forests. More generally, the simulations showed that explicit modelling of the nitrogen cycle can put important constraints on possible changes in soil-carbon stocks that may occur after land-use change.", "keywords": ["land use change", "Rainfall", "Mitigation", "ecophysiology", "nitrogen cyc Afforestation", "Greenhouse", "Nitrogen", "Rain", "CenW", "Land-use change", "lignin", "Greenhouse effect", "afforestation", "carbon cycle", "Forest", "Reforestation", "Keywords: Carbon", "2. Zero hunger", "atmospheric deposition", "Nitrogen dynamics", "04 agricultural and veterinary sciences", "15. Life on land", "Carbon", "13. Climate action", "Land use", "ecological modeling", "0401 agriculture", " forestry", " and fisheries", "grassland"], "contacts": [{"organization": "Roger M. Gifford, Miko U. F. Kirschbaum, Miko U. F. Kirschbaum, Lan Bin Guo,", "roles": ["creator"]}]}, "links": [{"href": "https://openresearch-repository.anu.edu.au/bitstream/1885/61047/5/Kirschbaum_Rainfall_affect_in_soil_carbon.pdf.jpg"}, {"href": "https://openresearch-repository.anu.edu.au/bitstream/1885/61047/7/01_Kirschbaum_Why_does_rainfall_affect_the_2008.pdf.jpg"}, {"href": "https://doi.org/10.1016/j.foreco.2008.02.005"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Forest%20Ecology%20and%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foreco.2008.02.005", "name": "item", "description": "10.1016/j.foreco.2008.02.005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foreco.2008.02.005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-04-01T00:00:00Z"}}, {"id": "10.1093/treephys/22.7.435", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:01Z", "type": "Journal Article", "created": "2012-01-20", "title": "Responses Of Deciduous Broadleaf Trees To Defoliation In A Co2 Enriched Atmosphere", "description": "Relatively little is known about the implications of atmospheric CO2 enrichment for tree responses to biotic disturbances such as folivory. We examined the combined effects of elevated CO2 concentration ([CO2]) and defoliation on growth and physiology of sugar maple (Acer saccharum Marsh.) and trembling aspen (Populus tremuloides Michx.). Seedlings were planted in the ground in eight open-top chambers. Four chambers were ventilated with CO2-enriched air (ambient + 283 micromol mol-1) and four chambers were supplied with ambient air. After 6 weeks of growth, half of the leaf area was removed on a subset of seedlings of each species in each CO2 treatment. We monitored subsequent biomass gain and allocation, along with leaf gas exchange and chemistry. Defoliation did not significantly affect final seedling biomass in either species or CO2 treatment. Growth recovery following defoliation was associated with increased allocation to leaf mass in maple and a slight enhancement of mean photosynthesis in aspen. Elevated [CO2] did not significantly affect aspen growth, and the observed stimulation of maple growth was significant only in mid-season. Correspondingly, simulated responses of whole-tree photosynthesis to elevated [CO2] were constrained by a decrease in photosynthetic capacity in maple, and were partially offset by reductions in specific leaf area and biomass allocation to foliage in aspen. There was a significant interaction between [CO2] and defoliation on only a few of the measured traits. Thus, the data do not support the hypothesis that atmospheric CO2 enrichment will substantially alter tree responses to folivory. However, our findings do provide further indication that regeneration-stage growth rates of certain temperate tree species may respond only moderately to a near doubling of atmospheric [CO2].", "keywords": ["defoliation-", "0106 biological sciences", "Ecophysiology", "Quaking aspen", "biomass-allocation", "growth-response", "Growth", "Environmental-Sciences)", "01 natural sciences", "plant-composition", "Trees", "biomass-", "Spermatophyta-", "Biomass", "Photosynthesis", "plant-physiology", "defoliation", "Angiospermae-", "leaf-area", "GLOBAL-ECOLOGY", "seedling-growth", "source-sink-relations", "Populus-tremuloides", "gas-exchange", "Populus", "broadleaves-", "deciduous-tree", "forest-trees", "atmosphere-", "trees-", "biomass-production", "Acer saccharum", "Nitrogen", "Carbohydrates", "Acer", "carbon-dioxide-enrichment", "photosynthesis-", "growth-", "species-differences", "seedlings-", "wisconsin-", "Populus tremuloides", "photosynthesis", "Climatic changes", "Carbon Dioxide", "15. Life on land", "Plant Leaves", "leaves-", "Aceraceae-: Dicotyledones-", "Carbon dioxide", "Sugar maple", "Seedlings", "Terrestrial-Ecology (Ecology-", "Acer-saccharum"], "contacts": [{"organization": "Volin, John C., Kruger, Eric L., Lindroth, Richard L.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1093/treephys/22.7.435"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Tree%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/treephys/22.7.435", "name": "item", "description": "10.1093/treephys/22.7.435", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/22.7.435"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2002-05-01T00:00:00Z"}}, {"id": "10.1101/117887", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:05Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics", "description": "Abstract

Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.Intrinsic water\uffe2\uff80\uff90use efficiency (iWUE) characterizes the physiological control on the simultaneous exchange of water and carbon dioxide in terrestrial ecosystems. Knowledge of iWUE is commonly gained from leaf\uffe2\uff80\uff90level gas exchange measurements, which are inevitably restricted in their spatial and temporal coverage. Flux measurements based on the eddy covariance (EC) technique can overcome these limitations, as they provide continuous and long\uffe2\uff80\uff90term records of carbon and water fluxes at the ecosystem scale. However, vegetation gas exchange parameters derived from EC data are subject to scale\uffe2\uff80\uff90dependent and method\uffe2\uff80\uff90specific uncertainties that compromise their ecophysiological interpretation as well as their comparability among ecosystems and across spatial scales. Here, we use estimates of canopy conductance and gross primary productivity (GPP) derived from EC data to calculate a measure of iWUE (G1, \uffe2\uff80\uff9cstomatal slope\uffe2\uff80\uff9d) at the ecosystem level at six sites comprising tropical, Mediterranean, temperate, and boreal forests. We assess the following six mechanisms potentially causing discrepancies between leaf and ecosystem\uffe2\uff80\uff90level estimates of G1: (i) non\uffe2\uff80\uff90transpirational water fluxes; (ii) aerodynamic conductance; (iii) meteorological deviations between measurement height and canopy surface; (iv) energy balance non\uffe2\uff80\uff90closure; (v) uncertainties in net ecosystem exchange partitioning; and (vi) physiological within\uffe2\uff80\uff90canopy gradients. Our results demonstrate that an unclosed energy balance caused the largest uncertainties, in particular if it was associated with erroneous latent heat flux estimates. The effect of aerodynamic conductance on G1 was sufficiently captured with a simple representation. G1 was found to be less sensitive to meteorological deviations between canopy surface and measurement height and, given that data are appropriately filtered, to non\uffe2\uff80\uff90transpirational water fluxes. Uncertainties in the derived GPP and physiological within\uffe2\uff80\uff90canopy gradients and their implications for parameter estimates at leaf and ecosystem level are discussed. Our results highlight the importance of adequately considering the sources of uncertainty outlined here when EC\uffe2\uff80\uff90derived water\uffe2\uff80\uff90use efficiency is interpreted in an ecophysiological context.

", "keywords": ["550", "ecophysiology", "Penman\u2013Monteith equation", "0207 environmental engineering", "577", "slope parameter", "02 engineering and technology", "Forests", "Models", " Biological", "01 natural sciences", "Trees", "Water Cycle", "XXXXXX - Unknown", "eddy covariance", "energy imbalance", "analysis of covariance", "0105 earth and related environmental sciences", "intrinsic water-use efficiency", "Water", "eddy flux", "Plant Transpiration", "Carbon Dioxide", "15. Life on land", "aerodynamic conductance", "water efficiency", "Carbon", "6. Clean water", "canopy gradients", "surface conductance", "Plant Leaves", "13. Climate action", "ecosystems"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.13893"}, {"href": "https://doi.org/10.1111/gcb.13893"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/gcb.13893", "name": "item", "description": "10.1111/gcb.13893", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.13893"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-10-11T00:00:00Z"}}, {"id": "10.1128/mBio.00799-17", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:55Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics", "description": "Abstract

Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.

", "keywords": ["Q Science", "0301 basic medicine", "330", "Supplementary Data", "ecophysiology", "Ecophysiology", "NE/E006353/1", "Bacterial Physiological Phenomena", "Microbiology", "Soil", "03 medical and health sciences", "Virology", "European Commission", "Ecosystem", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "655240", "metagenomics", "0303 health sciences", "Bacteria", "Natural Environment Research Council (NERC)", "Q", "NE/M017125/1", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Adaptation", " Physiological", "soil microbiology", "QR1-502", "United Kingdom", "3. Good health", "Soil microbiology", "Metagenomics", "Genome", " Bacterial", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/117887v1.full.pdf"}, {"href": "https://journals.asm.org/doi/pdf/10.1128/mBio.00799-17"}, {"href": "https://doi.org/10.1128/mBio.00799-17"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mBio", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/mBio.00799-17", "name": "item", "description": "10.1128/mBio.00799-17", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/mBio.00799-17"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-18T00:00:00Z"}}, {"id": "2164/15058", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:27:02Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics", "description": "Abstract

Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.