Arbuscular mycorrhizal fungi (AMF) perform key soil ecosystem services and, because of their symbiotic relationship with plant roots, may be exposed to the plant protection products (PPPs) applied to soils and crops. In 2017, the European Food Safety Authority (EFSA) released a scientific opinion addressing the state of the science on risk assessment of PPPs for in-soil organisms, recommending the inclusion of AMF ecotoxicological testing in the PPP regulatory process. However, it is not clear how this can be implemented in a tiered, robust, and ecologically relevant manner. Through a critical review of current literature, we examine the recommendations made within the EFSA report and the methodologies available to integrate AMF into the PPP risk assessment and provide perspective and commentary on their agronomic and ecological relevance. We conclude that considerable research questions remain to be addressed prior to the inclusion of AMF into the in-soil organism risk assessment, many of which stem from the unique challenges associated with including an obligate symbiont within the PPP risk assessment. Finally, we highlight critical knowledge gaps and the further research required to enable development of relevant, reliable, and robust scientific tests alongside pragmatic and scientifically sound guidance to ensure that any future risk-assessment paradigm is adequately protective of the ecosystem services it aims to preserve. Environ Toxicol Chem 2022;41:1808\uffe2\uff80\uff931823. \uffc2\uffa9 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.Responses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long\uffe2\uff80\uff90term field experiment which divides conventional and organic agriculture into component pest\uffe2\uff80\uff90control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles, microbial and nematode counts, and denaturing gradient gel electrophoresis (DGGE) to characterise soil microbial communities in plots used for onion (Allium cepa L.) cultivation.
RESULTSMicrobial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest\uffe2\uff80\uff90control treatment plots.
CONCLUSIONOrganic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. \uffc2\uffa9 2013 Society of Chemical Industry
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Microbial diversity", "Nematoda", "Soil", "03 medical and health sciences", "Onions", "Animals", "DNA", " Fungal", "Ecosystem", "Soil Microbiology", "2. Zero hunger", "Organic Agriculture", "0303 health sciences", "Bacteria", "Denaturing Gradient Gel Electrophoresis", "0402 animal and dairy science", "Fungi", "Denaturing gradient gel electrophoresis", "Agriculture", "Biolog Eco-plates", "04 agricultural and veterinary sciences", "15. Life on land", "Community level physiological profile", "Organic agriculture", "0405 other agricultural sciences"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.6206"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.6206", "name": "item", "description": "10.1002/jsfa.6206", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.6206"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-06-07T00:00:00Z"}}, {"id": "10.1002/ldr.3453", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:14:14Z", "type": "Journal Article", "created": "2019-10-15", "title": "Increases in aridity lead to drastic shifts in the assembly of dryland complex microbial networks", "description": "AbstractWe have little information on how and why soil microbial community assembly will respond to predicted increases in aridity by the end of this century. Here, we used correlation networks and structural equation modeling to assess the changes in the abundance of the ecological clusters including potential winner and loser microbial taxa associated with predicted increases in aridity. To do this, we conducted a field survey in an environmental gradient from eastern Australia and obtained information on bacterial and fungal community composition for 120 soil samples and multiple abiotic and biotic factors. Overall, our structural equation model explained 83% of the variance in the two mesic modules. Increases in aridity led to marked shifts in the abundance of the two major microbial modules found in our network, which accounted for >99% of all phylotypes. In particular, the relative abundance of one of these modules, the Mesic Module #1, which was positively related to multiple soil properties and plant productivity, declined strongly with aridity. Conversely, the relative abundance of a second dominant module (Xeric Module #2) was positively correlated with increases in aridity. Our study provides evidence that network analysis is a useful tool to identify microbial taxa that are either winners or losers under increasing aridity and therefore potentially under changing climates. Our work further suggests that climate change, and associated land degradation, could potentially lead to extensive microbial phylotypes exchange and local extinctions, as demonstrated by the reductions of up to 97% in the relative abundance of microbial taxa within Mesic Module #1.Rapidly growing global populations mandate greater crop productivity despite increasingly scarce natural resources, including freshwater. The adoption of sustainable agricultural practices seek to address such issues, but an unintended consequence is the exposure of agricultural soils and associated biota to emerging contaminants including azole pharmaceutical antifungals. We show that environmentally relevant exposure to three commonly prescribed azole antifungals can reduce mycorrhizal 33P transfer from the soil into the host plant. This suggests that exposure to azoles may have a significant impact on mycorrhizal\uffe2\uff80\uff90mediated transfer of nutrients in soil\uffe2\uff80\uff90plant systems. Understanding the unintended consequences of sustainable agricultural practices is needed to ensure the security and safety of future food production systems.
Summary
Sustainable farming practices are increasingly necessary to meet the demands of a growing population under constraints imposed by climate change. These practices, in particular the reuse of wastewater and amending soil with wastewater derived biosolids, provide a pathway for man\uffe2\uff80\uff90made chemicals to enter the agricultural environment.
Among the chemicals commonly detected in wastewater and biosolids are pharmaceutical azole antifungals. Fungi, in particular mycorrhiza\uffe2\uff80\uff90forming fungal symbionts of plant roots, are key drivers of nutrient cycling in the soil\uffe2\uff80\uff93plant system. As such, greater understanding of the impacts of azole antifungal exposure in agricultural systems is urgently needed.
We exposed wheat (Triticum aestivum L. cv. \uffe2\uff80\uff98Skyfall\uffe2\uff80\uff99) and arbuscular mycorrhizal fungi to environmentally relevant concentrations of three azole antifungals (clotrimazole, miconazole nitrate and fluconazole). We traced the mycorrhizal\uffe2\uff80\uff90acquired 33P from the soil into the host plant in contaminated versus non\uffe2\uff80\uff90contaminated soils and found 33P transfer from mycorrhizal fungi to host plants was reduced in soils containing antifungals. This represents a potentially major disruption to soil nutrient flows as a result of soil contamination.
Our work raises the major issue of exposure of soil biota to pharmaceuticals such as azole antifungals, introduced via sustainable agricultural practices, as a potentially globally important disruptive influence on soil nutrient cycles. The impacts of these compounds on non\uffe2\uff80\uff90target organisms, beneficial mycorrhizal fungi in particular, could have major implications on security and sustainability of future food systems.
Natural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off\uffe2\uff80\uff90target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co\uffe2\uff80\uff90operation and Development, which is a key international standard\uffe2\uff80\uff90setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5\uffe2\uff80\uff90dichloraniline). We determined the following in three different soils: (i) ammonium (NH4+) and nitrate (NO3\uffe2\uff88\uff92) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q\uffe2\uff80\uff90PCR).RESULTSAll pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose\uffe2\uff80\uff90dependent effects on NH4+ and NO3\uffe2\uff88\uff92 levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q\uffe2\uff80\uff90PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5\uffe2\uff80\uff90dichloraniline.
CONCLUSIONOur findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well\uffe2\uff80\uff90standardized tools. \uffc2\uffa9 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.Microplastics are increasingly recognized as a factor of global change. By altering soil inherent properties and processes, ripple-on effects on plants and their symbionts can be expected. Additionally, interactions with other factors of global change, such as drought, can influence the effect of microplastics. We designed a greenhouse study to examine effects of polyester microfibers, arbuscular mycorrhizal (AM) fungi and drought on plant, microbial and soil responses. We found that polyester microfibers increased the aboveground biomass of Allium cepa under well-watered and drought conditions, but under drought conditions the AM fungal-only treatment reached the highest biomass. Colonization with AM fungi increased under microfiber contamination, however, plant biomass did not increase when both AM fungi and fibers were present. The mean weight diameter of soil aggregates increased with AM fungal inoculation overall but decreased when the system was contaminated with microfibers or drought stressed. Our study adds additional support to the mounting evidence that microplastic fibers in soil can affect the plant-soil system by promoting plant growth, and favoring key root symbionts, AM fungi. Although soil aggregation is usually positively influenced by plant roots and AM fungi, and microplastic promotes both, our results show that plastic still had a negative effect on soil aggregates. Even though there are concerns that microplastic might interact with other factors of global change, our study revealed no such effect for drought.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "570", "Organic matter decomposition", "Drought", "Microplastic", "Arbuscular mycorrhizal fungi", "500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie", "Root traits", "15. Life on land", "01 natural sciences", "6. Clean water", "03 medical and health sciences", "13. Climate action", "Soil aggregation", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s42832-020-0060-4.pdf"}, {"href": "https://doi.org/10.1007/s42832-020-0060-4"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Ecology%20Letters", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s42832-020-0060-4", "name": "item", "description": "10.1007/s42832-020-0060-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s42832-020-0060-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-02T00:00:00Z"}}, {"id": "10.1016/j.agee.2010.12.011", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:35Z", "type": "Journal Article", "created": "2010-12-31", "title": "Impact On Soil Quality Of A 10-Year-Old Short-Rotation Coppice Poplar Stand Compared With Intensive Agricultural And Uncultivated Systems In A Mediterranean Area", "description": "Bioenergy crops play an ecologically and economically fundamental role as an alternative to agri-food productions and as renewable energy sources. Little attention has been focused on soil quality following conversion of agricultural lands to biomass crops. Here, we assessed the impact of a 10-year-old short-rotation coppice (SRC) poplar stand on the main soil chemical parameters, microbial biomass carbon, soil respiration, and arbuscular mycorrhizal fungi (AMF), compared with intensive agricultural and uncultivated systems. Three different harvest frequencies of poplar SRC (annual T1, biannual T2 and triennial T3 cutting cycles) were evaluated. Multivariate analysis showed that poplar SRC improved soil quality compared with intensive agricultural and uncultivated systems. T1 and T2 positively affected AMF inoculum potential and root colonisation of a co-occurring plant species, while T3 improved the majority of soil chemical and biochemical parameters. Moreover, three different AMF morphospecies belonging to the genera Glomus and Scutellospora were found in poplar SRC, while morphospecies belonging exclusively to genera Glomus were recorded in intensive agricultural and uncultivated systems. Such aspects have agro-ecological implications, since the positive changes of soil nutrient availability and carbon content together with a high abundance and diversity of soil biota show clear soil sustainability of poplar SRC.", "keywords": ["2. Zero hunger", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "Short-rotation forestry; Cutting cycle; Arbuscular mycorrhizal fungi; Microbial biomass carbon; Soil respiration; Multivariate analysis", "7. Clean energy"]}, "links": [{"href": "https://doi.org/10.1016/j.agee.2010.12.011"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agriculture%2C%20Ecosystems%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.agee.2010.12.011", "name": "item", "description": "10.1016/j.agee.2010.12.011", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.agee.2010.12.011"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-01-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2022.108754", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:25Z", "type": "Journal Article", "created": 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\u0627\u0644\u0645\u0631\u062a\u0628\u0637 \u0628\u0627\u0644\u0645\u0639\u0627\u062f\u0646 \u0648\u062a\u0645\u0639\u062f\u0646 \u0645\u064a\u0643\u0631\u0648\u0628\u064a \u0623\u0643\u0628\u0631 \u0644\u0640 SOM \u0645\u0639 \u0627\u0631\u062a\u0641\u0627\u0639 \u0627\u0644\u0637\u0644\u0628 \u0639\u0644\u0649 \u0627\u0644\u0645\u0648\u0627\u0631\u062f \u0627\u0644\u0645\u064a\u0643\u0631\u0648\u0628\u064a\u0629. \u062a\u0634\u064a\u0631 \u0627\u0644\u0646\u062a\u0627\u0626\u062c \u0625\u0644\u0649 \u0623\u0646 EA \u0628\u0648\u0633\u0627\u0637\u0629 \u0623\u0646\u0648\u0627\u0639 \u0627\u0644\u0623\u0634\u062c\u0627\u0631\u060c \u0648\u0627\u0644\u062d\u062f \u0645\u0646 \u0627\u0644\u0645\u0648\u0627\u0631\u062f \u0627\u0644\u0645\u064a\u0643\u0631\u0648\u0628\u064a\u0629 \u0648\u062a\u0643\u0648\u064a\u0646 \u0627\u0644\u0645\u062c\u062a\u0645\u0639 \u0627\u0644\u0645\u064a\u0643\u0631\u0648\u0628\u064a \u0647\u064a \u0645\u062d\u0631\u0643\u0627\u062a \u0645\u0647\u0645\u0629 \u0644\u0644\u0645\u062e\u0632\u0648\u0646\u0627\u062a \u0648\u0627\u0644\u062a\u0648\u0632\u064a\u0639 \u0627\u0644\u0631\u0623\u0633\u064a \u0644\u0645\u062e\u0632\u0648\u0646 \u0627\u0644\u0643\u0631\u0628\u0648\u0646 \u0627\u0644\u0639\u0636\u0648\u064a \u0641\u064a \u0627\u0644\u062a\u0631\u0628\u0629 \u0628\u064a\u0646 \u0623\u0646\u0648\u0627\u0639 \u0627\u0644\u0623\u0634\u062c\u0627\u0631 \u0648\u0628\u064a\u0646 \u0646\u0648\u0639\u064a\u0646 \u0645\u0646 \u0627\u0644\u062c\u0630\u0648\u0631 \u0627\u0644\u0641\u0637\u0631\u064a\u0629 \u0627\u0644\u0645\u0631\u062a\u0628\u0637\u0629 \u0628\u0647\u0627.", "keywords": ["Biomass (ecology)", "Microbial population biology", "Fagus sylvatica", "Soil Science", "Plant Science", "Plant litter", "Agricultural and Biological Sciences", "Mycorrhizal Fungi and Plant Interactions", "Soil water", "Genetics", "Monoculture", "Forest floor", "Saproxylic Insect Ecology and Forest Management", "Biology", "Beech", "Soil organic matter", "Soil Fertility", "Ecology", "Bacteria", "Picea abies", "Botany", "Life Sciences", "04 agricultural and veterinary sciences", "Soil carbon", "Agronomy", "Insect Science", "FOS: Biological sciences", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Nutrient"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2022.108754"}, {"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.2022.108754", "name": "item", "description": "10.1016/j.soilbio.2022.108754", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2022.108754"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-09-01T00:00:00Z"}}, {"id": "10.1016/j.biocontrol.2025.105723", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:57Z", "type": "Journal Article", "created": "2024-10-01", "title": "Advancing Strain-Specific Taqman Assays for Trichoderma Asperellum Detection in Commercial Agricultural Settings", "description": "The global agricultural sector is facing significant challenges in achieving higher sustainability, which has increased interest in using biological control agents (BCAs) to manage plant diseases. However, it is essential to ensure that microbial-based products, such as BCAs, are utilised in a manner that does not harm soil quality and fertility while decreasing reliance on synthetic pesticides. To accomplish this, it is crucial to monitor the fate and persistence of bioinoculants in the soil, which is essential for optimising their application over time, as well as for regulatory and commercial purposes and environmental risk assessment. A qPCR detection method utilising TaqMan chemistry is proposed, which has demonstrated high specificity and sensitivity in detecting Trichoderma asperellum, a common BCA species, in soil. The primers and probe were designed based on the \u03b2tubulin2 gene. The TaqMan-based assay was applied and validated on soils where tomatoes and strawberries were grown after a previous application of T. asperellum FC80 strain over three years. The TaqMan-based assay was able to detect the target strain accurately, meeting the stringent requirements for commercial and regulatory applications. Significance and impact of the study: The TaqMan assay developed here has the potential to impact the agricultural sector significantly. It can be used for regulatory, commercial, and scientific purposes to track, monitor, and determine the presence and fate of T. asperellum under field crop conditions, thereby contributing to adopting more sustainable and efficient agricultural practices.", "keywords": ["traceability qPCR", "Soil", "TaqMan Assay", "S", "QH301-705.5", "Fungi Trichoderma asperellum", "Agriculture", "Biology (General)", "Biological control agent"]}, "links": [{"href": "https://doi.org/10.1016/j.biocontrol.2025.105723"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biological%20Control", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biocontrol.2025.105723", "name": "item", "description": "10.1016/j.biocontrol.2025.105723", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biocontrol.2025.105723"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "10.1016/j.biortech.2006.11.027", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:59Z", "type": "Journal Article", "created": "2007-01-06", "title": "Effect Of Long-Term Application Of Manure And Fertilizer On Biological And Biochemical Activities In Soil During Crop Development Stages", "description": "A field experiment was conducted to investigate the effect of six long-term (34-year) fertilizer and farmyard manure (FYM) treatments (Control, N, NP, NPK, NPK+S, NPK+FYM) and three physiological stages of wheat growth on the microbial biomass carbon (MBC), nitrogen (MBN) and dehydrogenase, mineralizable N and phosphatase activities in soil. It was found that a balanced application of NPK+FYM gave the highest values for the measured parameters and lowest at the control. Values were generally highest at tillering, followed by the flowering and dough stages. A significant positive interaction between fertilizer treatments and physiological stages of wheat growth was observed, being highest at maximum tillering due to application of NPK+FYM. Stepwise regressions have revealed that grain yield of wheat was significantly associated with mineralizable N at tillering (R(2)=0.80), MBC at flowering (R(2)=0.90) and alkaline phosphatase activity (R(2)=0.70) at dough stages of wheat growth.", "keywords": ["Crops", " Agricultural", "2. Zero hunger", "Time Factors", "Bacteria", "Nitrogen", "Fungi", "04 agricultural and veterinary sciences", "Carbon", "Phosphoric Monoester Hydrolases", "Manure", "Soil", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Fertilizers", "Oxidoreductases", "Soil Microbiology", "Triticum"]}, "links": [{"href": "https://doi.org/10.1016/j.biortech.2006.11.027"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioresource%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biortech.2006.11.027", "name": "item", "description": "10.1016/j.biortech.2006.11.027", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biortech.2006.11.027"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-12-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2022.137472", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:05Z", "type": "Journal Article", "created": "2022-12-07", "title": "Assembled mixed co-cultures for emerging pollutant removal using native microorganisms from sewage sludge", "description": "The global pharmaceutical pollution caused by drug consumption (>100,000 tonnes) and its disposal into the environment is an issue which is currently being addressed by bioremediation techniques, using single or multiple microorganisms. Nevertheless, the low efficiency and the selection of non-compatible species interfere with the success of this methodology. This paper proposes a novel way of obtaining an effective multi-domain co-culture, with the capacity to degrade multi-pharmaceutical compounds simultaneously. To this end, seven microorganisms (fungi and bacteria) previously isolated from sewage sludge were investigated to enhance their degradation performance. All seven strains were factorially mixed and used to assemble different artificial co-cultures. Consequently, 127 artificial co-cultures were established and ranked, based on their fitness performance, by using the BSocial analysis web tool. The individual strains were categorized according to their social behaviour, whose net effect over the remaining strains was defined as 'Positive', 'Negative' or 'Neutral'. To evaluate the emerging-pollutant degradation rate, the best 10 co-cultures, and those which contained the social strains were then challenged with three different Pharmaceutical Active compounds (PhACs): diclofenac, carbamazepine and ketoprofen. The co-cultures with the fungi Penicillium oxalicum XD-3.1 and Penicillium rastrickii were able to degrade PhACs. However, the highest performance (>80% degradation) was obtained by the minimal active microbial consortia consisting of both Penicillium spp., Cladosporium cladosporoides and co-existing bacteria. These consortia transformed the PhACs to derivate molecules through hydroxylation and were released to the media, resulting in a low ecotoxicity effect. High-throughput screening of co-cultures provides a quick, reliable and efficient method to narrow down suitable degradation co-cultures for emerging PhAC contaminants while avoiding toxic metabolic derivatives.", "keywords": ["Sewage", "Bacteria", "Fungi", "HTGrowth", "Waste Disposal", " Fluid", "01 natural sciences", "Coculture Techniques", "6. Clean water", "12. Responsible consumption", "Biodegradation", " Environmental", "Pharmaceutical Preparations", "13. Climate action", "Environmental Pollutants", "BSocial", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2022.137472"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2022.137472", "name": "item", "description": "10.1016/j.chemosphere.2022.137472", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2022.137472"}, {"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": "10.1016/j.ecolind.2024.111796", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:11Z", "type": "Journal Article", "created": "2024-02-29", "title": "Ascomycota and Basidiomycota fungal phyla as indicators of land use efficiency for soil organic carbon accrual with woody plantations", "description": "As soil fungi are major players in the carbon accumulation process, the two main fungal degraders in topsoil, Ascomycetes and Basidiomycetes, were investigated as indicators of land use effectiveness in increasing soil carbon accumulation and soil function. The study focused on the soil organic carbon content increase in a 20-year short rotation forest cycle with broadleaf woody plantations compared to a nearby arable cropping system. Total fungi, Ascomycota and Basidiomycota, were quantified in terms of DNA copy number, with specific probes using SYBR\u00ae Green I dye on the QuantStudio\u2122 3D digital PCR system (dPCR). Previously, next generation sequencing analysis using a general primer confirmed that Ascomycota and Basidiomycota were the most represented phyla and that fungal community composition significantly differed between treatments. A range of key soil enzyme activities for the C-cycle were also assessed. Total organic carbon content (TOC), microbial biomass in term of dsDNA and enzyme activities significantly increased in woody plantations compared to arable soil. The TOC increase differed significantly also between wood species, Salix and Robina gave the greatest increase (+30 and 20\u00a0% respectively), followed by Populus (+12), microbial biomass highly correlated with TOC showing the same trend. Total fungi, Ascomycota and Basidiomycota increased significantly in three woody plantations compared to the arable soil system. Ascomycota in the woody plantations increased two to four times (average 3144 n copies \u00b5l\u22121 of DNA) compared to the arable soil (1419 n copies \u00b5l\u22121); Basidiomycota were almost absent in arable soil (av. 94n copies \u00b5l\u22121) and increased five to six times in woody plantations (av. 490 n copies \u00b5l\u22121). Total fungi and ascomycetes correlated strongly with microbial biomass and TOC, whereas basidiomycetes did not. These findings showed that Ascomycota represent the largest portion of fungi in agricultural soils even after a 20-years short rotation forest cycle and they can be taken as indicators of carbon accumulation processes. Therefore, this study suggests that joining the Ascomycetes quantity in the topsoil to the Ascomycota:Basidiomycota ratio seems a good option when setting regional strategies for improving C accrual in farmland with the short-term afforestation.", "keywords": ["Carbon sequestration", "2. Zero hunger", "Ecology", "04 agricultural and veterinary sciences", "15. Life on land", "Topsoil", "01 natural sciences", "Saproptrophic soil fungi", "Land use", "0401 agriculture", " forestry", " and fisheries", "Short rotation forest", "Digital PCR", "QH540-549.5", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Manici, Luisa M., Caputo, Francesco, Fornasier, Flavio, Paletto, Alessandro, Ceotto, Enrico, De Meo, Isabella,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.ecolind.2024.111796"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecological%20Indicators", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ecolind.2024.111796", "name": "item", "description": "10.1016/j.ecolind.2024.111796", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ecolind.2024.111796"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-03-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2005.08.017", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:19Z", "type": "Journal Article", "created": "2005-10-03", "title": "Responses To Ammonium And Nitrate Additions By Boreal Plants And Their Natural Enemies", "description": "Separate effects of ammonium (NH4+) and nitrate (NO3-) on boreal forest understorey vegetation were investigated in an experiment where 12.5 and 50.0 kg nitrogen (N) ha(-1) year(-1) was added to 2 m2 sized plots during 4 years. The dwarf-shrubs dominating the plant community, Vaccinium myrtillus and V. vitis-idaea, took up little of the added N independent of the chemical form, and their growth did not respond to the N treatments. The grass Deschampsia flexuosa increased from the N additions and most so in response to NO3-. Bryophytes took up predominately NH4+ and there was a negative correlation between moss N concentration and abundance. Plant pathogenic fungi increased from the N additions, but showed no differences in response to the two N forms. Because the relative contribution of NH4+ and NO3- to the total N deposition on a regional scale can vary substantially, the N load a habitat can sustain without substantial changes in the biota should be set considering specific vegetation responses to the predominant N form in deposition.", "keywords": ["Sweden", "0106 biological sciences", "Air Pollutants", "Nitrogen", "Fungi", "Plant Development", "Bryophyta", "Plants", "15. Life on land", "01 natural sciences", "Trees", "Quaternary Ammonium Compounds", "Biomass", "Ecosystem", "Environmental Monitoring", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Joachim Strengbom, Annika Nordin, Lars Ericson,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2005.08.017"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envpol.2005.08.017", "name": "item", "description": "10.1016/j.envpol.2005.08.017", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2005.08.017"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-05-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2008.06.038", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:19Z", "type": "Journal Article", "created": "2008-08-16", "title": "Bioconcentration Of Zinc And Cadmium In Ectomycorrhizal Fungi And Associated Aspen Trees As Affected By Level Of Pollution", "description": "Concentrations of Zn and Cd were measured in fruitbodies of ectomycorrhizal (ECM) fungi and leaves of co-occurring accumulator aspen. Samples were taken on three metal-polluted sites and one control site. Fungal bioconcentration factors (BCF = fruitbody concentration: soil concentration) were calculated on the basis of total metal concentrations in surface soil horizons (BCF(tot)) and NH(4)NO(3)-extractable metal concentrations in mineral soil (BCF(lab)). When plotted on log-log scale, values of BCF decreased linearly with increasing soil metal concentrations. BCF(lab) for both Zn and Cd described the data more closely than BCF(tot). Fungal genera differed in ZnBCF but not in CdBCF. The information on differences between fungi with respect to their predominant occurrence in different soil horizons did not improve relations of BCF with soil metal concentrations. Aspen trees accumulated Zn and Cd to similar concentrations as the ECM fungi. Apparently, the fungi did not act as an effective barrier against aspen metal uptake by retaining the metals.", "keywords": ["Fungi", "04 agricultural and veterinary sciences", "15. Life on land", "01 natural sciences", "Trees", "Zinc", "13. Climate action", "Mycorrhizae", "Soil Pollutants", "0401 agriculture", " forestry", " and fisheries", "Environmental Pollution", "Cadmium", "Environmental Monitoring", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2008.06.038"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envpol.2008.06.038", "name": "item", "description": "10.1016/j.envpol.2008.06.038", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2008.06.038"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-01-01T00:00:00Z"}}, {"id": "10.1890/12-1243.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:20:47Z", "type": "Journal Article", "created": "2012-10-29", "title": "Microbial Abundance And Composition Influence Litter Decomposition Response To Environmental Change", "description": "Rates of ecosystem processes such as decomposition are likely to change as a result of human impacts on the environment. In southern California, climate change and nitrogen (N) deposition in particular may alter biological communities and ecosystem processes. These drivers may affect decomposition directly, through changes in abiotic conditions, and indirectly through changes in plant and decomposer communities. To assess indirect effects on litter decomposition, we reciprocally transplanted microbial communities and plant litter among control and treatment plots (either drought or N addition) in a grassland ecosystem. We hypothesized that drought would reduce decomposition rates through moisture limitation of decomposers and reductions in plant litter quality before and during decomposition. In contrast, we predicted that N deposition would stimulate decomposition by relieving N limitation of decomposers and improving plant litter quality. We also hypothesized that adaptive mechanisms would allow microbes to decompose litter more effectively in their native plot and litter environments. Consistent with our first hypothesis, we found that drought treatment reduced litter mass loss from 20.9% to 15.3% after six months. There was a similar decline in mass loss of litter inoculated with microbes transplanted from the drought treatment, suggesting a legacy effect of drought driven by declines in microbial abundance and possible changes in microbial community composition. Bacterial cell densities were up to 86% lower in drought plots and at least 50% lower on litter derived from the drought treatment, whereas fungal hyphal lengths increased by 13\uffe2\uff80\uff9314% in the drought treatment. Nitrogen effects on decomposition rates and microbial abundances were weaker than drought effects, although N addition significantly altered initial plant litter chemistry and litter chemistry during decomposition. However, we did find support for microbial adaptation to N addition with N\uffe2\uff80\uff90derived microbes facilitating greater mass loss in N plots than in control plots. Our results show that environmental changes can affect rates of ecosystem processes directly through abiotic changes and indirectly through microbial abundances and communities. Therefore models of ecosystem response to global change may need to represent microbial biomass and community composition to make accurate predictions.
", "keywords": ["Time Factors", "Nitrogen", "Precipitation", "Nitrogen fertilization", "Environmental Microbiology", "Community composition", "Animals", "Home field advantage", "Global change", "Ecosystem", "2. Zero hunger", "Drought", "Bacteria", "Litter decomposition", "Fungi", "04 agricultural and veterinary sciences", "15. Life on land", "Grassland", "Reciprocal transplant", "6. Clean water", "Droughts", "Plant Leaves", "Microbes", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Environmental Monitoring"]}, "links": [{"href": "https://escholarship.org/content/qt5bg595vm/qt5bg595vm.pdf"}, {"href": "https://doi.org/10.1890/12-1243.1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1890/12-1243.1", "name": "item", "description": "10.1890/12-1243.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1890/12-1243.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-03-01T00:00:00Z"}}, {"id": "10.1016/j.funeco.2016.05.011", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:36Z", "type": "Journal Article", "created": "2016-06-26", "title": "Chronic Nitrogen Additions Fundamentally Restructure The Soil Fungal Community In A Temperate Forest", "description": "Abstract Fungi dominate the microbial biomass of temperate forest soils and are a key driver of ecosystem nutrient cycling. Chronic nitrogen (N) amendments frequently cause the accumulation of soil organic matter within soils, suggesting that elevated N disrupts decomposition by altering fungal communities. To link previously observed increases in soil organic matter with potential changes in the fungal community, we assessed the effects of soil N amendment on fungal community structure at a long-term N addition experiment at Harvard Forest (Petersham, MA, USA). A decline in the relative abundance of ectomycorrhizal fungi following long-term N addition was offset by an increase in the relative abundance of saprotrophs. Species richness and diversity of ectomycorrhizal fungi declined, while ascomycetes and saprotrophs responded positively to N enrichment. However, nitrophilic species included ectomycorrhizal as well as saprotrophic fungi, especially the ectomycorrhizal Russula vinacea, whose relative abundance increased from 10 to 37% of the entire community across N treatments. Two decades of soil N enrichment appears to have fundamentally altered the soil fungal community of this temperate forest.", "keywords": ["Basidiomycetes", "0106 biological sciences", "2. Zero hunger", "Diversity", "Community", "Soil fungi", "04 agricultural and veterinary sciences", "Biogeochemistry", "15. Life on land", "Nitrogen deposition", "01 natural sciences", "Ascomycetes", "0401 agriculture", " forestry", " and fisheries", "DNA barcoding"]}, "links": [{"href": "https://doi.org/10.1016/j.funeco.2016.05.011"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Fungal%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.funeco.2016.05.011", "name": "item", "description": "10.1016/j.funeco.2016.05.011", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.funeco.2016.05.011"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-10-01T00:00:00Z"}}, {"id": "10.1016/j.foreco.2022.120396", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:35Z", "type": "Journal Article", "created": "2022-07-04", "title": "Tree species identity is the predominant modulator of the effects of soil fauna on leaf litter decomposition", "description": "Open AccessLa faune du sol est l'un des principaux moteurs de la d\u00e9composition de la liti\u00e8re \u00e0 l'\u00e9chelle locale et mondiale, mais le r\u00f4le des esp\u00e8ces d'arbres dans la m\u00e9diation des effets de la faune du sol sur la d\u00e9composition de la liti\u00e8re reste insaisissable. Nous avons men\u00e9 une exp\u00e9rience sur le terrain en utilisant des sacs de liti\u00e8re avec trois tailles de maille diff\u00e9rentes qui ont permis l'acc\u00e8s \u00e0 la microfaune (0,1 mm), \u00e0 la micro et m\u00e9sofaune (2 mm) et \u00e0 la faune totale du sol (5 mm) pour \u00e9valuer la d\u00e9composition de la liti\u00e8re foliaire de deux esp\u00e8ces d'arbres associ\u00e9es \u00e0 des champignons mycorhiziens arbusculaires (MA) et de trois esp\u00e8ces d'arbres associ\u00e9es \u00e0 des champignons ectomycorhiziens (ECM) dans six sites de jardins communs danois. Nous avons \u00e9galement \u00e9valu\u00e9 comment les diff\u00e9rences dans la qualit\u00e9 initiale de la liti\u00e8re, les propri\u00e9t\u00e9s du sol et la composition de la communaut\u00e9 microbienne parmi les esp\u00e8ces d'arbres peuvent affecter la d\u00e9composition de la liti\u00e8re ainsi que les effets de la faune du sol sur la d\u00e9composition de la liti\u00e8re. Les r\u00e9sultats ont montr\u00e9 que (1) la perte de masse de la liti\u00e8re variait consid\u00e9rablement selon la taille des mailles et les esp\u00e8ces d'arbres, avec des taux de d\u00e9composition de la liti\u00e8re (k) allant de 0,273 \u00e0 3,482\u00a0; (2) l'acc\u00e8s \u00e0 la m\u00e9sofaune augmentait significativement la liti\u00e8re k de 0,658 pour la MA et de 0,396 pour les esp\u00e8ces d'arbres ECM sans acc\u00e8s \u00e0 la faune du sol, respectivement de 255 et 92%, tandis que l'acc\u00e8s \u00e0 la fois \u00e0 la m\u00e9so- et \u00e0 la macrofaune augmentait k de 265 et 108% pour les arbres AM et ECM, respectivement\u00a0; (3) l'identit\u00e9 des esp\u00e8ces d'arbres, l'association mycorhizienne, la qualit\u00e9 initiale de la liti\u00e8re, les propri\u00e9t\u00e9s du sol, la composition des communaut\u00e9s microbiennes et la biomasse de la faune du sol ambiant \u00e9taient tous des facteurs influen\u00e7ant significativement la d\u00e9composition de la liti\u00e8re, mais l'identit\u00e9 des esp\u00e8ces d'arbres \u00e9tait le facteur dominant ind\u00e9pendamment de la taille des mailles des sacs de liti\u00e8re\u00a0; et (4) les effets de la m\u00e9sofaune sur la d\u00e9composition de la liti\u00e8re \u00e9taient principalement contr\u00f4l\u00e9s par l'identit\u00e9 des esp\u00e8ces d'arbres, la concentration initiale en Mg de la liti\u00e8re et le rapport lignine\u00a0:N, tandis que le petit impact suppl\u00e9mentaire de l'acc\u00e8s \u00e0 la macrofaune n'\u00e9tait pas bien expliqu\u00e9 par aucun des facteurs \u00e9valu\u00e9s. Dans l'ensemble, nos r\u00e9sultats sugg\u00e8rent que les esp\u00e8ces d'arbres affectent la d\u00e9composition de la liti\u00e8re via une stimulation diff\u00e9rente du fonctionnement de la faune du sol, et que les esp\u00e8ces d'arbres associ\u00e9es \u00e0 la MA et \u00e0 la mec diff\u00e8rent dans le degr\u00e9 auquel la faune du sol stimule la d\u00e9composition de la liti\u00e8re. Cependant, le mod\u00e8le n'\u00e9tait pas enti\u00e8rement coh\u00e9rent car les taux de d\u00e9composition de la liti\u00e8re pour la chaux associ\u00e9e \u00e0 la mec \u00e9taient stimul\u00e9s dans la m\u00eame mesure que les taux pour les esp\u00e8ces d'arbres associ\u00e9es \u00e0 la MA, le fr\u00eane et l'\u00e9rable. Dans l'ensemble, nos r\u00e9sultats sugg\u00e8rent que les communaut\u00e9s de m\u00e9so- et de macrofaune du sol peuvent am\u00e9liorer les effets des esp\u00e8ces d'arbres sur la d\u00e9composition de la liti\u00e8re ainsi que l'incorporation de la liti\u00e8re C dans le sol min\u00e9ral.", "keywords": ["Biomass (ecology)", "0106 biological sciences", "Litter quality", "Microfauna", "Plant Science", "Soil mesofauna", "01 natural sciences", "Plant litter", "Soil fauna", "Agricultural and Biological Sciences", "Biodiversity Conservation and Ecosystem Management", "Soil biology", "Microbial community", "Mycorrhizal Fungi and Plant Interactions", "Litter", "Soil water", "Wood Decomposition", "Saproxylic Insect Ecology and Forest Management", "Plant Interactions", "Biology", "Ecosystem", "Nature and Landscape Conservation", "Ecology", "Soil property", "Life Sciences", "04 agricultural and veterinary sciences", "15. Life on land", "Fauna", "Insect Science", "FOS: Biological sciences", "Environmental Science", "Physical Sciences", "Common garden", "0401 agriculture", " forestry", " and fisheries", "Litterbag mesh size"]}, "links": [{"href": "https://doi.org/10.1016/j.foreco.2022.120396"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Forest%20Ecology%20and%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foreco.2022.120396", "name": "item", "description": "10.1016/j.foreco.2022.120396", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foreco.2022.120396"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-09-01T00:00:00Z"}}, {"id": "10.1016/j.funbio.2010.04.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:36Z", "type": "Journal Article", "created": "2010-04-26", "title": "Afforestation Alters Community Structure Of Soil Fungi", "description": "Relatively little is known about the effect of afforestation on soil fungal communities. This study demonstrated that afforestation altered fungal community structure and that changes were correlated to pools of soil C. Pasture at three locations on the same soil type was afforested with Eucalyptus globulus or Pinus pinaster. The structure of fungal communities under the three land uses was measured after 13y using automated ribosomal intergenic spacer analysis (ARISA). Afforestation significantly altered the structure of fungal communities. The effect of location on the structure of fungal communities was limited to pasture soils; although these contained the same plant species, the relative composition of each species varied between locations. Differences in the structure of fungal communities between pasture, E. globulus and P. pinaster were significantly correlated with changes in the amount of total organic C and microbial biomass-C in soil. Afforestation of patches of agricultural land may contribute to conserving soil fungi in agricultural landscapes by supporting fungal communities with different composition to agricultural soils.", "keywords": ["2. Zero hunger", "Soil", "Fungi", "0401 agriculture", " forestry", " and fisheries", "Agriculture", "Biodiversity", "04 agricultural and veterinary sciences", "15. Life on land", "Soil Microbiology", "Trees"]}, "links": [{"href": "https://doi.org/10.1016/j.funbio.2010.04.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Fungal%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.funbio.2010.04.008", "name": "item", "description": "10.1016/j.funbio.2010.04.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.funbio.2010.04.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-07-01T00:00:00Z"}}, {"id": "10.1016/j.jbiotec.2023.07.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:49Z", "type": "Journal Article", "created": "2023-07-25", "title": "Fast and reliable method to estimate global DNA methylation in plants and fungi with high-pressure liquid chromatography (HPLC)-ultraviolet detection and even more sensitive one with HPLC-mass spectrometry", "description": "DNA (Deoxyribonucleic acid) methylation is one of the epigenetic modifications of DNA, acting as a bridge between genotype and phenotype. Thus, disruption of DNA methylation pattern has tremendous consequences for organism development. Current methods to determine DNA methylation suffer from methodological drawbacks like high requirement of DNA and poor reproducibility of chromatograms. Here we provide a fast and reliable method using high-pressure liquid chromatography (HPLC)-ultraviolet (UV) detector and even more sensitive one with HPLC- mass spectrometry (MS) and we test this method with various plant and fungal DNA isolates. We optimized the preparation of the DNA degradation step to decrease background noise, we improved separation conditions to provide reliable and reproducible chromatograms and conditions to measure nucleotides in HPLC-MS. We showed that global DNA methylation level can be accurately and reproducibly measured with as little as 0.2\u00a0\u00b5M for HPLC-UV and 0.02\u00a0\u00b5M for HPLC-MS of methylated cytosine.", "keywords": ["Chromatography", "Plant DNA", "DNA methylation", "ta1183", "ta1182", "Fungi", "610", "Reproducibility of Results", "DNA Methylation", "Mass Spectrometry", "Fungal DNA", "chromatography", "DNA", " Fungal", "ta116", "Chromatography", " High Pressure Liquid"]}, "links": [{"href": "https://doi.org/10.1016/j.jbiotec.2023.07.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jbiotec.2023.07.008", "name": "item", "description": "10.1016/j.jbiotec.2023.07.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jbiotec.2023.07.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-09-01T00:00:00Z"}}, {"id": "10.1111/nph.15014", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:47Z", "type": "Journal Article", "created": "2018-02-09", "title": "Native soils with their microbiotas elicit a state of alert in tomato plants", "description": "Summary
Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas.
Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium).
Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam\uffe2\uff80\uff90disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.
The \uffe2\uff80\uff98state of alert\uffe2\uff80\uff99 detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.
", "keywords": ["0301 basic medicine", "Proteome", "Propanols", "Arbuscular mycorrhizal fungi", "arbuscular mycorrhizal fungi", "tomato", "Lignin", "Models", " Biological", "Plant Roots", "defence responses", "Tomato", "Soil", "03 medical and health sciences", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Stress", " Physiological", "microbiota", "Plant Immunity", "Soil Microbiology", "suppressive and conducive soils", "susceptible and resistant genotypes", "2. Zero hunger", "0303 health sciences", "Defence responses", "Microbiota", "15. Life on land", "Lignin biosynthesis", "Gene Ontology", "Susceptible and resistant genotypes", "Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science", "Suppressive and conducive soils", "Transcriptome", "lignin biosynthesis"]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1660820/1/Chialva%20et%20al%20Iris.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014"}, {"href": "https://doi.org/10.1111/nph.15014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.15014", "name": "item", "description": "10.1111/nph.15014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.15014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-09T00:00:00Z"}}, {"id": "10.1111/nph.15230", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:48Z", "type": "Journal Article", "created": "2018-05-28", "title": "Partner communication and role of nutrients in the arbuscular mycorrhizal symbiosis", "description": "Contents Summary 1031 I. Introduction 1031 II. Interkingdom communication enabling symbiosis 1032 III. Nutritional and regulatory roles for key metabolites in the AM symbiosis 1035 IV. The plant\uffe2\uff80\uff93fungus genotype combination determines the outcome of the symbiosis 1039 V. Perspectives 1039 Acknowledgements 1041 References 1041
SummaryThe evolutionary and ecological success of the arbuscular mycorrhizal (AM) symbiosis relies on an efficient and multifactorial communication system for partner recognition, and on a fine\uffe2\uff80\uff90tuned and reciprocal metabolic regulation of each symbiont to reach an optimal functional integration. Besides strigolactones, N\uffe2\uff80\uff90acetylglucosamine\uffe2\uff80\uff90derivatives released by the plant were recently suggested to trigger fungal reprogramming at the pre\uffe2\uff80\uff90contact stage. Remarkably, N\uffe2\uff80\uff90acetylglucosamine\uffe2\uff80\uff90based diffusible molecules also are symbiotic signals produced by AM fungi (AMF) and clues on the mechanisms of their perception by the plant are emerging. AMF genomes and transcriptomes contain a battery of putative effector genes that may have conserved and AMF\uffe2\uff80\uff90 or host plant\uffe2\uff80\uff90specific functions. Nutrient exchange is the key feature of AM symbiosis. A mechanism of phosphate transport inside fungal hyphae has been suggested, and first insights into the regulatory mechanisms of root colonization in accordance with nutrient transfer and status were obtained. The recent discovery of the dependency of AMF on fatty acid transfer from the host has offered a convincing explanation for their obligate biotrophism. Novel studies highlighted the importance of plant and fungal genotypes for the outcome of the symbiosis. These findings open new perspectives for fundamental research and application of AMF in agriculture.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Nitrogen", "Phosphorus", "Plants", "15. Life on land", "symbiosis", "lipids", "03 medical and health sciences", "nutrients", "Mycorrhizae", "arbuscular mycorrhizal fungi (AMF)", "Metabolome", "natural variation", "signalling", "Symbiosis", "effectors", "phosphate"]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1667502/1/Pre-print%20IRIS_%20review%20New%20Phytol%202018.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15230"}, {"href": "https://doi.org/10.1111/nph.15230"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.15230", "name": "item", "description": "10.1111/nph.15230", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.15230"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-05-28T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2024.134231", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:54Z", "type": "Journal Article", "created": "2024-04-06", "title": "Soil microbial community fragmentation reveals indirect effects of fungicide exposure mediated by biotic interactions between microorganisms", "description": "Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.", "keywords": ["2. Zero hunger", "570", "Bacteria", "hymexazol", "[SDV]Life Sciences [q-bio]", "Microbiota", "Fungi", "500", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "15. Life on land", "Fungicides", " Industrial", "[SDV] Life Sciences [q-bio]", "nitrogen cycling", "13. Climate action", "network", "ammonia-oxidizing microorganism", "Soil Pollutants", "Microbial Interactions", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "pesticide", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2024.134231"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2024.134231", "name": "item", "description": "10.1016/j.jhazmat.2024.134231", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2024.134231"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-05-01T00:00:00Z"}}, {"id": "10.1016/j.mib.2019.08.004", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:57Z", "type": "Journal Article", "created": "2019-10-22", "title": "The mycobiota: fungi take their place between plants and bacteria", "description": "Eukaryotes host numerous intracellular and associated microbes in their microbiota. Fungi, the so-called Mycobiota, are important members of both human and plant microbiota. Moreover, members of the plant mycobiota host their own microbiota on their surfaces and inside their hyphae. The microbiota of the mycobiota includes mycorrhizal helper bacteria (for mycorrhizal fungi) and fungal endobacteria, which are critical for the fungal host and, as such, likely affect the plant. This review discusses the contribution that these often-overlooked members make to the composition and performance of the plant microbiota.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Bacteria", "Host Microbial Interactions", "RNA", " Ribosomal", " 16S", "Fungi", "Microbial Interactions", "Plants", "Bacterial Physiological Phenomena", "Symbiosis", "Phylogeny", "Mycobiome"], "contacts": [{"organization": "Bonfante P., Venice F., Lanfranco L.,", "roles": ["creator"]}]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1728500/7/Bonfante%2c%20Venice%20and%20Lanfranco_Current%20Opinion%20Author%20final%20version.pdf"}, {"href": "https://doi.org/10.1016/j.mib.2019.08.004"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Opinion%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.mib.2019.08.004", "name": "item", "description": "10.1016/j.mib.2019.08.004", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.mib.2019.08.004"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2016.07.135", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:06Z", "type": "Journal Article", "created": "2016-07-27", "title": "Biochar Decreased Microbial Metabolic Quotient And Shifted Community Composition Four Years After A Single Incorporation In A Slightly Acid Rice Paddy From Southwest China", "description": "While numerous studies both in laboratory and field have showed short term impacts of biochar on soil microbial community, there have been comparatively few reports addressing its long term impacts particular in field condition. This study investigated the changes of microbial community activity and composition in a rice paddy four years after a single incorporation of biochar at 20 and 40t/ha. The results indicated that biochar amendment after four years increased soil pH, soil organic C (SOC), total N and C/N ratio and decreased bulk density, particularly for the 40t/ha treatment compared to the control (0t/ha). Though no significant difference was observed in soil basal respiration, biochar amendment increased soil microbial biomass C and resulted in a significantly lower metabolic quotient. Besides, dehydrogenase and \u03b2-glucosidase activities were significantly decreased under biochar amendment relative to the control. The results of Illumina Miseq sequencing showed that biochar increased \u03b1-diversity of bacteria but decreased that of fungi and changed both bacterial and fungal community structures significantly. Biochar did not change the relative abundances of majority of bacteria at phylum level with the exception of a significant reduction of Actinobacteria, but significantly changed most of bacterial groups at genus level, particularly at 40t/ha. In contrast, biochar significantly decreased the relative abundances of Ascomycota and Basidiomycota by 11% and 66% and increased the relative abundances of Zygomycota by 147% at 40t/ha compared to the non-amended soil. Redundancy analysis (RDA) indicated that biochar induced changes in soil chemical properties, such as pH, SOC and C/N, were important factors driving community composition shifts. This study suggested that biochar amendment may increase microbial C use efficiency and reduce some microorganisms that are capable of decomposing more recalcitrant soil C, which may help stabilization of soil organic matter in paddy soil in long term.", "keywords": ["2. Zero hunger", "China", "Microbiota", "Fungi", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "Bacterial Physiological Phenomena", "6. Clean water", "Soil", "Biodegradation", " Environmental", "13. Climate action", "Charcoal", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Seasons", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2016.07.135"}, {"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.2016.07.135", "name": "item", "description": "10.1016/j.scitotenv.2016.07.135", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2016.07.135"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-11-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2009.08.045", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:04Z", "type": "Journal Article", "created": "2009-09-23", "title": "Application Of Temporal Temperature Gradient Gel Electrophoresis For Characterisation Of Fungal Endophyte Communities Of Salix Caprea L. In A Heavy Metal Polluted Soil", "description": "Fungal endophytes can affect the heavy metal uptake of their host plants and increase the tolerance of their host plants to heavy metal stress. Therefore, in the present study, a wide-range screening of the fungal endophyte communities was conducted to determine the fungal distribution and diversity on S. caprea roots on a metal polluted site. Fungal communities were screened using amplification with the 5.8S-ITS2-28S part of the rDNA operon, with the resulting amplicons analysed by temporal temperature gradient gel electrophoresis (TTGE) and sequencing. This technique is reproducible and shows good coverage of ascomycete and basidiomycete taxa, as 68% and 32% of all of the sequences, respectively. No clear shift in fungal ITS-TTGE profiles from S. caprea roots was seen along the secondary succession stages. Ascomycetes dominated the more polluted plots, while there was a greater diversity of basidiomycetes in the less polluted and control plots, suggesting greater tolerance of ascomycetes in comparison with basidiomycete fungi. The high diversity of DSEs was confirmed at the highly metal-enriched locations, with species belonging to the genera Phialophora, Phialocephala and Leptodontidium. Furthermore, the DSE colonisation of S. caprea roots and the frequency of the sequences showing affinity towards DSE genus Phialophora, showed good correspondence with soil Pb, Cd and plant-available P concentrations, possibly indicating that DSEs improve metal tolerance of willows to high heavy metal contamination.", "keywords": ["Electrophoresis", " Agar Gel", "0301 basic medicine", "dark septate endophytes", "Fungi", "Temperature", "mycorrhiza", "Salix", "04 agricultural and veterinary sciences", "info:eu-repo/classification/udc/581", "15. Life on land", "heavy metal pollution", "community fingerprinting", "Soil", "03 medical and health sciences", "13. Climate action", "Metals", " Heavy", "Soil Pollutants", "0401 agriculture", " forestry", " and fisheries", "DNA", " Fungal", "Phylogeny", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2009.08.045"}, {"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.2009.08.045", "name": "item", "description": "10.1016/j.scitotenv.2009.08.045", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2009.08.045"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-12-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2013.07.064", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:04Z", "type": "Journal Article", "created": "2013-08-19", "title": "Effect Of Long Term Organic Amendments And Vegetation Of Vineyard Soils On The Microscale Distribution And Biogeochemistry Of Copper", "description": "In this study we evaluated the effect of the long term organic management of a vineyard-soil on the biogeochemistry of copper at the micro-aggregate scale. The model vineyard-soil (M\u00e2con-France) experienced a long-term field-experiment that consisted in amendments and vegetations with various materials and plants. We studied specifically the effect of Straw (S) and Conifer Compost (CC) organic amendments and Clover (Cl) and Fescue (F) vegetation on the fate of copper (fungicide) in the surface layer of this loamy soil, through a comparison with the Non Amended soil (NA). After collection the five soils were immediately physically fractionated in order to obtain 5 granulometric size-fractions. All soils and size-fractions were quantitatively characterized in terms of granulometry, chemical content and copper distribution, speciation and bioavailability to bacteria and plants. The results showed strong increases of soil-constituents aggregation for all treatments (Cl>CC>S>F>NA), in relation with the increased cementation of soil-constituents by organic matter (OM). The distribution patterns of all major elements and organic carbon were found highly variable within the soil sub-fractions and also between the 5 treatments. Due to their specific inorganic and organic composition, soil sub-fractions can thus be considered as a specific microbial habitat. Added OM accumulated preferentially in the 20-2 \u03bcm and in the >250 \u03bcm of the 5 soils. The distribution patterns of copper as well as its speciation and bioavailability to bacteria in the soil sub-fractions were shown to be strongly different among the five soils, in relation with OM distribution. Our results also suggest that Cu-bioavailability to plants is controlled by soil-rhizosphere structure. Altogether our results permitted to show that long-term organic management of a vineyard soil induced stable modifications of soil physical and chemical properties at both macro and micro-scales. These modifications affected in turn the micro-scale biogeochemistry of copper, and especially its bioavailability to bacteria and plants.", "keywords": ["2. Zero hunger", "Organic Agriculture", "Bacteria", "Spectrophotometry", " Atomic", "Biological Availability", "04 agricultural and veterinary sciences", "Plants", "15. Life on land", "01 natural sciences", "Fungicides", " Industrial", "Soil", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "France", "Seasons", "Copper", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2013.07.064"}, {"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.2013.07.064", "name": "item", "description": "10.1016/j.scitotenv.2013.07.064", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2013.07.064"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-01-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2014.07.098", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:05Z", "type": "Journal Article", "created": "2014-08-12", "title": "Effects Of Different Types Of N Deposition On The Fungal Decomposition Activities Of Temperate Forest Soils", "description": "Nitrogen (N) deposition significantly affects soil microbial activities and litter decomposition processes in forest ecosystems. However, the changes in soil fungi during litter decomposition remain unclear. In this study, ammonium nitrate was selected as inorganic N (IN), whereas urea and glycine were selected as organic N (ON). N fertilizer with different IN-to-ON ratios (1:4, 2:3, 3:2, 4:1, and 5:0) was mixed in equal amounts and then added to temperate forest soils. Half of each treatment was simultaneously added with streptomycin to inhibit soil bacteria. The activities of enzymes involved in litter decomposition (invertase, \u03b2-glucosidase, cellulase, polyphenol oxidase, and phosphatase) were assayed after a three-year field experiment. The results showed that enzymatic activities were inhibited by IN addition but accelerated by ON addition in the non-antibiotic addition treatments. An increase in ON in the mixed N fertilizer also shifted enzymatic activities from N inhibition to N stimulation. Similarly, in the antibiotic addition treatments, fungal activities revealed the same trends, but they were seriously inhibited by IN and significantly accelerated by ON. These results indicated that soil fungi were more sensitive to N deposition, particularly to ON. A large amount of ON may convert soil microbial communities into a fungi-dominated system. However, excessive ON deposition (20% IN+80% ON) caused N saturation and repressed fungal activities. These results suggested that soil fungi were sensitive to N type and that different IN-to-ON ratios may induce diverse ecological effects on soil fungi.", "keywords": ["beta-Fructofuranosidase", "Nitrogen", "Fungi", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "Forests", "Nitrogen Cycle", "15. Life on land", "01 natural sciences", "Ecosystem", "Soil Microbiology", "6. Clean water", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Guo Lida, Kaiyue Qu, He Jianping, Shushan Li, Peng Guo, Yuhan Du,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2014.07.098"}, {"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.2014.07.098", "name": "item", "description": "10.1016/j.scitotenv.2014.07.098", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2014.07.098"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-11-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2019.01.095", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:07Z", "type": "Journal Article", "created": "2019-01-10", "title": "The Cover Crop Determines The Amf Community Composition In Soil And In Roots Of Maize After A Ten-Year Continuous Crop Rotation", "description": "Intensive agricultural practices are responsible for soil biological degradation. By stimulating indigenous arbuscular mycorrhizal fungi (AMF), cover cropping enhances soil health and promotes agroecosystem sustainability. Still, the legacy effects of cover crops (CCs) and the major factors driving the AM fungal community are not well known; neither is the influence of the specific CC. This work describes a field experiment established in Central Spain to test the effect of replacing winter fallow by barley (Hordeum vulgare L.) or vetch (Vicia sativa L.) during the intercropping of maize (Zea mays L.). We examined the community composition of the AMF in the roots and rhizosphere soil associated with the subsequent cash crop after 10\u202fyears of cover cropping, using Illumina technology. The multivariate analysis showed that the AMF communities under the barley treatment differed significantly from those under fallow, whereas no legacy effect of the vetch CC was detected. Soil organic carbon, electrical conductivity, pH, Ca and microbial biomass carbon were identified as major factors shaping soil AMF communities. Specific AMF taxa were found to play a role in plant uptake of P, Fe, Zn, Mn, and Cd, which may shed light on the functionality of these taxa. In our conditions, the use of barley as a winter CC appears to be an appropriate choice with respect to promotion of AMF populations and biological activity in agricultural soils with intercropping systems. However, more research on CC species and their legacy effect on the microbial community composition and functionality are needed to guide decisions in knowledge-based agriculture.", "keywords": ["Crops", " Agricultural", "2. Zero hunger", "Diversity", "Cover cropping", "Grass", "Arbuscular mycorrhizal fungi", "Agriculture", "Hordeum", "04 agricultural and veterinary sciences", "15. Life on land", "Plant Roots", "Zea mays", "Crop Production", "Legume", "Spain", "Long-term experiment", "Mycorrhizae", "Long-term experiments", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Illumina technology", "Mediterranean climate", "Soil Microbiology", "Mycobiome"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2019.01.095"}, {"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.2019.01.095", "name": "item", "description": "10.1016/j.scitotenv.2019.01.095", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2019.01.095"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2023.165179", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:09Z", "type": "Journal Article", "created": "2023-06-28", "title": "Intensive vegetable production under plastic mulch: A field study on soil plastic and pesticide residues and their effects on the soil microbiome", "description": "Intensive agriculture relies on external inputs to reach high productivity and profitability. Plastic mulch, mainly in the form of Low-Density Polyethylene (LDPE), is widely used in agriculture to decrease evaporation, increase soil temperature and prevent weeds. The incomplete removal of LDPE mulch after use causes plastic contamination in agricultural soils. In conventional agriculture, the use of pesticides also leaves residues accumulating in soils. Thus, the objective of this study was to measure plastic and pesticide residues in agricultural soils and their effects on the soil microbiome. For this, we sampled soil (0-10\u00a0cm and 10-30\u00a0cm) from 18 parcels from 6 vegetable farms in SE Spain. The farms were under either organic or conventional management, where plastic mulch had been used for >25\u00a0years. We measured the macro- and micro-light density plastic debris contents, the pesticide residue levels, and a range of physiochemical properties. We also carried out DNA sequencing on the soil fungal and bacterial communities. Plastic debris (>100\u00a0\u03bcm) was found in all samples with an average number of 2\u00a0\u00d7\u00a0103\u00a0particles\u00a0kg-1 and area of 60\u00a0cm2\u00a0kg-1. We found 4-10 different pesticide residues in all conventional soils, for an average of 140\u00a0\u03bcg\u00a0kg-1. Overall, pesticide content was \u223c100 times lower in organic farms. The soil microbiomes were farm-specific and related to different soil physicochemical parameters and contaminants. Regarding contaminants, bacterial communities responded to the total pesticide residues, the fungicide Azoxystrobin and the insecticide Chlorantraniliprole as well as the plastic area. The fungicide Boscalid was the only contaminant to influence the fungal community. The wide spread of plastic and pesticide residues in agricultural soil and their effects on soil microbial communities may impact crop production and other environmental services. More studies are required to evaluate the total costs of intensive agriculture.", "keywords": ["2. Zero hunger", "Plastic mulch", "Soil microbiome", "Microbiota", "Microplastic", "Pesticide Residues", "Pesticides residues", "Agriculture", "12. Garantizar modalidades de consumo y producci\u00f3n sostenibles", "15. Life on land", "Fungicides", " Industrial", "Edafolog\u00eda y Qu\u00edmica Agr\u00edcola", "Soil", "Intensive vegetable production", "13. Climate action", "Agriculture contamination", "Polyethylene", "Vegetables", "31 Ciencias Agrarias::3101 Agroqu\u00edmica", "Pesticides"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2023.165179"}, {"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.2023.165179", "name": "item", "description": "10.1016/j.scitotenv.2023.165179", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2023.165179"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2024.175008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:10Z", "type": "Journal Article", "created": "2024-07-23", "title": "Mycorrhizal association controls soil carbon-degrading enzyme activities and soil carbon dynamics under nitrogen addition: A systematic review", "description": "Recent evidence suggests that changes in carbon-degrading extracellular enzyme activities (C-EEAs) can help explain soil organic carbon (SOC) dynamics under nitrogen (N) addition. However, the factors controlling C-EEAs remain unclear, impeding the inclusion of microbial mechanisms in global C cycle models. Using meta-analysis, we show that the responses of C-EEAs to N addition were best explained by mycorrhizal association across a wide range of environmental and experimental factors. In ectomycorrhizal (ECM) dominated ecosystems, N addition suppressed C-EEAs targeting the decomposition of structurally complex macromolecules by 13.1\u00a0%, and increased SOC stocks by 5.2\u00a0%. In contrast, N addition did not affect C-EEAs and SOC stocks in arbuscular mycorrhizal (AM) dominated ecosystems. Our results indicate that earlier studies may have overestimated SOC changes under N addition in AM-dominated ecosystems and underestimated SOC changes in ECM-dominated ecosystems. Incorporating this mycorrhizal-dependent impact of EEAs on SOC dynamics into Earth system models could improve predictions of SOC dynamics under environmental changes.", "keywords": ["Free-living decomposers", "2. Zero hunger", "Soil organic carbon", "Nitrogen", "Nitrogen availability", "15. Life on land", "Carbon", "Carbon Cycle", "Soil", "13. Climate action", "Mycorrhizae", "Soil extracellular enzyme", "Mycorrhizal fungi", "Soil Microbiology", "Ecosystem"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2024.175008"}, {"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.2024.175008", "name": "item", "description": "10.1016/j.scitotenv.2024.175008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.175008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-10-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2024.177557", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:10Z", "type": "Journal Article", "created": "2024-11-20", "title": "Dynamic response of soil microbial communities and network to hymexazol exposure", "description": "Fungicides are an essential component of current agricultural practices, but their extensive use has raised concerns about their effects on non-target soil microorganisms, which carry out essential ecosystem functions. However, despite the complexity of microbial communities, many studies investigating their response to fungicides focus only on bacteria or fungi at one point in time. In this study, we used amplicon sequencing to assess the effect of the fungicide hymexazol on the diversity, composition, and co-occurrence network of soil bacteria, fungi, and protists at 7, 21, and 60\u00a0days after application. We found that hymexazol had very little effect on microbial alpha-diversity, but that microbial community composition and OTU differential abundance were altered over the duration of the experiment, even after hymexazol concentrations were undetectable. The co-occurrence patterns within and between microbial kingdoms were affected by hymexazol dose, suggesting that indirect effects may play a role in the microbial community response. Nitrogen cycling was also affected, with a transient hymexazol-associated increase in the abundance of ammonia-oxidizing microorganisms and soil nitrate concentration. These findings highlight that the effects of fungicides on soil microorganisms are dynamic and extensive, spanning several taxonomic kingdoms.", "keywords": ["570", "Bacteria", "Fungicide", "Microbiota", "Fungi", "Protists", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "Nitrification", "630", "Fungicides", " Industrial", "Pesticide", "Soil", "Soil Pollutants", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "Soil Microbiology", "Nitrogen cycling"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2024.177557"}, {"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.2024.177557", "name": "item", "description": "10.1016/j.scitotenv.2024.177557", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.177557"}, {"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.2007.02.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:14Z", "type": "Journal Article", "created": "2007-03-13", "title": "Nitrogen Fertilization Reduces Diversity And Alters Community Structure Of Active Fungi In Boreal Ecosystems", "description": "Nitrogen (N) availability is increasing in many ecosystems due to anthropogenic disturbance. We used a nucleotide analog technique and sequencing of ribosomal RNA genes to test whether N fertilization altered active fungal communities in two boreal ecosystems. In decaying litter from a recently burned spruce forest, Shannon diversity decreased significantly with N fertilization, and taxonomic richness declined from 44 to 33 operational taxonomic units (OTUs). In soils from a mature spruce forest, richness also declined with N fertilization, from 67 to 52 OTUs. Fungal community structure in litter differed significantly with N fertilization, primarily because fungi of the order Ceratobasidiales increased in abundance. We observed similar changes in fungal diversity and community structure with starch addition to litter, suggesting that N fertilization may affect fungal communities by altering plant carbon inputs. These changes could have important consequences for ecosystem processes such as decomposition and nutrient mineralization.", "keywords": ["ribosomal genes", "0301 basic medicine", "nucleotide analog", "carbon", "04 agricultural and veterinary sciences", "15. Life on land", "nitrogen", "diversity", "03 medical and health sciences", "fertilization", "litter quality", "0401 agriculture", " forestry", " and fisheries", "fungi", "boreal forest", "community structure"]}, "links": [{"href": "https://escholarship.org/content/qt2rs399mh/qt2rs399mh.pdf"}, {"href": "https://doi.org/10.1016/j.soilbio.2007.02.001"}, {"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.2007.02.001", "name": "item", "description": "10.1016/j.soilbio.2007.02.001", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2007.02.001"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-08-01T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Fungi&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Fungi&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Fungi&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Fungi&offset=50", "hreflang": "en-US"}], "numberMatched": 329, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-04-16T06:41:49.193979Z"}