Despite the global significance of the subsurface biosphere, the degree to which it depends on surface organic carbon (OC) is still poorly understood. Here, we compare stable and radiogenic carbon isotope compositions of microbial phospholipid fatty acids (PLFAs) with those of in situ potential microbial C sources to assess the major C sources for subsurface microorganisms in biogeochemical distinct shallow aquifers (Critical Zone Exploratory, Thuringia Germany). Despite the presence of younger OC, the microbes assimilated 14C\uffe2\uff80\uff90free OC to varying degrees; ~31% in groundwater within the oxic zone, ~47% in an iron reduction zone, and ~70% in a sulfate reduction/anammox zone. The persistence of trace amounts of mature and partially biodegraded hydrocarbons suggested that autochthonous petroleum\uffe2\uff80\uff90derived hydrocarbons were a potential 14C\uffe2\uff80\uff90free C source for heterotrophs in the oxic zone. In this zone, \uffce\uff9414C values of dissolved inorganic carbon (\uffe2\uff88\uff92366\uffc2\uffa0\uffc2\uffb1\uffc2\uffa018\uffe2\uff80\uffb0) and 11MeC16:0 (\uffe2\uff88\uff92283\uffc2\uffa0\uffc2\uffb1\uffc2\uffa032\uffe2\uff80\uffb0), an important component in autotrophic nitrite oxidizers, were similar enough to indicate that autotrophy is an important additional C fixation pathway. In anoxic zones, methane as an important C source was unlikely since the 13C\uffe2\uff80\uff90fractionations between the PLFAs and CH4 were inconsistent with kinetic isotope effects associated with methanotrophy. In the sulfate reduction/anammox zone, the strong 14C\uffe2\uff80\uff90depletion of 10MeC16:0 (\uffe2\uff88\uff92942\uffc2\uffa0\uffc2\uffb1\uffc2\uffa022\uffe2\uff80\uffb0), a PLFA common in sulfate reducers, indicated that those bacteria were likely to play a critical part in 14C\uffe2\uff80\uff90free sedimentary OC cycling. Results indicated that the 14C\uffe2\uff80\uff90content of microbial biomass in shallow sedimentary aquifers results from complex interactions between abundance and bioavailability of naturally occurring OC, hydrogeology, and specific microbial metabolisms.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "assimilation", "Environmental Engineering", "Environmental engineering", "Geology", "subsurface", "15. Life on land", "Civil Engineering", "Physical Geography and Environmental Geoscience", "6. Clean water", "03 medical and health sciences", "Geochemistry", "13. Climate action", "C cycling", "Earth Sciences", "radiocarbon", "PLFA", "microbial function", "Civil engineering", "Hydrology", "Research Articles"]}, "links": [{"href": "https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2017WR022067"}, {"href": "https://escholarship.org/content/qt28c3v5mf/qt28c3v5mf.pdf"}, {"href": "https://doi.org/10.1029/2017wr022067"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Resources%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1029/2017wr022067", "name": "item", "description": "10.1029/2017wr022067", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1029/2017wr022067"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-01T00:00:00Z"}}, {"id": "10.1007/s00442-005-0191-4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:15:42Z", "type": "Journal Article", "created": "2005-07-22", "title": "Fine Root Chemistry And Decomposition In Model Communities Of North-Temperate Tree Species Show Little Response To Elevated Atmospheric Co2 And Varying Soil Resource Availability", "description": "Rising atmospheric [CO2] has the potential to alter soil carbon (C) cycling by increasing the content of recalcitrant constituents in plant litter, thereby decreasing rates of decomposition. Because fine root turnover constitutes a large fraction of annual NPP, changes in fine root decomposition are especially important. These responses will likely be affected by soil resource availability and the life history characteristics of the dominant tree species. We evaluated the effects of elevated atmospheric [CO2] and soil resource availability on the production and chemistry, mycorrhizal colonization, and decomposition of fine roots in an early- and late-successional tree species that are economically and ecologically important in north temperate forests. Open-top chambers were used to expose young trembling aspen (Populus tremuloides) and sugar maple (Acer saccharum) trees to ambient (36 Pa) and elevated (56 Pa) atmospheric CO2. Soil resource availability was composed of two treatments that bracketed the range found in the Upper Lake States, USA. After 2.5 years of growth, sugar maple had greater fine root standing crop due to relatively greater allocation to fine roots (30% of total root biomass) relative to aspen (7% total root biomass). Relative to the low soil resources treatment, aspen fine root biomass increased 76% with increased soil resource availability, but only under elevated [CO2]. Sugar maple fine root biomass increased 26% with increased soil resource availability (relative to the low soil resources treatment), and showed little response to elevated [CO2]. Concentrations of N and soluble phenolics, and C/N ratio in roots were similar for the two species, but aspen had slightly higher lignin and lower condensed tannins contents compared to sugar maple. As predicted by source-sink models of carbon allocation, pooled constituents (C/N ratio, soluble phenolics) increased in response to increased relative carbon availability (elevated [CO2]/low soil resource availability), however, biosynthetically distinct compounds (lignin, starch, condensed tannins) did not always respond as predicted. We found that mycorrhizal colonization of fine roots was not strongly affected by atmospheric [CO2] or soil resource availability, as indicated by root ergosterol contents. Overall, absolute changes in root chemical composition in response to increases in C and soil resource availability were small and had no effect on soil fungal biomass or specific rates of fine root decomposition. We conclude that root contributions to soil carbon cycling will mainly be influenced by fine root production and turnover responses to rising atmospheric [CO2], rather than changes in substrate chemistry.", "keywords": ["0106 biological sciences", "Science", "Climate", "Ecology and Evolutionary Biology", "Plant Roots", "01 natural sciences", "Trees", "Sugar Maple", "Soil", "Ergosterol", "Health Sciences", "Carbon-based Secondary Compounds", "Biomass", "Cellular and Developmental Biology", "Ecosystem", "Soil Microbiology", "Atmosphere", "Fungi", "Natural Resources and Environment", "Molecular", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "Soil C Cycling", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Trembling Aspen"]}, "links": [{"href": "https://doi.org/10.1007/s00442-005-0191-4"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-005-0191-4", "name": "item", "description": "10.1007/s00442-005-0191-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-005-0191-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-07-23T00:00:00Z"}}, {"id": "10.1007/s11104-022-05508-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:16:26Z", "type": "Journal Article", "created": "2022-06-22", "title": "Harnessing belowground processes for sustainable intensification of agricultural systems", "description": "AbstractIncreasing 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.We determined soil microbial community composition and function in a field experiment in which plant communities of increasing species richness were exposed to factorial elevated CO2 and nitrogen (N) deposition treatments. Because elevated CO2 and N deposition increased plant productivity to a greater extent in more diverse plant assemblages, it is plausible that heterotrophic microbial communities would experience greater substrate availability, potentially increasing microbial activity, and accelerating soil carbon (C) and N cycling. We, therefore, hypothesized that the response of microbial communities to elevated CO2 and N deposition is contingent on the species richness of plant communities. Microbial community composition was determined by phospholipid fatty acid analysis, and function was measured using the activity of key extracellular enzymes involved in litter decomposition. Higher plant species richness, as a main effect, fostered greater microbial biomass, cellulolytic and chitinolytic capacity, as well as the abundance of saprophytic and arbuscular mycorrhizal (AM) fungi. Moreover, the effect of plant species richness on microbial communities was significantly modified by elevated CO2 and N deposition. For instance, microbial biomass and fungal abundance increased with greater species richness, but only under combinations of elevated CO2 and ambient N, or ambient CO2 and N deposition. Cellobiohydrolase activity increased with higher plant species richness, and this trend was amplified by elevated CO2. In most cases, the effect of plant species richness remained significant even after accounting for the influence of plant biomass. Taken together, our results demonstrate that plant species richness can directly regulate microbial activity and community composition, and that plant species richness is a significant determinant of microbial response to elevated CO2 and N deposition. The strong positive effect of plant species richness on cellulolytic capacity and microbial biomass indicate that the rates of soil C cycling may decline with decreasing plant species richness.
", "keywords": ["Extracellular Enzymes", "Complementary Resource Use", "Science", "Ecology and Evolutionary Biology", "Grassland Ecosystem", "Phospholipid Fatty Acid (PLFA)", "Global Change", "14. Life underwater", "complimentary resource use", "global change", "580", "2. Zero hunger", "Plant Diversity", "microbial biomass", "Geology and Earth Sciences", "grasslands", "Soil Fungi", "extracellular enzymes", "04 agricultural and veterinary sciences", "15. Life on land", "Microbial Biomass", "Soil C Cycling", "plant diversity", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "FACE (Free-air Carbon Dioxide Enrichment)"]}, "links": [{"href": "https://doi.org/10.1111/j.1365-2486.2007.01313.x"}, {"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/j.1365-2486.2007.01313.x", "name": "item", "description": "10.1111/j.1365-2486.2007.01313.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-2486.2007.01313.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-01-19T00:00:00Z"}}, {"id": "10.5061/dryad.b7f53", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-06-25T16:25:59Z", "type": "Dataset", "title": "Data from: Arbuscular mycorrhizal fungi increase organic carbon decomposition under elevated CO2", "description": "unspecifiedThe extent to which terrestrial ecosystems can sequester carbon to mitigate climate change is a matter of debate. The stimulation of arbuscular mycorrhizal fungi (AMF) by elevated atmospheric carbon dioxide (CO2) has been assumed to be a major mechanism facilitating soil carbon sequestration by increasing carbon inputs to soil and by protecting organic carbon from decomposition via aggregation. We present evidence from four independent microcosm and field experiments demonstrating that CO2 enhancement of AMF results in considerable soil carbon losses. Our findings challenge the assumption that AMF protect against degradation of organic carbon in soil and raise questions about the current prediction of terrestrial ecosystem carbon balance under future climate-change scenarios.", "keywords": ["N cycling", "13. Climate action", "C cycling", "Arbuscular mycorrhizal fungi", "15. Life on land"], "contacts": [{"organization": "Cheng, Lei, Booker, Fitzgerald L., Tu, Cong, Burkey, Kent O., Zhou, Lishi, Shew, H. David, Rufty, Thomas W., Hu, Shuijin,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.b7f53"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.b7f53", "name": "item", "description": "10.5061/dryad.b7f53", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.b7f53"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-08-31T00:00:00Z"}}, {"id": "21.11116/0000-0003-863B-4", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-25T16:32:37Z", "type": "Journal Article", "created": "2019-01-04", "title": "14C\u2010Free Carbon Is a Major Contributor to Cellular Biomass in Geochemically Distinct Groundwater of Shallow Sedimentary Bedrock Aquifers", "description": "AbstractDespite the global significance of the subsurface biosphere, the degree to which it depends on surface organic carbon (OC) is still poorly understood. Here, we compare stable and radiogenic carbon isotope compositions of microbial phospholipid fatty acids (PLFAs) with those of in situ potential microbial C sources to assess the major C sources for subsurface microorganisms in biogeochemical distinct shallow aquifers (Critical Zone Exploratory, Thuringia Germany). Despite the presence of younger OC, the microbes assimilated 14C\uffe2\uff80\uff90free OC to varying degrees; ~31% in groundwater within the oxic zone, ~47% in an iron reduction zone, and ~70% in a sulfate reduction/anammox zone. The persistence of trace amounts of mature and partially biodegraded hydrocarbons suggested that autochthonous petroleum\uffe2\uff80\uff90derived hydrocarbons were a potential 14C\uffe2\uff80\uff90free C source for heterotrophs in the oxic zone. In this zone, \uffce\uff9414C values of dissolved inorganic carbon (\uffe2\uff88\uff92366\uffc2\uffa0\uffc2\uffb1\uffc2\uffa018\uffe2\uff80\uffb0) and 11MeC16:0 (\uffe2\uff88\uff92283\uffc2\uffa0\uffc2\uffb1\uffc2\uffa032\uffe2\uff80\uffb0), an important component in autotrophic nitrite oxidizers, were similar enough to indicate that autotrophy is an important additional C fixation pathway. In anoxic zones, methane as an important C source was unlikely since the 13C\uffe2\uff80\uff90fractionations between the PLFAs and CH4 were inconsistent with kinetic isotope effects associated with methanotrophy. In the sulfate reduction/anammox zone, the strong 14C\uffe2\uff80\uff90depletion of 10MeC16:0 (\uffe2\uff88\uff92942\uffc2\uffa0\uffc2\uffb1\uffc2\uffa022\uffe2\uff80\uffb0), a PLFA common in sulfate reducers, indicated that those bacteria were likely to play a critical part in 14C\uffe2\uff80\uff90free sedimentary OC cycling. Results indicated that the 14C\uffe2\uff80\uff90content of microbial biomass in shallow sedimentary aquifers results from complex interactions between abundance and bioavailability of naturally occurring OC, hydrogeology, and specific microbial metabolisms.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.