Natural nitrogen isotopic signature reveals deprotonation during ammonium transport across living organisms.
The biodegradation of total petroleum hydrocarbon (TPH) in soil is very challenging due to the complex recalcitrant nature of hydrocarbon, hydrophobicity, indigenous microbial adaptation and competition, and harsh environmental conditions. This work further confirmed that limited natural attenuation of petroleum hydrocarbons (TPHs) (15% removal) necessitates efficient bioremediation strategies. Hence, a scaling-up experiment for testing and optimizing the use of biopiles for bioremediation of TPH polluted soils was conducted with three 500-kg pilots of polluted soil, and respective treatments were implemented: including control soil (CT), bioaugmentation and vermicompost treatment (BAVC), and a combined application of BAVC along with bioelectrochemical snorkels (BESBAVC), all maintained at 40% field capacity. This study identified that at pilot scale level, a successful application of BAVC treatment can achieve 90.3% TPH removal after 90 days. BAVC\uffe2\uff80\uff99s effectiveness stemmed from synergistic mechanisms. Introduced microbial consortia were capable of TPH degradation, while vermicompost provided essential nutrients, enhanced aeration, and, potentially, acted as a biosorbent. Hence, it can be concluded that the combined application of BAVC significantly enhances TPH removal compared to natural attenuation. While the combined application of a bioelectrochemical snorkel (BES) with BAVC also showed a significant TPH removal, it did not differ statistically from the individual application of BAVC, under applied conditions. Further research is needed to optimize BES integration with BAVC for broader applicability. This study demonstrates BAVC as a scalable and mechanistically sound approach for TPH bioremediation in soil.The present study reports findings related to the treatment of polluted groundwater using macrophyte-assisted phytoremediation. The potential of three macrophyte species (Phragmites australis, Scirpus holoschoenus, and Typha angustifolia) to tolerate exposure to multi-metal(loid) polluted groundwater was first evaluated in mesocosms for 7- and 14-day batch testing. In the 7-day batch test, the polluted water was completely replaced\uffc2\uffa0and renewed after 7\uffc2\uffa0days, while for\uffc2\uffa014\uffc2\uffa0days exposure, the same polluted water, added in the first week, was maintained. The initial biochemical screening\uffc2\uffa0results of macrophytes indicated that the selected plants were more tolerant to the provided conditions with 14\uffc2\uffa0days of exposure. Based on these findings, the plants were exposed to HRT regimes of 15 and 30\uffc2\uffa0days. The results showed that P. australis and S. holoschoenus performed better than T. angustifolia, in terms of metal(loid) accumulation and removal, biomass production, and toxicity reduction. In addition, the translocation and compartmentalization of metal(loid)s were dose-dependent. At the 30-day loading rate (higher HRT), below-ground phytostabilization was greater than phytoaccumulation, whereas at the 15-day loading rate (lower HRT), below- and above-ground phytoaccumulation was the dominant metal(loid) removal mechanism. However, higher levels of toxicity were noted in the water at the 15-day loading rate. Overall, this\uffc2\uffa0study provides valuable insights for macrophyte-assisted phytoremediation of polluted (ground)water streams that can help to improve the design and implementation of phytoremediation systems.Enzymes are on high demand for very diverse biotechnological applications. However, natural biocatalysts often need to be engineered for fine-tuning their properties towards the end applications, such as the activity, selectivity, stability to temperature or co-solvents, and solubility. Computational methods are increasingly used in this task, providing predictions that narrow down the space of possible mutations significantly and can enormously reduce the experimental burden. Many computational tools are available as web-based platforms, making them accessible to non-expert users. These platforms are typically user-friendly, contain walk-throughs, and do not require deep expertise and installations. Here we describe some of the most recent outstanding web-tools for enzyme engineering and formulate future perspectives in this field.
", "keywords": ["0301 basic medicine", "Internet", "0303 health sciences", "03 medical and health sciences", "Solubility", "biochemistry", "Computational Biology", "PROTEIN; STABILITY; DYNAMICS; VIEW", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.sbi.2021.01.010"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Opinion%20in%20Structural%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.sbi.2021.01.010", "name": "item", "description": "10.1016/j.sbi.2021.01.010", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.sbi.2021.01.010"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-03T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2024.176720", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:16:42Z", "type": "Journal Article", "created": "2024-10-07", "title": "Environmental and socio-economic evaluation of a groundwater bioremediation technology using social Cost-Benefit Analysis: Application to an in-situ metal(loid) precipitation case study", "description": "Bioremediation can be an alternative or complementary approach to conventional soil and water treatment technologies. Determining the environmental and socio-economic impacts of bioremediation is important but rarely addressed. This work presents a comprehensive sustainability assessment for a specific groundwater bioremediation case study based on In-situ Metal(loid) Precipitation (ISMP) by conducting a social Cost-Benefit Analysis (CBA) using two different approaches: environmental Life Cycle Costing (eLCC) and Impact Pathway Approach (IPA). Externalities are calculated in two ways: i) using Environmental Prices (EP) to monetize Life Cycle Assessment (LCA) results and metal(loid)s removed at field scale, and ii) following the IPA steps to determine the social costs avoided by removing arsenic contamination at full scale. The results show that, in the baseline scenario, the project is not socio-economically viable in both cases as the Net Present Value (NPV) is -129,512.61 \u20ac and\u00a0-\u00a0415,185,140 \u20ac respectively. Sensitivity and scenario analyses are performed to identify the key parameters and actions needed to reach a positive NPV. For instance, increasing the amount of water treated per year to 90 m3 and assuming a 20\u00a0% increase in operation costs and a 60\u00a0% increase in construction costs can make the project socio-economically viable at the field scale, while a reduction in the social discount rate from a 4\u00a0% to a 2\u00a0% can lead to a positive NPV at the full scale. The approaches proposed in this work may be useful for practitioners and policymakers when evaluating the environmental and socio-economic impacts of bioremediation technologies at different scales and regions, as well as human health impacts caused by contaminants at the current legal limits.", "keywords": ["Bioqu\u00edmica", "570", "550", "Environmental Life Cycle Costing", "Cost-Benefit Analysis", "Life Cycle Assessment", "Biochemistry", "Biorremediaci\u00f3n", "Water Purification", "Biodegradation", " Environmental", "Metals", "mpact Pathway Approach", "Social Cost-Benefit Analysis", "Groundwater", "Bioremediation", "Water Pollutants", " Chemical"], "contacts": [{"organization": "Ib\u00e1\u00f1ez, Jes\u00fas, P\u00e9rez-de-Mora, Alfredo, Santiago-Herrera, Mario, Belloncle, Benjamine, de Wilde, Herwig, Martel-Mart\u00edn, Sonia, Blanco-Alc\u00e1ntara, David, Barros, Roc\u00edo,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2024.176720"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2024.176720", "name": "item", "description": "10.1016/j.scitotenv.2024.176720", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.176720"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-12-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2022.108918", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:16:55Z", "type": "Journal Article", "created": "2022-12-22", "title": "Litter chemistry of common European tree species drives the feeding preference and consumption rate of soil invertebrates, and shapes the diversity and structure of gut and faecal microbiomes", "description": "Open AccessTerrestrial isopods and millipedes are key drivers of a litter decomposition in terrestrial ecosystems but the effects of litter chemistry on feeding preference and litter consumption rate as well as on the diversity and composition of gut and faecal microbiome still entails several challenges. We established a mesocosm experiment with terrestrial isopods (Oniscus asellus) and millipedes (Glomeris marginata) fed by leaf litter from six common European tree species (ash, maple, lime, beech, oak and Norway spruce) to reveal the effect of litter chemistry on consumption rate and feeding preference as well as on the compositions of gut and faecal microbiomes. The total percentage of consumed litter showed that O. asellus preferred nutrient-rich and labile-C litter of ash over more recalcitrant litter of oak, beech, and Norway spruce, while G. marginata preferred calcium-rich ash, maple and lime litter over beech and Norway spruce. Consumption of litter by O. asellus and G. marginata increased with concentrations of magnesium, sulphur and potassium but decreased with concentrations of iron, phosphorus, lignin, cellulose and TOC. The millipede G. marginata harboured higher bacterial OTU richness (73.5 \u00b1 12.5) than the isopod O. asellus (49.1 \u00b1 15.9), but fungal OTU richness was similar with 25.8 \u00b1 6.7 in O. asellus and 25.7 \u00b1 2.7 in G. marginata. In total, faeces of both animals hosted higher diversity than gut. In gut and faeces of O. asellus, the fungal OTU richness was highest for individuals fed by litter of Norway spruce, while lowest OTU richness was recorded for individuals fed by litter of more palatable ash. In contrast, the highest diversity of the fungal community in gut and faeces of G. marginata was recorded for individuals fed by palatable lime litter, while the lowest OTUs richness was recorded when millipedes were fed by maple and spruce. The structures of bacterial and fungal communities generally separated between O. asellus and G. marginata. The fungal community structure in gut and faeces differed between animals fed by different foliar litters, while the bacterial community structure mainly differed between gut and faeces regardless of the offered type of litter. The fungal community structure in gut and faeces of O. asellus and G. marginata were shaped by concentrations of magnesium, sulphur, lignin and cellulose. The bacterial communities in gut and faeces of both O. asellus and G. marginata were dominated by copiotrophic bacteria, while fungal communities were dominated by unspecified saprotrophs. Our study suggest that litter quality is a strong driver of feeding preference and consumption rates as well as composition of bacterial and fungal communities in gut and faeces of two species representing the main groups of litter feeding soil fauna in European forests.", "keywords": ["0301 basic medicine", "Genomic Insights into Social Insects and Symbiosis", "Plant Science", "Plant litter", "Agricultural and Biological Sciences", "03 medical and health sciences", "Biochemistry", " Genetics and Molecular Biology", "Litter", "Genetics", "Ecological Niche", "Biology", "Ecosystem", "Beech", "0303 health sciences", "Species Distribution Modeling and Climate Change Impacts", "Ecology", "Ecological Modeling", "Botany", "Life Sciences", "15. Life on land", "Plant-Parasitic Nematodes in Molecular Plant Pathology", "Detritus", "FOS: Biological sciences", "Detritivore", "Environmental Science", "Physical Sciences", "Species richness"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2022.108918"}, {"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.2022.108918", "name": "item", "description": "10.1016/j.soilbio.2022.108918", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2022.108918"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-01T00:00:00Z"}}, {"id": "10.1038/s41467-020-15622-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:34Z", "type": "Journal Article", "created": "2020-05-05", "title": "Sustained fluvial deposition recorded in Mars\u2019 Noachian stratigraphic record", "description": "AbstractOrbital observation has revealed a rich record of fluvial landforms on Mars, with much of this record dating 3.6\uffe2\uff80\uff933.0 Ga. Despite widespread geomorphic evidence, few analyses of Mars\uffe2\uff80\uff99 alluvial sedimentary-stratigraphic record exist, with detailed studies of alluvium largely limited to smaller sand-bodies amenable to study in-situ by rovers. These typically metre-scale outcrop dimensions have prevented interpretation of larger scale channel-morphology and long-term basin evolution, vital for understanding the past Martian climate. Here we give an interpretation of a large sedimentary succession at Izola mensa within the NW Hellas Basin rim. The succession comprises channel and barform packages which together demonstrate that river deposition was already well established >3.7 Ga. The deposits mirror terrestrial analogues subject to low-peak discharge variation, implying that river deposition at Izola was subject to sustained, potentially perennial, fluvial flow. Such conditions would require an environment capable of maintaining large volumes of water for extensive time-periods, necessitating a precipitation-driven hydrological cycle.
", "keywords": ["550", "Science", "General Biochemistry", "Genetics and Molecular Biology", "Q", "500", "General Physics and Astronomy", "Geomorphology", "General Chemistry", "15. Life on land", "01 natural sciences", "Article", "12. Responsible consumption", "Sedimentology", " Stratigraphy", " Fluvial Deposits", " Mars", " Sedimentary Deposits", "[SDU.STU.PL]Sciences of the Universe [physics]/Earth Sciences/Planetology", "13. Climate action", "Inner planets", "[SDU.STU.PL] Sciences of the Universe [physics]/Earth Sciences/Planetology", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://oro.open.ac.uk/70442/1/70442.pdf"}, {"href": "https://www.nature.com/articles/s41467-020-15622-0.pdf"}, {"href": "https://doi.org/10.1038/s41467-020-15622-0"}, {"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/s41467-020-15622-0", "name": "item", "description": "10.1038/s41467-020-15622-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-020-15622-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-05T00:00:00Z"}}, {"id": "10.1016/j.talanta.2018.09.033", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:07Z", "type": "Journal Article", "created": "2018-09-12", "title": "Assessment of the DGT technique in digestate to fraction twelve trace elements", "description": "This study proposes an evaluation of the diffusive gradients in thin films technique (DGT) for studying trace elements in digested sewage sludge samples. Twelve elements were monitored by Chelex (Al, Cd, Co, Cr (III), Cu, Fe, Mn, Ni, Pb) and zirconia-DGT (As, Mo, Se) samplers exposed from 4\u202fh to 9 days. Twenty-four hours' deployment time was suitable for most of the studied elements. However, short deployment led to insufficient element accumulation or non-establishment of steady state while long deployment (from 18 to 144\u202fh depending on the element) led to saturation of the binding gels and/or competing effects with other major elements. In addition, this study showed that the matrix of the digested sewage sludge lowers the accumulation of some trace elements in the DGT samplers, leading to labile concentrations underestimation of roughly 10-30% (depending on the element). Moreover, compared to the conventional total dissolved elements measurement, DGT technique allowed to quantify 7 out of 12 labile elements whereas only 3 out of 12 dissolved elements were quantified. These results highlight the potential of DGT technique to assess labile trace elements in digestate samples, provided a careful adaptation of the deployment time as well as an evaluation of the matrix effect is performed.", "keywords": ["550", "[SDE.IE]Environmental Sciences/Environmental Engineering", "Matrix interferences", "Speciation", "Metalloids Speciation", "Chemistry (all)", "Biochemistry", "01 natural sciences", "6. Clean water", "Analytical Chemistry", "0104 chemical sciences", "Passive sampling", "[CHIM.ANAL]Chemical Sciences/Analytical chemistry", "Digested sewage sludge", "Metals", "628", "Digested sewage sludge; Matrix interferences; Metalloids; Metals; Passive sampling; Speciation; Analytical Chemistry; Chemistry (all); Biochemistry; Spectroscopy", "Spectroscopy", "Metalloids", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.talanta.2018.09.033"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Talanta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.talanta.2018.09.033", "name": "item", "description": "10.1016/j.talanta.2018.09.033", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.talanta.2018.09.033"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-01T00:00:00Z"}}, {"id": "10.1017/s0266467400007409", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:13Z", "type": "Journal Article", "created": "2009-07-10", "title": "Ecosystem Dynamics Of Disturbed And Undisturbed Sites In North Queensland Wet Tropical Rain-Forest .1. Floristic Composition, Climate And Soil Chemistry", "description": "ABSTRACTThis paper introduces studies of nutrient cycling in disturbed and undisturbed rain forest plots in the upper catchment of Birthday Creek, near Paluma, North Queensland. The catchment is underlain by granite and has soils of comparatively low fertility. Differences between unlogged plots and plots disturbed 25 years previously by selective logging are still apparent. Disturbed plots have soils with higher bulk densities and pH, lower CEC, kjeldahl nitrogen and available phosphorus concentrations, and changed species composition. The data suggest that recovery from selective logging is dependent on soil fertility and intensity of disturbance.
", "keywords": ["disturbance", "0106 biological sciences", "Australia", "selective logging", "15. Life on land", "tropical rain forest", "01 natural sciences", "FoR 0601 (Biochemistry and Cell Biology)", "north Queensland", "soil compaction", "soil nutrients", "FoR 0602 (Ecology)", "climate", "floristics"]}, "links": [{"href": "https://doi.org/10.1017/s0266467400007409"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Tropical%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1017/s0266467400007409", "name": "item", "description": "10.1017/s0266467400007409", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1017/s0266467400007409"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1993-08-01T00:00:00Z"}}, {"id": "10.1021/jf0613987", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:18Z", "type": "Journal Article", "created": "2006-10-03", "title": "Distribution Of Selenium In Different Biochemical Fractions And Raw Darkening Degree Of Potato (Solanum Tuberosum L.) Tubers Supplemented With Selenate", "description": "Effects of Se fertilization on potato processing quality, possible changes in Se concentration and form in tubers during storage, and retransfer of Se from seed tubers were examined. Potato plants were grown at five selenate (SeO4(2-)) concentrations. Tubers were harvested 16 weeks after planting and were stored at 3-4 degrees C prior to analysis. The results showed that the Se concentration did not decrease during storage for 1-12 months. In tubers, 49-65% of total Se was allocated in protein fraction, which is less than found in plant leaves in a previous study. The next-generation tubers produced by the Se-enriched seed tubers had increased Se concentrations, which evidenced the relocation of Se from the seed tubers. At low levels, Se improved the processing quality of potato tubers by diminishing and retarding their raw darkening. The value of Se-enriched potato tubers as a Se source in the human diet was discussed.", "keywords": ["0106 biological sciences", "0301 basic medicine", "2. Zero hunger", "Selenium", "03 medical and health sciences", "Time Factors", "Biochemical Phenomena", "Darkness", "Biochemistry", "01 natural sciences", "Solanum tuberosum"], "contacts": [{"organization": "Helin\u00e4 Hartikainen, Mervi Sepp\u00e4nen, P\u00e4ivi Ekholm, Marja Turakainen,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1021/jf0613987"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Agricultural%20and%20Food%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/jf0613987", "name": "item", "description": "10.1021/jf0613987", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/jf0613987"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-10-03T00:00:00Z"}}, {"id": "10.1029/2005jg000152", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:26Z", "type": "Journal Article", "created": "2006-08-08", "title": "Nutrient Control Of Microbial Carbon Cycling Along An Ombrotrophic-Minerotrophic Peatland Gradient", "description": "Future climate change and other anthropogenic activities are likely to increase nutrient availability in many peatlands, and it is important to understand how these additional nutrients will influence peatland carbon cycling. We investigated the effects of nitrogen and phosphorus on aerobic CH4oxidation, anaerobic carbon mineralization (as CO2and CH4production), and anaerobic nutrient mineralization in a bog, an intermediate fen, and a rich fen in the Upper Peninsula of Michigan. We utilized a 5\uffe2\uff80\uff90week laboratory nutrient amendment experiment in conjunction with a 6\uffe2\uff80\uff90year field nutrient fertilization experiment to consider how the relative response to nitrogen and phosphorus differed among these wetlands over the short and long term. Field fertilizations generally increased nutrient availability in the upper 15 cm of peat and resulted in shifts in the vegetation community in each peatland. High nitrogen concentrations inhibited CH4oxidation in bog peat during short\uffe2\uff80\uff90term incubations; however, long\uffe2\uff80\uff90term fertilization with lower concentrations of nitrogen stimulated rates of CH4oxidation in bog peat. In contrast, no nitrogen effects on CH4oxidation were observed in the intermediate or rich fen peat. Anaerobic carbon mineralization in bog peat was consistently inhibited by increased phosphorus availability, but similar phosphorus additions had few effects in the intermediate fen and stimulated CH4production and nutrient mineralization in the rich fen. Our results demonstrate that nitrogen and phosphorus are important controls of peatland microbial carbon cycling; however, the role of these nutrients can differ over the short and long term and is strongly mediated by peatland type.
", "keywords": ["Other Ecology and Evolutionary Biology", "2. Zero hunger", "Terrestrial and Aquatic Ecology", "Nutrients", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "Peatlands", "Biochemistry", "01 natural sciences", "6. Clean water", "Microbial Carbon Cycling", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Methane", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1029/2005jg000152"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Geophysical%20Research%3A%20Biogeosciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1029/2005jg000152", "name": "item", "description": "10.1029/2005jg000152", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1029/2005jg000152"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-08-09T00:00:00Z"}}, {"id": "10.1038/s41467-018-05824-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:33Z", "type": "Journal Article", "created": "2018-08-20", "title": "Biogenic volatile release from permafrost thaw is determined by the soil microbial sink", "description": "AbstractWarming in the Arctic accelerates thawing of permafrost-affected soils, which leads to a release of greenhouse gases to the atmosphere. We do not know whether permafrost thaw also releases non-methane volatile organic compounds that can contribute to both negative and positive radiative forcing on climate. Here we show using proton transfer reaction\uffe2\uff80\uff93time of flight\uffe2\uff80\uff93mass spectrometry that substantial amounts of ethanol and methanol and in total 316 organic ions were released from Greenlandic permafrost soils upon thaw in laboratory incubations. We demonstrate that the majority of this release is taken up in the active layer above. In an experiment using 14C-labeled ethanol and methanol, we demonstrate that these compounds are consumed by microorganisms. Our findings highlight that the thawing permafrost soils are not only a considerable source of volatile organic compounds but also that the active layer regulates their release into the atmosphere.
", "keywords": ["0301 basic medicine", "Ethanol", "Science", "Climate", "Methanol", "General Biochemistry", "Genetics and Molecular Biology", "Q", "General Physics and Astronomy", "Permafrost", "General Chemistry", "15. Life on land", "01 natural sciences", "Article", "03 medical and health sciences", "13. Climate action", "11. Sustainability", "SDG 13 - Climate Action", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.nature.com/articles/s41467-018-05824-y.pdf"}, {"href": "https://doi.org/10.1038/s41467-018-05824-y"}, {"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/s41467-018-05824-y", "name": "item", "description": "10.1038/s41467-018-05824-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-018-05824-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-08-24T00:00:00Z"}}, {"id": "10.1038/s41467-018-05980-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:33Z", "type": "Journal Article", "created": "2018-08-29", "title": "Land use driven change in soil pH affects microbial carbon cycling processes", "description": "AbstractSoil microorganisms act as gatekeepers for soil\uffe2\uff80\uff93atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates.Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.Diversified cropping systems, especially those including legumes, have been proposed to enhance food production with reduced inputs and environmental impacts. However, the impact of legume pre-crops on main crop yield and its drivers has never been systematically investigated in a global context. Here, we synthesize 11,768 yield observations from 462 field experiments comparing legume-based and non-legume cropping systems and show that legumes enhanced main crop yield by 20%. These yield advantages decline with increasing N fertilizer rates and crop diversity of the main cropping system. The yield benefits are consistent among main crops (e.g., rice, wheat, maize) and evident across pedo-climatic regions. Moreover, greater yield advantages (32% vs. 7%) are observed in low- vs. high-yielding environments, suggesting legumes increase crop production with low inputs (e.g., in Africa or organic agriculture). In conclusion, our study suggests that legume-based rotations offer a critical pathway for enhancing global crop production, especially when integrated into low-input and low-diversity agricultural systems.Increasing atmospheric CO2 stimulates photosynthesis which can increase net primary production (NPP), but at longer timescales may not necessarily increase plant biomass. Here we analyse the four decade-long CO2-enrichment experiments in woody ecosystems that measured total NPP and biomass. CO2 enrichment increased biomass increment by 1.05\uffe2\uff80\uff89\uffc2\uffb1\uffe2\uff80\uff890.26\uffe2\uff80\uff89kg\uffe2\uff80\uff89C\uffe2\uff80\uff89m\uffe2\uff88\uff922 over a full decade, a 29.1\uffe2\uff80\uff89\uffc2\uffb1\uffe2\uff80\uff8911.7% stimulation of biomass gain in these early-secondary-succession temperate ecosystems. This response is predictable by combining the CO2 response of NPP (0.16\uffe2\uff80\uff89\uffc2\uffb1\uffe2\uff80\uff890.03\uffe2\uff80\uff89kg\uffe2\uff80\uff89C\uffe2\uff80\uff89m\uffe2\uff88\uff922\uffe2\uff80\uff89y\uffe2\uff88\uff921) and the CO2-independent, linear slope between biomass increment and cumulative NPP (0.55\uffe2\uff80\uff89\uffc2\uffb1\uffe2\uff80\uff890.17). An ensemble of terrestrial ecosystem models fail to predict both terms correctly. Allocation to wood was a driver of across-site, and across-model, response variability and together with CO2-independence of biomass retention highlights the value of understanding drivers of wood allocation under ambient conditions to\uffc2\uffa0correctly interpret\uffc2\uffa0and predict CO2 responses.
", "keywords": ["[SDE] Environmental Sciences", "0106 biological sciences", "0301 basic medicine", "TREE MORTALITY", "550", "Climate", "Plant Biology", "Biochemistry", "01 natural sciences", "Trees", "atmospheric carbon dioxide", "ddc:550", "Biomass", "Photosynthesis", "Ecology", "Q", "FOREST PRODUCTIVITY", "Forestry", "Biological Sciences", "woody", "decadal biomass", "Wood", "[SDE]Environmental Sciences", "GROWTH", "ecosystems", "CARBON ALLOCATION", "570", "Science", "Biophysics", "333", "SWEETGUM PLANTATION", "Article", "03 medical and health sciences", "XXXXXX - Unknown", "forest ecology", "plant biomass", "Biochemistry", " Biophysics", " and Structural Biology", "Ecosystem", "photosynthesis", "Carbon Dioxide", "15. Life on land", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "NITROGEN", "CLIMATE", "13. Climate action", "and Structural Biology", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "ELEVATED CO2", "SOIL CARBON", "RESPONSES"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-08348-1.pdf"}, {"href": "https://arrow.tudublin.ie/context/scschbioart/article/1214/viewcontent/nature.pdf"}, {"href": "https://escholarship.org/content/qt5m5806sh/qt5m5806sh.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-08348-1"}, {"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/s41467-019-08348-1", "name": "item", "description": "10.1038/s41467-019-08348-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-08348-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-14T00:00:00Z"}}, {"id": "10.1038/s41467-019-09448-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:33Z", "type": "Journal Article", "created": "2019-03-29", "title": "Multiple plant diversity components drive consumer communities across ecosystems", "description": "AbstractHumans modify ecosystems and biodiversity worldwide, with negative consequences for ecosystem functioning. Promoting plant diversity is increasingly suggested as a mitigation strategy. However, our mechanistic understanding of how plant diversity affects the diversity of heterotrophic consumer communities remains limited. Here, we disentangle the relative importance of key components of plant diversity as drivers of herbivore, predator, and parasitoid species richness in experimental forests and grasslands. We find that plant species richness effects on consumer species richness are consistently positive and mediated by elevated structural and functional diversity of the plant communities. The importance of these diversity components differs across trophic levels and ecosystems, cautioning against ignoring the fundamental ecological complexity of biodiversity effects. Importantly, plant diversity effects on higher trophic-level species richness are in many cases mediated by modifications of consumer abundances. In light of recently reported drastic declines in insect abundances, our study identifies important pathways connecting plant diversity and consumer diversity across ecosystems.
", "keywords": ["0106 biological sciences", "2. Zero hunger", "570", "/dk/atira/pure/core/keywords/nachhaltigkeitswissenschaft; name=Sustainability Science", "Science", "/dk/atira/pure/subjectarea/asjc/1600; name=Chemistry(all)", "Q", "/dk/atira/pure/subjectarea/asjc/1300; name=Biochemistry", " Genetics and Molecular Biology(all)", "634", "Biodiversity", "/dk/atira/pure/core/keywords/biology; name=Ecosystems Research", "Plants", "15. Life on land", "/dk/atira/pure/subjectarea/asjc/1000; name=General", "01 natural sciences", "Article", "ddc:", "/dk/atira/pure/subjectarea/asjc/3100; name=Physics and Astronomy(all)", "Species Specificity", "Animals", "14. Life underwater", "Arthropods"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-09448-8.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-09448-8"}, {"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/s41467-019-09448-8", "name": "item", "description": "10.1038/s41467-019-09448-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-09448-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-29T00:00:00Z"}}, {"id": "10.1039/d0mt00043d", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:41Z", "type": "Journal Article", "created": "2020-05-20", "title": "Biomolecular approaches to understanding metal tolerance and hyperaccumulation in plants", "description": "AbstractTrace metal elements are essential for plant growth but become toxic at high concentrations, while some non-essential elements, such as Cd and As, show toxicity even in traces. Thus, metal homeostasis is tightly regulated in plants. Plant species colonising metalliferous soils have evolved mechanisms to hypertolerate metals and, in rare cases, can hyperaccumulate them in excess amounts in their shoots. The molecular mechanisms of metal hypertolerance and hyperaccumulation are likely derived from alterations in the basic mechanisms involved in general metal homeostasis. Genes involved in metal transport, synthesis of metal chelators and oxidative stress responses are constitutively and highly expressed in metal hypertolerant and hyperaccumulator species. Plant specialized metabolites and cell wall components have been proposed as major players in these mechanisms. In addition, the high intra-specific natural variation of metal hypertolerance and hyperaccumulation suggests that various molecular mechanisms might be involved in the evolution of these traits. To date, the potential of wild plant populations as systems to study metal tolerance and hyperaccumulation has not been fully exploited. The advent of next-generation sequencing (NGS) has enabled the study of non-model species, providing an opportunity to study natural populations and new tolerant and/or hyperaccumulating species, and will provide new insights into metal tolerance and hyperaccumulation. In this review we highlight background knowledge about metal tolerance and hyperaccumulation in plants and the current state-of-the-art techniques to study and identify the underlying mechanisms of metal hypertolerance and hyperaccumulation. We also outline for the reader the importance of the multidisciplinarity of this research field and how the integration of multiomic approaches will benefit facing the future scientific challenges.Magnesium is the metal at the center of all types of chlorophyll and is thus crucial to photosynthesis. When an element is involved in a biosynthetic pathway its isotopes are fractionated based on the difference of vibrational frequency between the different molecules. With the technical advance of multi-collectors plasma-mass-spectrometry and improvement in analytical precision, it has recently been found that two types of chlorophylls (a and b) are isotopically distinct. These results have very significant implications with regards to the use of Mg isotopes to understand the biosynthesis of chlorophyll. Here we present theoretical constraints on the origin of these isotopic fractionations through ab initio calculations. We present the fractionation factor for chlorphyll a, b, d, and f. We show that the natural isotopic variations among chlorophyll a and b are well explained by isotopic fractionation under equilibrium, which implies exchanges of Mg during the chlorophyll cycle. We predict that chlorophyll d and f should be isotopically fractionated compared to chlorophyll a and that this could be used in the future to understand the biosynthesis of these molecules.
", "keywords": ["Chlorophyll", "0301 basic medicine", "0303 health sciences", "RELEVANT", "Molecular Structure", "PHOTOSYNTHESIS", "Science", "Q", "POTENTIALS", "R", "Chemical Fractionation", "Fe", "Article", "3. Good health", "[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry", "[CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry", "03 medical and health sciences", "Isotopes", "Zn", "Medicine", "PLANTS", "Magnesium", "[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry", " Molecular Biology/Biochemistry [q-bio.BM]", "GEOCHEMISTRY", "[SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry", " Molecular Biology/Biochemistry [q-bio.BM]"], "contacts": [{"organization": "Fr\u00e9d\u00e9ric Moynier, Fr\u00e9d\u00e9ric Moynier, Toshiyuki Fujii,", "roles": ["creator"]}]}, "links": [{"href": "https://www.nature.com/articles/s41598-017-07305-6.pdf"}, {"href": "https://doi.org/10.1038/s41598-017-07305-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-017-07305-6", "name": "item", "description": "10.1038/s41598-017-07305-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-017-07305-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-08-01T00:00:00Z"}}, {"id": "10.1038/s41598-023-49194-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:38Z", "type": "Journal Article", "created": "2023-12-13", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "description": "AbstractBacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes. Soil compaction represents a major agronomic challenge, inhibiting root elongation and impacting crop yields. Roots use ethylene to sense soil compaction as the restricted air space causes this gaseous signal to accumulate around root tips. Ethylene inhibits root elongation and promotes radial expansion in compacted soil, but its mechanistic basis remains unclear. Here, we report that ethylene promotes abscisic acid (ABA) biosynthesis and cortical cell radial expansion. Rice mutants of ABA biosynthetic genes had attenuated cortical cell radial expansion in compacted soil, leading to better penetration. Soil compaction-induced ethylene also up-regulates the auxin biosynthesis gene OsYUC8 . Mutants lacking OsYUC8 are better able to penetrate compacted soil. The auxin influx transporter OsAUX1 is also required to mobilize auxin from the root tip to the elongation zone during a root compaction response. Moreover, osaux1 mutants penetrate compacted soil better than the wild-type roots and do not exhibit cortical cell radial expansion. We conclude that ethylene uses auxin and ABA as downstream signals to modify rice root cell elongation and radial expansion, causing root tips to swell and reducing their ability to penetrate compacted soil. Underlying physiological mechanisms of intraspecific variation in growth response to elevated CO2 concentration [CO2] were investigated using two spring wheat (Triticum aestivum L.) cultivars: Yitpi and H45. Leaf blade elongation rate (LER), leaf carbon (C), nitrogen (N) in the expanding leaf blade (ELB, sink) and photosynthesis (A) and C and N status in the last fully expanded leaf blade (LFELB, source) were measured. Plants were grown at ambient [CO2] (~384\uffc2\uffb5molmol\uffe2\uff80\uff931) and elevated [CO2] (~550\uffc2\uffb5molmol\uffe2\uff80\uff931) in the Australian Grains Free Air CO2 Enrichment facility. Elevated [CO2] increased leaf area and total dry mass production, respectively, by 42 and 53% for Yitpi compared with 2 and 13% for H45. Elevated [CO2] also stimulated the LER by 36% for Yitpi compared with 5% for H45. Yitpi showed a 99% increase in A at elevated [CO2] but no A stimulation was found for H45. There was a strong correlation (r2=0.807) between LER of the ELB and soluble carbohydrate concentration in LFELB. In ELB, the highest spatial N concentration was observed in the cell division zone, where N concentrations were 67.3 and 60.6mg g\uffe2\uff80\uff931 for Yitpi compared with 51.1 and 39.2mg g\uffe2\uff80\uff931 for H45 at ambient and elevated [CO2]. In contrast, C concentration increased only in the cell division and cell expansion zone of the ELB of Yitpi. These findings suggest that C supply from the source (LFELB) is cultivar dependent and well correlated with LER, leaf area expansion and whole-plant growth response to elevated [CO2].
", "keywords": ["Diurnal regulation of LER", "580", "0106 biological sciences", "0301 basic medicine", "2. Zero hunger", "070303 Crop and Pasture Biochemistry and Physiology", "leaf blade elongation rate", "diurnal regulation of LER", "gas exchange", "Growth analysis", "15. Life on land", "01 natural sciences", "Leaf blade elongation rate", "03 medical and health sciences", "Elevated (CO2)", "elevated [CO2]", "Gas exchange", "growth analysis"]}, "links": [{"href": "https://doi.org/10.1071/fp14125"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Functional%20Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1071/fp14125", "name": "item", "description": "10.1071/fp14125", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1071/fp14125"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-01-01T00:00:00Z"}}, {"id": "10.1093/plcell/koac263", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:12Z", "type": "Journal Article", "created": "2022-08-26", "title": "Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress", "description": "AbstractWe present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.Transformation products (TPs) of man-made chemicals, formed through microbially mediated transformation in the environment, can have serious adverse environmental effects, yet the analytical identification of TPs is challenging. Rule-based prediction tools are successful in predicting TPs, especially in environmental chemistry applications that typically have to rely on small datasets, by imparting the existing knowledge on enzyme-mediated biotransformation reactions. However, the rules extracted from biotransformation reaction databases usually face the issue of being over/under-generalized and are not flexible to be updated with new reactions.
ResultsWe developed an automatic rule extraction tool called enviRule. It clusters biotransformation reactions into different groups based on the similarities of reaction fingerprints, and then automatically extracts and generalizes rules for each reaction group in SMARTS format. It optimizes the genericity of automatic rules against the downstream TP prediction task. Models trained with automatic rules outperformed the models trained with manually curated rules by 30% in the area under curve (AUC) scores. Moreover, automatic rules can be easily updated with new reactions, highlighting enviRule\uffe2\uff80\uff99s strengths for both automatic extraction of optimized reactions rules and automated updating thereof.
Availability and implementationenviRule code is freely available at https://github.com/zhangky12/enviRule.
", "keywords": ["10120 Department of Chemistry", "Statistics and Probability", "Original Paper", "1303 Biochemistry", "Computational Biology", "Biochemistry", "Computer Science Applications", "Computational Mathematics", "Computational Theory and Mathematics", "13. Climate action", "540 Chemistry", "1312 Molecular Biology", "1706 Computer Science Applications", "2613 Statistics and Probability", "2605 Computational Mathematics", "Molecular Biology", "Biotransformation", "1703 Computational Theory and Mathematics"]}, "links": [{"href": "https://doi.org/10.1093/bioinformatics/btad407"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/bioinformatics/btad407", "name": "item", "description": "10.1093/bioinformatics/btad407", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/bioinformatics/btad407"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-24T00:00:00Z"}}, {"id": "10.1093/femsle/fnab100", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:10Z", "type": "Journal Article", "created": "2021-07-30", "title": "Transcriptomic markers of fungal growth, respiration and carbon-use efficiency", "description": "ABSTRACTFungal metabolic carbon acquisition and its subsequent partitioning between biomass production and respiration, i.e. the carbon-use efficiency (CUE), are central parameters in biogeochemical modeling. However, current available techniques for estimating these parameters are all associated with practical and theoretical shortcomings, making assessments unreliable. Gene expression analyses hold the prospect of phenotype prediction by indirect means, providing new opportunities to obtain information about metabolic priorities. We cultured four different fungal isolates (Chalara longipes, Laccaria bicolor, Serpula lacrymans and Trichoderma harzianum) in liquid media with contrasting nitrogen availability and measured growth rates and respiration to calculate CUE. By relating gene expression markers to measured carbon fluxes, we identified genes coding for 1,3-\uffce\uffb2-glucan synthase and 2-oxoglutarate dehydrogenase as suitable markers for growth and respiration, respectively, capturing both intraspecific variation as well as within-strain variation dependent on growth medium. A transcript index based on these markers correlated significantly with differences in CUE between the fungal isolates. Our study paves the way for the use of these markers to assess differences in growth, respiration and CUE in natural fungal communities, using metatranscriptomic or the RT-qPCR approach. This theme issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). The papers in this issue show that soils can contribute positively to the delivery of all NCP. These contributions can be maximized through careful soil management to provide healthy soils, but poorly managed, degraded or polluted soils may contribute negatively to the delivery of NCP. Soils are also shown to contribute positively to the UN Sustainable Development Goals. Papers in the theme issue emphasize the need for careful soil management. Priorities for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation, (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health, productivity and sustainability and to prevent degradation, and (iii) for degraded soils, restore to full soil health. Our knowledge of what constitutes sustainable soil management is mature enough to implement best management practices, in order to maintain and improve soil health. The papers in this issue show the vast potential of soils to contribute to NCP. This is not only desirable, but essential to sustain a healthy planet and if we are to deliver sustainable development in the decades to come.
This article is part of the theme issue \uffe2\uff80\uff98The role of soils in delivering Nature\uffe2\uff80\uff99s Contributions to People\uffe2\uff80\uff99.
The ability of soil microbial communities to withstand and recover from disturbance or stress is important for the functional stability of forest ecosystems. However, the relationship between the community responses of soil microbes and variation in tree mixtures vs functional composition remains poorly understood.
We investigated soil biochemical properties and soil microbial resistance and resilience to drought in three 4\uffe2\uff80\uff90year\uffe2\uff80\uff90old tree monocultures (Acer saccharum Marsh, Larix laricina (Duroi) K. Koch and Pinus strobus L.) and two tree species combinations (L.\uffc2\uffa0laricina/A.\uffc2\uffa0saccharum and L.\uffc2\uffa0laricina/P.\uffc2\uffa0strobus) planted in a high\uffe2\uff80\uff90density tree field experiment located in southern Quebec, Canada. The experimentally imposed drought stress consisted of maintaining soil material for 30\uffc2\uffa0days at 25% of water\uffe2\uff80\uff90holding capacity (WHC). Microbial biomass was assessed immediately after the water stress (resistance) and 15 and 30\uffc2\uffa0days following drought (resilience).
Results showed that tree communities influenced soil chemistry, soil respirometry properties and microbial resistance and resilience. We measured significant non\uffe2\uff80\uff90additive (i.e. both synergistic and antagonistic) effects of mixing tree species in some of the soil biochemical properties measured, mostly in the L.\uffc2\uffa0laricina/A.\uffc2\uffa0saccharum mixture. However, we did not find non\uffe2\uff80\uff90additive effects of tree mixtures on microbial resistance and resilience. A structural equation modelling analysis revealed that resistance and resilience were mostly modulated by direct effects of community\uffe2\uff80\uff90weighted means (CWM) of leaf litter lignin content and mineralizable N, and by indirect links from tree density and CWM of leaf litter N content via mineralizable N.
This study suggests that tree species identity surpassed species mixtures as a key driver of soil microbial resistance and resilience. We showed a trade\uffe2\uff80\uff90off between microbial resistance and resilience in soil food webs, which is consistent with ecological theory. Our results indicate that differences in functional traits between tree species may rapidly be reflected in divergent soil biochemical properties and that these differences can in turn drive soil microbial resistance and resilience to drought.
", "keywords": ["2. Zero hunger", "0106 biological sciences", "droughts", "XXXXXX - Unknown", "ecology", "15. Life on land", "ecosystems", "soil biochemistry", "01 natural sciences", "6. Clean water", "biodiversity"]}, "links": [{"href": "https://doi.org/10.1111/1365-2435.12364"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Functional%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1365-2435.12364", "name": "item", "description": "10.1111/1365-2435.12364", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1365-2435.12364"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-12-20T00:00:00Z"}}, {"id": "10.1101/2024.05.03.592357", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:18Z", "type": "Journal Article", "created": "2025-06-27", "title": "The evolutionary history and functional specialization of microRNA genes in Arabidopsis halleri and A. lyrata", "description": "AbstractMicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in plant genomes. While some miRNA genes are deeply conserved, the majority appear to be species-specific, raising the question of how they emerge and integrate into cellular regulatory networks. To address this question, we first performed a detailed annotation of miRNA genes in the closely related Arabidopsis halleri and A. lyrata, then evaluated their phylogenetic conservation across 87 plant species. We then characterized the process by which newly emerged miRNA genes progressively acquire the properties of \uffe2\uff80\uff9ccanonical\uffe2\uff80\uff9d miRNA genes, in terms of size and stability of the hairpin precursor, loading of their cleavage products into Argonaute proteins, and potential to regulate downstream target genes. Analysis of nucleotide polymorphism distribution along the hairpin sequence (stem, mature miRNA, terminal loop) revealed that the selective constraints on recently emerged miRNA genes were initially weak, gradually increasing toward evolutionarily conserved miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary progression toward canonical miRNAs by which a small fraction of de novo formed miRNA genes eventually integrate into \uffe2\uff80\uff9ccore\uffe2\uff80\uff9d biological processes.Biochar amendment is one of the most promising agricultural approaches to tackle climate change by enhancing soil carbon (C) sequestration. Microbial\uffe2\uff80\uff90mediated decomposition processes are fundamental for the fate and persistence of sequestered C in soil, but the underlying mechanisms are uncertain. Here, we synthesise 923 observations regarding the effects of biochar addition (over periods ranging from several weeks to several years) on soil C\uffe2\uff80\uff90degrading enzyme activities from 130 articles across five continents worldwide. Our results showed that biochar addition increased soil ligninase activity targeting complex phenolic macromolecules by 7.1%, but suppressed cellulase activity degrading simpler polysaccharides by 8.3%. These shifts in enzyme activities explained the most variation of changes in soil C sequestration across a wide range of climatic, edaphic and experimental conditions, with biochar\uffe2\uff80\uff90induced shift in ligninase:cellulase ratio correlating negatively with soil C sequestration. Specifically, short\uffe2\uff80\uff90term (<1\uffc2\uffa0year) biochar addition significantly reduced cellulase activity by 4.6% and enhanced soil organic C sequestration by 87.5%, whereas no significant responses were observed for ligninase activity and ligninase:cellulase ratio. However, long\uffe2\uff80\uff90term (\uffe2\uff89\uffa51\uffc2\uffa0year) biochar addition significantly enhanced ligninase activity by 5.2% and ligninase:cellulase ratio by 36.1%, leading to a smaller increase in soil organic C sequestration (25.1%). These results suggest that shifts in enzyme activities increased ligninase:cellulase ratio with time after biochar addition, limiting long\uffe2\uff80\uff90term soil C sequestration with biochar addition. Our work provides novel evidence to explain the diminished soil C sequestration with long\uffe2\uff80\uff90term biochar addition and suggests that earlier studies may have overestimated soil C sequestration with biochar addition by failing to consider the physiological acclimation of soil microorganisms over time.Retreating glaciers, icons of climate change, release new potential habitats for both aquatic and terrestrial organisms. High\uffe2\uff80\uff90elevation species are threatened by temperature increases and the upward migration of lowlands species. Improving our understanding of successional processes after glacier retreat becomes urgent, especially in the tropics, where glacier shrinkage is particularly fast. We examined the successional patterns of aquatic invertebrates, ground beetles, terrestrial plants, soil eukaryotes (algae, invertebrates, plants) in an equatorial glacier foreland (Carihuairazo, Ecuador). Based on both taxonomical identification and eDNA metabarcoding, we analysed the effects of both environmental conditions and age of deglacierization on community composition. Except for algae, diversity increased with time since deglacierization, especially among passive dispersers, suggesting that dispersal was a key driver structuring the glacier foreland succession. Spatial \uffce\uffb2\uffe2\uff80\uff90diversity was mainly attributed to nestedness for aquatic invertebrates, terrestrial plants and soil algae, likely linked to low environmental variability within the studied glacier foreland; and to turnover for soil invertebrates, suggesting competition exclusion at the oldest successional stage. Pioneer communities were dominated by species exhibiting flexible feeding strategies and high dispersal ability (mainly transported by wind), probably colonising from lower altitudes, or from the glacier in the case of algae. Overall, glacier foreland colonisation in the tropics exhibit common characteristics to higher latitudes. High\uffe2\uff80\uff90elevation species are nevertheless threatened, as the imminent extinction of many tropical glaciers will affect species associated to glacier\uffe2\uff80\uff90influenced habitats but also prevent cold\uffe2\uff80\uff90adapted and hygrophilous species from using these habitats as refuges in a warming world.
", "keywords": ["Colonization", "[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", "550", "Early succession", "glacier retreat", "Sociology", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "Environmental DNA Sequencing", "Glacier", "Ecology", "Geography", "early succession", "Life Sciences", "Phylogenetics and taxonomy", "Biodiversity", "[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics", "Threatened species", "FOS: Sociology", "Multiple-taxa", "multiple-taxa", "Habitat", "[SDE]Environmental Sciences", "Physical Sciences", "environment/Ecosystems", "570", "Physical geography", "Population", "Global Diversity of Microbial Eukaryotes and Their Evolution", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics", "Ecological succession", "Biochemistry", " Genetics and Molecular Biology", "Biological dispersal", "[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "equatorial glacier foreland", "Equatorial glacier foreland", "Glacier retreat", "Molecular Biology", "Biology", "Demography", "Marine Microbial Diversity and Biogeography", "Colonisation", "South America", "15. Life on land", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "13. Climate action", "FOS: Biological sciences", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "Environmental Science", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "early succession; equatorial glacier foreland; glacier retreat; multiple-taxa", "Environmental DNA in Biodiversity Monitoring"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/851699/2/rosero%202021.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.05478"}, {"href": "https://doi.org/10.1111/ecog.05478"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecography", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/ecog.05478", "name": "item", "description": "10.1111/ecog.05478", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/ecog.05478"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-05-06T00:00:00Z"}}, {"id": "10.1111/gcb.15420", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:31Z", "type": "Journal Article", "created": "2021-03-04", "title": "Microbial inputs at the litter layer translate climate into altered organic matter properties", "description": "<p>Plant litter chemistry is altered during decomposition but it remains unknown if these alterations, and thus the composition of residual litter, will change in response to climate. Selective microbial mineralization of litter components and the accumulation of microbial necromass can drive litter compositional change, but the extent to which these mechanisms respond to climate remains poorly understood. We addressed this knowledge gap by studying needle litter decomposition along a boreal forest climate transect. Specifically, we investigated how the composition and/or metabolism of the decomposer community varies with climate, and if that variation is associated with distinct modifications of litter chemistry during decomposition. We analyzed the composition of microbial phospholipid fatty acids (PLFAs) in the litter layer and measured natural abundance &#948;<sup>13</sup>C<sub>PLFA</sub> values as an integrated measure of microbial metabolisms. Changes in litter chemistry and &#948;<sup>13</sup>C values were measured in litterbag experiments conducted at each transect site. A warmer climate was associated with higher litter nitrogen concentrations as well as altered microbial community structure (lower fungi:bacteria ratios) and microbial metabolism (higher &#948;<sup>13</sup>C<sub>PLFA</sub>). Litter in warmer transect regions accumulated less aliphatic&#8208;C (lipids, waxes) and retained more O&#8208;alkyl&#8208;C (carbohydrates), consistent with enhanced <sup>13</sup>C&#8208;enrichment in residual litter, than in colder regions. These results suggest that chemical changes during litter decomposition will change with climate, driven primarily by indirect climate effects (e.g., greater nitrogen availability and decreased fungi:bacteria ratios) rather than direct temperature effects. A positive correlation between microbial biomass &#948;<sup>13</sup>C values and <sup>13</sup>C&#8208;enrichment during decomposition suggests that change in litter chemistry is driven more by distinct microbial necromass inputs than differences in the selective removal of litter components. Our study highlights the role that microbial inputs during early litter decomposition can play in shaping surface litter contribution to soil organic matter as it responds to climate warming effects such as greater nitrogen availability.</p>
", "keywords": ["DECOMPOSITION", "C-13", "CP‐", "necromass", "litter decomposition", "COMMUNITY COMPOSITION", "Soil", "CARBON SEQUESTRATION", "Taiga", "boreal forest", "bacteria", "C-13 NMR", "TEMPERATURE", "Biochemistry", " cell and molecular biology", "Soil Microbiology", "FUNGAL", "2. Zero hunger", "MAS C-13‐", "Fungi", "04 agricultural and veterinary sciences", "15. Life on land", "NMR", "6. Clean water", "climate transect", "Plant Leaves", "13. Climate action", "FOREST SOILS", "PLFA", "0401 agriculture", " forestry", " and fisheries", "fungi", "FATTY-ACIDS", "BULK CARBON", "LIGNIN"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15420"}, {"href": "https://doi.org/10.1111/gcb.15420"}, {"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.15420", "name": "item", "description": "10.1111/gcb.15420", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.15420"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-16T00:00:00Z"}}, {"id": "10.1371/journal.pone.0029642", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:17Z", "type": "Journal Article", "created": "2012-01-04", "title": "Carbon Stocks And Fluxes In Tropical Lowland Dipterocarp Rainforests In Sabah, Malaysian Borneo", "description": "Deforestation in the tropics is an important source of carbon C release to the atmosphere. To provide a sound scientific base for efforts taken to reduce emissions from deforestation and degradation (REDD+) good estimates of C stocks and fluxes are important. We present components of the C balance for selectively logged lowland tropical dipterocarp rainforest in the Malua Forest Reserve of Sabah, Malaysian Borneo. Total organic C in this area was 167.9 Mg C ha\u207b\u00b9\u00b13.8 (SD), including: Total aboveground (TAGC: 55%; 91.9 Mg C ha\u207b\u00b9\u00b12.9 SEM) and belowground carbon in trees (TBGC: 10%; 16.5 Mg C ha\u207b\u00b9\u00b10.5 SEM), deadwood (8%; 13.2 Mg C ha\u207b\u00b9\u00b13.5 SEM) and soil organic matter (SOM: 24%; 39.6 Mg C ha\u207b\u00b9\u00b10.9 SEM), understory vegetation (3%; 5.1 Mg C ha\u207b\u00b9\u00b11.7 SEM), standing litter (<1%; 0.7 Mg C ha\u207b\u00b9\u00b10.1 SEM) and fine root biomass (<1%; 0.9 Mg C ha\u207b\u00b9\u00b10.1 SEM). Fluxes included litterfall, a proxy for leaf net primary productivity (4.9 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b10.1 SEM), and soil respiration, a measure for heterotrophic ecosystem respiration (28.6 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b11.2 SEM). The missing estimates necessary to close the C balance are wood net primary productivity and autotrophic respiration.Twenty-two years after logging TAGC stocks were 28% lower compared to unlogged forest (128 Mg C ha\u207b\u00b9\u00b113.4 SEM); a combined weighted average mean reduction due to selective logging of -57.8 Mg C ha\u207b\u00b9 (with 95% CI -75.5 to -40.2). Based on the findings we conclude that selective logging decreased the dipterocarp stock by 55-66%. Silvicultural treatments may have the potential to accelerate the recovery of dipterocarp C stocks to pre-logging levels.", "keywords": ["0106 biological sciences", "1000 Multidisciplinary", "Tropical Climate", "Science", "Rain", "Q", "R", "1100 General Agricultural and Biological Sciences", "Biodiversity", "15. Life on land", "01 natural sciences", "Carbon", "Dipterocarpaceae", "Trees", "10127 Institute of Evolutionary Biology and Environmental Studies", "Soil", "1300 General Biochemistry", " Genetics and Molecular Biology", "Borneo", "Seedlings", "13. Climate action", "570 Life sciences; biology", "590 Animals (Zoology)", "Medicine", "Biomass", "Research Article"], "contacts": [{"organization": "Saner, Philippe, Loh, Yen Yee, Ong, Robert C., Hector, Andy,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0029642"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0029642", "name": "item", "description": "10.1371/journal.pone.0029642", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0029642"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-01-03T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:01Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACTDue to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s V = 0.857, and Theil\uffe2\uff80\uff99s U = 0.316). For species-level community profiling, we found strong correlations ( r s > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average r s = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.
IMPORTANCEA quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.
", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/10.1128/msystems.00859-24"}, {"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.00859-24", "name": "item", "description": "10.1128/msystems.00859-24", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00859-24"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "10.1126/sciadv.aar3599", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:59Z", "type": "Journal Article", "created": "2018-09-12", "title": "Nitrogen isotope signature evidences ammonium deprotonation as a common transport mechanism for the AMT-Mep-Rh protein superfamily", "description": "Natural nitrogen isotopic signature reveals deprotonation during ammonium transport across living organisms.
How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.
Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a \uffe2\uff80\uff9ctop 10\uffe2\uff80\uff9d list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.
", "keywords": ["Naturgeografi", "Earth", " Planet", "Climate Change", "Microbiology", "traits", "biogeochemistry", "Humans", "Ecosystem", "Biomedical and Clinical Sciences", "Bacteria", "biogeochemistry; modeling; traits; climate change", "modeling", "Opinion/Hypothesis", "Biodiversity", "Biological Sciences", "Medical microbiology", "Models", " Theoretical", "15. Life on land", "QR1-502", "6. Clean water", "Climate Science", "3. Good health", "Climate Action", "climate change", "Physical Geography", "Medical Microbiology", "13. Climate action", "Biochemistry and cell biology", "Biochemistry and Cell Biology", "Generic health relevance", "Klimatvetenskap"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mbio.00455-24"}, {"href": "https://doi.org/10.1128/mbio.00455-24"}, {"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.00455-24", "name": "item", "description": "10.1128/mbio.00455-24", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/mbio.00455-24"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-05-08T00:00:00Z"}}, {"id": "10.1371/journal.pone.0124096", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:20Z", "type": "Journal Article", "created": "2015-04-16", "title": "Effects Of Different Organic Manures On The Biochemical And Microbial Characteristics Of Albic Paddy Soil In A Short-Term Experiment", "description": "Open AccessCette \u00e9tude visait \u00e0 \u00e9valuer les effets des engrais chimiques (NPK), NPK avec du fumier de b\u00e9tail (NPK+M), NPK avec de la paille (NPK+S) et NPK avec du fumier vert (NPK+G) sur les activit\u00e9s enzymatiques du sol et les caract\u00e9ristiques microbiennes du sol de paddy albique, qui est un sol typique avec une faible productivit\u00e9 en Chine. Les r\u00e9ponses des activit\u00e9s enzymatiques extracellulaires et de la diversit\u00e9 des communaut\u00e9s microbiennes (d\u00e9termin\u00e9es par analyse des acides gras phospholipidiques [PLFA] et \u00e9lectrophor\u00e8se sur gel \u00e0 gradient d\u00e9naturant [DGGE]) ont \u00e9t\u00e9 mesur\u00e9es. Les r\u00e9sultats ont montr\u00e9 que NPK+M et NPK+S augmentaient significativement le rendement du riz, NPK+M \u00e9tant sup\u00e9rieur d'environ 24\u00a0% \u00e0 NPK. Le NPK+M a significativement augment\u00e9 le carbone organique du sol (SOC) et les phosphates disponibles (P) et am\u00e9lior\u00e9 les activit\u00e9s de la phosphatase, de la \u03b2-cellobiosidase, de la L-leucine aminopeptidase et de l'ur\u00e9ase. Le NPK+S a significativement augment\u00e9 le COS et le potassium disponible (K) et significativement augment\u00e9 les activit\u00e9s de la N-ac\u00e9tyl-glucosamidase, de la \u03b2-xylosidase, de l'ur\u00e9ase et de la ph\u00e9nol oxydase. Le NPK+G a significativement am\u00e9lior\u00e9 l'azote total (N), l'ammonium N, le P disponible et l'activit\u00e9 de la N-ac\u00e9tyl-glucosamidase. La biomasse de PLFA \u00e9tait la plus \u00e9lev\u00e9e sous NPK+S, suivie des traitements NPK+M et NPK+G. L'analyse en composantes principales (ACP) du PLFA a indiqu\u00e9 que les sols avec NPK+M et NPK+S contenaient des proportions plus \u00e9lev\u00e9es d'acides gras insatur\u00e9s et de cyclopropane (biomarqueurs de champignons et de bact\u00e9ries \u00e0 Gram n\u00e9gatif) et que les sols sous NPK+G contenaient plus d'acides gras satur\u00e9s \u00e0 cha\u00eene droite (repr\u00e9sentant des bact\u00e9ries \u00e0 Gram positif). La PCA des patrons DGGE a montr\u00e9 que les amendements organiques avaient une plus grande influence sur la communaut\u00e9 fongique. L'analyse en grappes des profils DGGE fongiques a r\u00e9v\u00e9l\u00e9 que NPK+G \u00e9tait clairement s\u00e9par\u00e9. Pendant ce temps, la communaut\u00e9 bact\u00e9rienne du traitement NPK+M \u00e9tait la plus distincte. L'analyse RDA a r\u00e9v\u00e9l\u00e9 que les changements dans la composition de la communaut\u00e9 microbienne d\u00e9pendaient principalement de la \u03b2-xylosidase, des activit\u00e9s de la \u03b2-cellobiosidase, de l'azote total et des teneurs en K disponibles. Les abondances de PLFA bact\u00e9riens et fongiques gram-n\u00e9gatifs probablement efficaces pour am\u00e9liorer la fertilit\u00e9 des sols de paddy albique \u00e0 faible rendement en raison de leur influence significative sur le profil DGGE.", "keywords": ["China", "Mechanics and Transport in Unsaturated Soils", "Microbial population biology", "Science", "Materials Science", "Soil Science", "Organic chemistry", "Thermal Effects on Soil", "Biochemistry", "Gene", "Agricultural and Biological Sciences", "Biomaterials", "Food science", "Soil", "Engineering", "Genetics", "Biology", "Soil Microbiology", "Civil and Structural Engineering", "Applications of Clay Nanotubes in Various Fields", "2. Zero hunger", "Temperature gradient gel electrophoresis", "Bacteria", "Q", "R", "Fungi", "Life Sciences", "Straw", "Oryza", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Urease", "Agronomy", "6. Clean water", "Manure", "Chemistry", "Enzyme", "FOS: Biological sciences", "Physical Sciences", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Animal science", "Research Article", "16S ribosomal RNA"], "contacts": [{"organization": "Qian Zhang, Wei Zhou, Gaofeng Liang, Xiu\u2010Bin Wang, Jingwen Sun, Ping He, LI Lu-jiu,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0124096"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0124096", "name": "item", "description": "10.1371/journal.pone.0124096", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0124096"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-04-16T00:00:00Z"}}, {"id": "10.1371/journal.pone.0161694", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:20Z", "type": "Journal Article", "created": "2016-09-02", "title": "Short-Term Responses Of Soil Respiration And C-Cycle Enzyme Activities To Additions Of Biochar And Urea In A Calcareous Soil", "description": "Open AccessBiochar (BC) addition to soil is a proposed strategy to enhance soil fertility and crop productivity. However, there is limited knowledge regarding responses of soil respiration and C-cycle enzyme activities to BC and nitrogen (N) additions in a calcareous soil. A 56-day incubation experiment was conducted to investigate the combined effects of BC addition rates (0, 0.5, 1.0, 2.5 and 5.0% by mass) and urea (U) application on soil nutrients, soil respiration and C-cycle enzyme activities in a calcareous soil in the North China Plain. Our results showed soil pH values in both U-only and U plus BC treatments significantly decreased within the first 14 days and then stabilized, and CO2emission rate in all U plus BC soils decreased exponentially, while there was no significant difference in the contents of soil total organic carbon (TOC), dissolved organic carbon (DOC), total nitrogen (TN), and C/N ratio in each treatment over time. At each incubation time, soil pH, electrical conductivity (EC), TOC, TN, C/N ratio, DOC and cumulative CO2 emission significantly increased with increasing BC addition rate, while soil potential activities of the four hydrolytic enzymes increased first and then decreased with increasing BC addition rate, with the largest values in the U + 1.0%BC treatment. However, phenol oxidase activity in all U plus BC soils showed a decreasing trend with the increase of BC addition rate. Our results suggest that U plus BC application at a rate of 1% promotes increases in hydrolytic enzymes, does not highly increase C/N and C mineralization, and can improve in soil fertility.", "keywords": ["Organic chemistry", "Soil pH", "Biochemistry", "Agricultural and Biological Sciences", "Soil", "Calcareous", "Engineering", "Soil water", "Urea", "2. Zero hunger", "Ecology", "Soil Water Retention", "Respiration", "Q", "Total organic carbon", "R", "Life Sciences", "Soil respiration", "Carbon cycle", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Soil carbon", "6. Clean water", "Chemistry", "Charcoal", "Physical Sciences", "Environmental chemistry", "Respiration rate", "Medicine", "Incubation", "Pyrolysis", "Research Article", "Mechanics and Transport in Unsaturated Soils", "Nitrogen", "Science", "Materials Science", "Soil Science", "Soil fertility", "Thermal Effects on Soil", "Biomaterials", "Biology", "Ecosystem", "Applications of Clay Nanotubes in Various Fields", "Civil and Structural Engineering", "Biochar Application", "Botany", "15. Life on land", "Carbon", "Agronomy", "Biochar", "Unsaturated Soil Mechanics", "13. Climate action", "FOS: Biological sciences", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Animal science"], "contacts": [{"organization": "Dali Song, XI Xiang-yin, Shaomin Huang, Gaofeng Liang, Jingwen Sun, Wei Zhou, Xiu\u2010Bin Wang,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0161694"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0161694", "name": "item", "description": "10.1371/journal.pone.0161694", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0161694"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-09-02T00:00:00Z"}}, {"id": "10.20944/preprints202106.0434.v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:47Z", "type": "Journal Article", "created": "2021-06-16", "title": "Going beyond Soil Conservation with the Use of Cover Crops in Mediterranean Sloping Olive Orchards", "description": "Among the agricultural practices promoted by the Common Agricultural Policy to increase soil functions, the use of cover crops is a recommended tool to improve the sustainability of Mediter-ranean woody crops such as olive orchards. However, there is a broad range of cover crop ty-pologies in relation to its implementation, control and species composition. In that sense, the in-fluence of different plant species on soil quality indicators in olive orchards remains unknown yet. This study describes the effects of four treatments based on the implementation of different ground covers (CC-NAT, CC-GRA and CC-MIX) and conventional tillage (TILL) on soil erosion, soil physicochemical and biological properties, and soil microbial communities after 8 years of cover crop establishment. Our results have demonstrated that the presence of a temporary cover crop (CC), compared to a soil under tillage (TILL), can reduce soil losses and maintain good soil physicochemical properties and modify greatly the structure and diversity of soil bacterial com-munities and its functioning. The presence of a homogeneous CC of gramineous (Lolium rigidum or Lolilum multiflorum) (CC-GR) for 8 years significantly increased the functional properties of the soil as compared to TILL; although the most significant change was a modification on the bacte-rial community composition that was clearly different from the rest of treatments. On the other hand, the use of a mixture of plant species (CC-MIX) as a CC for only two years although did not modify greatly the structure and diversity of soil bacterial communities compared to the TILL soil, induced significant changes on the functional properties of the soil, and reverted those properties to a level similar to that of an undisturbed soil that had maintained a natural cover of spontaneous vegetation for decades (CC-NAT).