We studied the dominant protists found in soils across the globe and their contributions to belowground food webs.
Long\uffe2\uff80\uff90term elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long\uffe2\uff80\uff90term N input alone or in combination with phosphorus (P) and potassium (K) is poorly understood. We explored the effect of long\uffe2\uff80\uff90term N and NPK fertilization on soil bacterial diversity and community composition using meta\uffe2\uff80\uff90analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effect of N fertilization on bacterial diversity varied with soil texture and water management, but was independent of crop type or N application rate. Changes in bacterial diversity were positively related to both soil pH and organic C content under N fertilization alone, but only to soil organic C under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long\uffe2\uff80\uff90term N fertilization. Nitrogen fertilization increased the relative abundance of Proteobacteria and Actinobacteria, but reduced the abundance of Acidobacteria, consistent with the general life history strategy theory for bacteria. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long\uffe2\uff80\uff90term N and NPK fertilization that differentially affects bacterial diversity and community composition provides a reference for nutrient management strategies for maintaining belowground microbial diversity in agro\uffe2\uff80\uff90ecosystems worldwide.
", "keywords": ["2. Zero hunger", "Nitrogen", "Microbiota", "Agriculture", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Actinobacteria", "13. Climate action", "Proteobacteria", "Potassium", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/gcb.14163"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/gcb.14163", "name": "item", "description": "10.1111/gcb.14163", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.14163"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-25T00:00:00Z"}}, {"id": "10.1111/gcb.17522", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-24T16:19:23Z", "type": "Journal Article", "created": "2024-10-03", "title": "Recovery of Soil Microbial Metabolism After Rewetting Depends on Interacting Environmental Conditions and Changes in Functional Groups and Life History Strategies", "description": "ABSTRACTClimate change is causing an intensification of soil drying and rewetting events, altering microbial functioning and potentially destabilizing soil organic carbon. After rewetting, changes in microbial community carbon use efficiency (CUE), investment in life history strategies, and fungal to bacterial dominance co\uffe2\uff80\uff90occur. Still, we have yet to generalize what drives these dynamic responses. Here, we collated 123 time series of microbial community growth (G, sum of fungal and bacterial growth, evaluated by leucine and acetate incorporation, respectively) and respiration (R) after rewetting and calculated CUE\uffe2\uff80\uff89=\uffe2\uff80\uff89G/(G\uffe2\uff80\uff89+\uffe2\uff80\uff89R). First, we characterized CUE recovery by two metrics: maximum CUE and time to maximum CUE. Second, we translated microbial growth and respiration data into microbial investments in life history strategies (high yield (Y), resource acquisition (A), and stress tolerance (S)). Third, we characterized the temporal change in fungal to bacterial dominance. Finally, the metrics describing the CUE recovery, investment in life history strategies, and fungal to bacterial dominance after rewetting were explained by environmental factors and microbial properties. CUE increased after rewetting as fungal dominance declined, but the maximum CUE was explained by the CUE under moist conditions, rather than specific environmental factors. In contrast, higher soil pH and carbon availability accelerated the decline of microbial investment in stress tolerance and fungal dominance. We conclude that microbial CUE recovery is mostly driven by the shifting microbial community composition and the metabolic capacity of the community, whereas changes in microbial investment in life history strategies and fungal versus bacterial dominance depend on soil pH and carbon availability.Warming alters soil microbial traits through ecological and evolutionary processes, directly influencing the decomposition of organic matter, which significantly affects global soil carbon emissions. Yet, soil carbon models largely ignore these processes and their implications for global responses to warming. Here, we incorporate eco\uffe2\uff80\uff90evolutionary theory into a mechanistic model describing microbial soil carbon decomposition to address the question of whether such processes could have consequential effects on climate carbon feedbacks globally. We assume that a key trait of microbes, their resource allocation to production of exoenzymes (which facilitate decomposition of organic matter)\uffe2\uff80\uff94is optimized to environmental temperatures by natural selection. We find that eco\uffe2\uff80\uff90evolutionary optimization results in microbes allocating more resources to enzyme production under warming. When applied at the global scale, eco\uffe2\uff80\uff90evolutionary optimization enhances the biological realism of soil carbon models and significantly amplifies global soil carbon loss by 2100. Our results highlight the significant potential of microbial eco\uffe2\uff80\uff90evolutionary responses to influence carbon cycle feedbacks to climate change, and motivate an urgent need for more comprehensive data to accurately quantify the adaptive potential of microbiomes in response to climate change.In Arctic regions, thawing permafrost soils are projected to release 50 to 250 Gt of carbon by 2100. This data is mostly derived from carbon\uffe2\uff80\uff90rich wetlands, although 71% of this carbon pool is stored in faster\uffe2\uff80\uff90thawing mineral soils, where ecosystems close to the outer boundaries of permafrost regions are especially vulnerable. Although extensive data exists from currently thawing sites and short\uffe2\uff80\uff90term thawing experiments, investigations of the long\uffe2\uff80\uff90term changes following final thaw and co\uffe2\uff80\uff90occurring drainage are scarce. Here we show ecosystem changes at two comparable tussock tundra sites with distinct permafrost thaw histories, representing 15 and 25\uffc2\uffa0years of natural drainage, that resulted in a 10\uffe2\uff80\uff90fold decrease in CH4 emissions (3.2\uffc2\uffa0\uffc2\uffb1\uffc2\uffa02.2 vs. 0.3\uffc2\uffa0\uffc2\uffb1\uffc2\uffa00.4\uffc2\uffa0mg C\uffe2\uff80\uff90CH4\uffc2\uffa0m\uffe2\uff88\uff922\uffc2\uffa0day\uffe2\uff88\uff921), while CO2 emissions were comparable. These data extend the time perspective from earlier studies based on short\uffe2\uff80\uff90term experimental drainage. The overall microbial community structures did not differ significantly between sites, although the drier top soils at the most advanced site led to a loss of methanogens and their syntrophic partners in surface layers while the abundance of methanotrophs remained unchanged. The resulting deeper aeration zones likely increased CH4 oxidation due to the longer residence time of CH4 in the oxidation zone, while the observed loss of aerenchyma plants reduced CH4 diffusion from deeper soil layers directly to the atmosphere. Our findings highlight the importance of including hydrological, vegetation and microbial specific responses when studying long\uffe2\uff80\uff90term effects of climate change on CH4 emissions and underscores the need for data from different soil types and thaw histories.Soil microbial communities in Chihuahuan Desert grasslands generally experience highly variable spatiotemporal rainfall patterns. Changes in precipitation regimes can affect belowground ecosystem processes such as decomposition and nutrient cycling by altering soil microbial community structure and function. The objective of this study was to determine if increased seasonal precipitation frequency and magnitude over a 7\uffe2\uff80\uff90year period would generate a persistent shift in microbial community characteristics and soil nutrient availability. We supplemented natural rainfall with large events (one/winter and three/summer) to simulate increased precipitation based on climate model predictions for this region. We observed a 2\uffe2\uff80\uff90year delay in microbial responses to supplemental precipitation treatments. In years 3\uffe2\uff80\uff935, higher microbial biomass, arbuscular mycorrhizae abundance, and soil enzyme C and P acquisition activities were observed in the supplemental water plots even during extended drought periods. In years 5\uffe2\uff80\uff937, available soil P was consistently lower in the watered plots compared to control plots. Shifts in soil P corresponded to higher fungal abundances, microbial C utilization activity, and soilpH. This study demonstrated that 25% shifts in seasonal rainfall can significantly influence soil microbial and nutrient properties, which in turn may have long\uffe2\uff80\uff90term effects on nutrient cycling and plant P uptake in this desert grassland.
", "keywords": ["precipitation manipulation", "Climate Change", "Rain", "extreme climate events", "Soil", "XXXXXX - Unknown", "Big Bend National Park", "Soil Microbiology", "2. Zero hunger", "Ecology", "Bacteria", "Microbiota", "Fungi", "04 agricultural and veterinary sciences", "Biological Sciences", "15. Life on land", "Grassland", "Texas", "6. Clean water", "desert ecosystems", "13. Climate action", "soil microbial communities", "0401 agriculture", " forestry", " and fisheries", "Seasons", "Desert Climate", "Environmental Sciences"]}, "links": [{"href": "https://escholarship.org/content/qt4v79d7f4/qt4v79d7f4.pdf"}, {"href": "https://doi.org/10.1111/gcb.12418"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/gcb.12418", "name": "item", "description": "10.1111/gcb.12418", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.12418"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-04-04T00:00:00Z"}}, {"id": "10.1093/femsec/fiaa119", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:00Z", "type": "Journal Article", "created": "2020-06-14", "title": "Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables", "description": "ABSTRACTMicrobes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.Domestic wastewater is a recognized source of antibiotic resistant bacteria and antibiotic resistance genes (ARB&ARGs), whose risk of transmission to humans cannot be ignored. The fitness of wastewater ARB in the complex fecal microbiota of a healthy human was investigated in feces-based microcosm assays (FMAs). FMAs were inoculated with two wastewater isolates, Escherichia coli strain A2FCC14 (MLST ST131) and Enterococcus faecium strain H1EV10 (MLST ST78), harboring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The FMAs, incubated in the presence or absence of oxygen or in the presence or absence of the antibiotics cefotaxime or vancomycin, were monitored based on cultivation, ARGs quantification and bacterial community analysis. The fecal bacterial community was dominated by members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The ARGs harbored by the wastewater isolates could be quantified after one week, in FMAs incubated under both aerobic and anaerobic conditions. These observations were not significantly different in FMAs incubated anaerobically, supplemented with sub-inhibitory concentrations of cefotaxime or vancomycin. The observation that ARGs of wastewater ARB persisted in presence of the human fecal microbiota for at least one week supports the hypothesis of a potential transmission to humans, a topic that deserves further investigation.
", "keywords": ["0301 basic medicine", "Microcosm assays", "0303 health sciences", "Bacteria", "Angiotensin-Converting Enzyme Inhibitors", "Wastewater", "Human fecal microbiota", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "Angiotensin Receptor Antagonists", "Feces", "03 medical and health sciences", "Antibiotic resistance genes", "Antibiotic resistant bacteria", "Genes", " Bacterial", "11. Sustainability", "Humans", "Antibiotic resistance transmission", "Microcosm effect", "Multilocus Sequence Typing"]}, "links": [{"href": "http://academic.oup.com/femsec/article-pdf/96/6/fiaa058/33327470/fiaa058.pdf"}, {"href": "https://doi.org/10.1093/femsec/fiaa058"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiaa058", "name": "item", "description": "10.1093/femsec/fiaa058", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiaa058"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-02T00:00:00Z"}}, {"id": "10.1093/femsec/fiad080", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:00Z", "type": "Journal Article", "created": "2023-07-21", "title": "Vegetation, topography, and soil depth drive microbial community structure in two Swedish grasslands", "description": "AbstractSoil microbial diversity and community composition are shaped by various factors linked to land management, topographic position, and vegetation. To study the effects of these drivers, we characterized fungal and bacterial communities from bulk soil at four soil depths ranging from the surface to below the rooting zone of two Swedish grasslands with differing land-use histories, each including both an upper and a lower catenary position. We hypothesized that differences in plant species richness and plant functional group composition between the four study sites would drive the variation in soil microbial community composition and correlate with microbial diversity, and that microbial biomass and diversity would decrease with soil depth following a decline in resource availability. While vegetation was identified as the main driver of microbial community composition, the explained variation was significantly higher for bacteria than for fungi, and the communities differed more between grasslands than between catenary positions. Microbial biomass derived from DNA abundance decreased with depth, but diversity remained relatively stable, indicating diverse microbial communities even below the rooting zone. Finally, plant-microbial diversity correlations were significant only for specific plant and fungal functional groups, emphasizing the importance of functional interactions over general species richness.Many experiments that measure the response of microbial communities to heavy metals increase metal concentrations abruptly in the soil. However, it is unclear whether abrupt additions mimic the gradual and often long-term accumulation of these metals in the environment where microbial populations may adapt. In a greenhouse experiment that lasted 26 months, we tested whether bacterial communities and soil respiration differed between soils that received an abrupt or a gradual addition of copper or no copper at all. Bacterial richness and other diversity indices were consistently lower in the abrupt treatment compared to the ambient treatment that received no copper. The abrupt addition of copper yielded different initial bacterial communities than the gradual addition; however, these communities appeared to converge once copper concentrations were approximately equal. Soil respiration in the abrupt treatment was initially suppressed but recovered after four months. Afterwards, respiration in both the gradual and abrupt treatments wavered between being below or equal to the ambient treatment. Overall, our study indicates that gradual and abrupt additions of copper can yield similar bacterial communities and respiration, but these responses may drastically vary until copper concentrations are equal.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Microbiota", "Bacterial Physiological Phenomena", "Soil", "03 medical and health sciences", "13. Climate action", "Metals", " Heavy", "Soil Pollutants", "Copper", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "http://academic.oup.com/femsec/article-pdf/95/1/fiy212/29189709/fiy212.pdf"}, {"href": "https://doi.org/10.1093/femsec/fiy212"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiy212", "name": "item", "description": "10.1093/femsec/fiy212", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiy212"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-10-23T00:00:00Z"}}, {"id": "10.1093/femsec/fiz133", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:01Z", "type": "Journal Article", "created": "2019-08-22", "title": "Restriction of plant roots in boreal forest organic soils affects the microbial community but does not change the dominance from ectomycorrhizal to saprotrophic fungi", "description": "ABSTRACTBoreal forest soils store significant amounts of carbon and are cohabited by saprotrophic and ectomycorrhizal fungi (ECM). The \uffe2\uff80\uff98Gadgil effect\uffe2\uff80\uff99 implies antagonistic interactions between saprotrophic fungi and ECM. Plant photosynthates support the competitive fitness of the ECM, and may also shape the soil bacterial communities. Many \uffe2\uff80\uff98Gadgil effect\uffe2\uff80\uff99 experiments have focused on litter layer (OL) or have litter and root-fragments present, and thus possibly favor the saprotrophs. We compared how the restriction of plant roots and exudates affect soil microbial community structures in organic soil (mixed OF and OH). For this, we established a 3-yr field experiment with 3 different mesh treatments affecting the penetration of plant roots and external fungal hyphae. Exclusion of plant photosynthates induced modest changes in both fungal and bacterial community structures, but not to potential functionality of the microbial community. The microbial community was resilient towards rather short-term disturbances. Contrary to the \uffe2\uff80\uff98Gadgil effect\uffe2\uff80\uff99, mesh treatments restricting the entrance of plant roots and external fungal hyphae did not favor saprotrophs that originally inhabited the soil. Thus, we propose that different substrate preferences (fresh litter vs. fermented or humified soil), rather than antagonism, maintain the spatial separation of saprotrophs and mycorrhizal fungi in boreal forest soils.
", "keywords": ["0301 basic medicine", "570", "Hyphae", "577", "Plant Roots", "ectomycorrhiza", "Trees", "Soil", "03 medical and health sciences", "boreal forest soil", "Mycorrhizae", "Taiga", "saprotrophs", "Soil Microbiology", "2. Zero hunger", "0303 health sciences", "Microbiota", "Fungi", "Plants", "15. Life on land", "Gadgil effect", "Carbon", "functional gene profile", "13. Climate action", "ta1181", "microbial community"]}, "links": [{"href": "http://academic.oup.com/femsec/article-pdf/95/9/fiz133/29808832/fiz133.pdf"}, {"href": "https://doi.org/10.1093/femsec/fiz133"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiz133", "name": "item", "description": "10.1093/femsec/fiz133", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiz133"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-23T00:00:00Z"}}, {"id": "10.1093/ismejo/wrae156", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-24T16:19:02Z", "type": "Journal Article", "created": "2024-08-06", "title": "Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates", "description": "AbstractSoils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3\uffe2\uff80\uff934 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%\uffe2\uff80\uff9330% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.Chemical exchange often serves as the first step in plant\uffe2\uff80\uff93microbe interactions and exchanges of various signals, nutrients, and metabolites continue throughout the interaction. Here, we highlight the role of metabolite exchanges and metabolic crosstalk in the microbiome\uffe2\uff80\uff93root\uffe2\uff80\uff93shoot\uffe2\uff80\uff93environment nexus. Roots secret a diverse set of metabolites; this assortment of root exudates, including secondary metabolites such as benzoxazinoids, coumarins, flavonoids, indolic compounds, and terpenes, shapes the rhizosphere microbiome. In turn, the rhizosphere microbiome affects plant growth and defense. These inter-kingdom chemical interactions are based on a metabolic circular economy, a seemingly wasteless system in which rhizosphere members exchange (i.e. consume, reuse, and redesign) metabolites. This review also describes the recently discovered phenomenon \uffe2\uff80\uff9cSystemically Induced Root Exudation of Metabolites\uffe2\uff80\uff9d in which the rhizosphere microbiome governs plant metabolism by inducing systemic responses that shift the metabolic profiles of root exudates. Metabolic exchange in the rhizosphere is based on chemical gradients that form specific microhabitats for microbial colonization and we describe recently developed high-resolution methods to study chemical interactions in the rhizosphere. Finally, we propose an action plan to advance the metabolic circular economy in the rhizosphere for sustainable solutions to the cumulative degradation of soil health in agricultural lands. There is widespread concern that cessation of grazing in historically grazed ecosystems is causing biotic homogenization and biodiversity loss. We used 12 montane grassland sites along an 800 km north\uffe2\uff80\uff93south gradient across the UK, to test whether cessation of grazing affects local \uffce\uffb1 - and \uffce\uffb2 -diversity of below-ground food webs. We show cessation of grazing leads to strongly decreased \uffce\uffb1 -diversity of most groups of soil microbes and fauna, particularly of relatively rare taxa. By contrast, the \uffce\uffb2 -diversity varied between groups of soil organisms. While most soil microbial communities exhibited increased homogenization after cessation of grazing, we observed decreased homogenization for soil fauna after cessation of grazing. Overall, our results indicate that exclusion of domesticated herbivores from historically grazed montane grasslands has far-ranging negative consequences for diversity of below-ground food webs. This underscores the importance of grazers for maintaining the diversity of below-ground communities, which play a central role in ecosystem functioning. Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology. Here, we performed metagenomic analyses on rocks from across Antarctica comprising >75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities potentially influencing bacterial adaptation and biogeochemistry. This catalog lays the foundation for expanding knowledge of the virosphere in extreme environments.An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the \uffe2\uff80\uff98cry\uffe2\uff80\uff90for\uffe2\uff80\uff90help\uffe2\uff80\uff99 hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto\uffe2\uff80\uff90extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by\uffe2\uff80\uff90products with a higher toxicity. We propose that the \uffe2\uff80\uff98cry\uffe2\uff80\uff90for\uffe2\uff80\uff90help\uffe2\uff80\uff99 mechanism could drive the exudation\uffe2\uff80\uff90mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Microbiota", "Minireviews", "15. Life on land", "Polychlorinated Biphenyls", "6. Clean water", "Soil", "03 medical and health sciences", "Biodegradation", " Environmental", "13. Climate action", "Soil Pollutants", "Environmental Pollution", "Soil Microbiology"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/857922/2/Rolli%20et%20al.%202021_EM.pdf"}, {"href": "https://air.unimi.it/bitstream/2434/857922/4/1462-2920.15647.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15647"}, {"href": "https://doi.org/10.1111/1462-2920.15647"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.15647", "name": "item", "description": "10.1111/1462-2920.15647", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.15647"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-23T00:00:00Z"}}, {"id": "10.1111/1751-7915.13654", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:16Z", "type": "Journal Article", "created": "2020-08-31", "title": "An underappreciated DIET for anaerobic petroleum hydrocarbon\u2010degrading microbial communities", "description": "Direct interspecies electron transfer (DIET) via electrically conductive minerals can play a role in the anaerobic oxidation of petroleum hydrocarbons in contaminated sites and can be exploited for the development of new, more effective bioremediation approaches.", "keywords": ["0301 basic medicine", "H100", "0303 health sciences", "petroleum hydrocarbon", "anaerobic degradation", "Microbiota", "H800", "Hydrocarbons", "6. Clean water", "DIET", "03 medical and health sciences", "Biodegradation", " Environmental", "Petroleum", "Soil Pollutants", "Anaerobiosis", "Crystal Ball", "TP248.13-248.65", "Biotechnology"]}, "links": [{"href": "https://nrl.northumbria.ac.uk/id/eprint/44983/8/1751-7915.13654.pdf"}, {"href": "https://iris.cnr.it/bitstream/20.500.14243/394172/1/An%20underappreciated%20DIET%20for%20anaerobic%20petroleum.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.13654"}, {"href": "https://eprints.ncl.ac.uk/fulltext.aspx?url=270998/E5D81B02-CB5D-4798-8D73-9D54E5057C34.pdf&pub_id=270998"}, {"href": "https://doi.org/10.1111/1751-7915.13654"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1751-7915.13654", "name": "item", "description": "10.1111/1751-7915.13654", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1751-7915.13654"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-30T00:00:00Z"}}, {"id": "10.1126/science.aay2832", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:49Z", "type": "Journal Article", "created": "2019-11-15", "title": "The role of multiple global change factors in driving soil functions and microbial biodiversity", "description": "Many factors influence global changeGlobal environmental change is driven by multiple natural and anthropogenic factors. With a focus on global change as it affects soils, Rilliget al.point out that nearly all published studies consider just one or two factors at a time (see the Perspective by Manning). In a laboratory experiment, they tested 10 drivers of global change both individually and in combination, at levels ranging from 2 to 10 factors. They found that soil properties, processes, and microbial communities could not be predicted from single-effect responses and that multiple factors in combination produced unsuspected responses. They concluded that single-factor studies remain important for uncovering mechanisms but that global change biology needs to embrace more fully the multitude of drivers impinging on ecosystems.
Science, this issue p.886; see also p.801
", "keywords": ["2. Zero hunger", "Soil", "13. Climate action", "Microbiota", "15. Life on land", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1126/science.aay2832"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1126/science.aay2832", "name": "item", "description": "10.1126/science.aay2832", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1126/science.aay2832"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-15T00:00:00Z"}}, {"id": "10.1111/jam.13606", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:43Z", "type": "Journal Article", "created": "2017-10-09", "title": "Soil Microbiota Respond To Green Manure In Organic Vineyards", "description": "The aim of this work was to investigate the effects of biodynamic management with and without the addition of green manure, in comparison with organic management, on the microbiota in vineyards soil.High throughput sequencing was used to compare the taxonomic structure of the soil bacterial and fungal communities from vineyards managed with different methods (organic, biodynamic or biodynamic with green manure). Our results showed that microbial communities associated with biodynamic and organic farming systems were very similar, while green manure was the greatest source of soil microbial biodiversity and significantly changed microbial richness and community composition compared with other soils. Green manure also significantly enriched bacterial taxa involved in the soil nitrogen cycle (e.g. Microvirga sp., Pontibacter sp. and Nitrospira sp.).Our results showed that the diversity and composition of the microbial communities associated with biodynamic and organic farming systems were similar, indicating that the use of biodynamic preparations 500 and 501 did not cause any significant detectable changes to the soil microbial community in the short term, while the effects of green manure were significant in soil microbiota.The microbiological richness and structure of soil are used as a sensitive indicator of soil quality. The extension of organic/biodynamic farming, associated with green manure application, could contribute to increase the abundance of functional groups of biological and agronomical relevance and maintaining microbial biodiversity in vineyard soils.", "keywords": ["0301 basic medicine", "2. Zero hunger", "570", "Microbial diversity", "Organic Agriculture", "0303 health sciences", "bacteria; biodynamic vineyard; fungi; green manure; microbial community structure; microbial diversity; organic vineyard; soil microbiology; soil vineyard", "Microbiota", "Green manure", "Microbial community structure", "Biodiversity", "15. Life on land", "630", "Manure", "Soil vineyard", "Soil", "03 medical and health sciences", "Soil microbiology", "13. Climate action", "Settore AGR/16 - MICROBIOLOGIA AGRARIA", "Vitis", "Soil Microbiology"]}, "links": [{"href": "https://iris.unitn.it/bitstream/11572/283669/1/jam.13606.pdf"}, {"href": "https://doi.org/10.1111/jam.13606"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Applied%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/jam.13606", "name": "item", "description": "10.1111/jam.13606", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/jam.13606"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-11-03T00:00:00Z"}}, {"id": "10.1111/mec.13620", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-06-24T16:19:43Z", "type": "Journal Article", "created": "2016-03-19", "title": "The Impact Of Tropical Forest Logging And Oil Palm Agriculture On The Soil Microbiome", "description": "AbstractSelective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land\uffe2\uff80\uff90use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once\uffe2\uff80\uff90logged and twice\uffe2\uff80\uff90logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell\uffe2\uff80\uff93cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land\uffe2\uff80\uff90use changes on the interaction of soil microbes.
", "keywords": ["0301 basic medicine", "Conservation of Natural Resources", "0303 health sciences", "Bacteria", "Microbiota", "Agriculture", "Forestry", "Biodiversity", "Arecaceae", "Forests", "15. Life on land", "03 medical and health sciences", "Borneo", "international", "RNA", " Ribosomal", " 16S", "Metagenome", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/mec.13620"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecular%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/mec.13620", "name": "item", "description": "10.1111/mec.13620", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/mec.13620"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-20T00:00:00Z"}}, {"id": "10.1111/nph.12569", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:44Z", "type": "Journal Article", "created": "2013-10-31", "title": "Experimental Drought Reduces The Transfer Of Recently Fixed Plant Carbon To Soil Microbes And Alters The Bacterial Community Composition In A Mountain Meadow", "description": "Summary
Drought affects plants and soil microorganisms, but it is still not clear how it alters the carbon (C) transfer at the plant\uffe2\uff80\uff93microbial interface. Here, we tested direct and indirect effects of drought on soil microbes and microbial turnover of recent plant\uffe2\uff80\uff90derived C in a mountain meadow.
Microbial community composition was assessed using phospholipid fatty acids (PLFAs); the allocation of recent plant\uffe2\uff80\uff90derived C to microbial groups was analysed by pulse\uffe2\uff80\uff90labelling of canopy sections with 13CO2 and the subsequent tracing of the label into microbial PLFAs.
Microbial biomass was significantly higher in plots exposed to a severe experimental drought. In addition, drought induced a shift of the microbial community composition, mainly driven by an increase of Gram\uffe2\uff80\uff90positive bacteria. Drought reduced belowground C allocation, but not the transfer of recently plant\uffe2\uff80\uff90assimilated C to fungi, and in particular reduced tracer uptake by bacteria. This was accompanied by an increase of 13C in the extractable organic C pool during drought, which was even more pronounced after plots were mown.
We conclude that drought weakened the link between plant and bacterial, but not fungal, C turnover, and facilitated the growth of potentially slow\uffe2\uff80\uff90growing, drought\uffe2\uff80\uff90adapted soil microbes, such as Gram\uffe2\uff80\uff90positive bacteria.
", "keywords": ["Time Factors", "Nitrogen", "Mowing", "Mountain grassland", "Carbon Cycle", "Microbial community composition", "Soil", "Biomass", "Ecosystem", "Soil Microbiology", "2. Zero hunger", "106022 Mikrobiologie", "Carbon Isotopes", "Drought", "Research", "Microbiota", "Water", "Carbon allocation", "Microclimate", "04 agricultural and veterinary sciences", "15. Life on land", "Carbon", "6. Clean water", "Droughts", "C pulse-labelling", "13. Climate action", "Austria", "Phospholipid fatty acids", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries"]}, "links": [{"href": "https://doi.org/10.1111/nph.12569"}, {"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.12569", "name": "item", "description": "10.1111/nph.12569", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.12569"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-10-31T00:00:00Z"}}, {"id": "10.1111/nph.15014", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:44Z", "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.15161", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:44Z", "type": "Journal Article", "created": "2018-04-19", "title": "Plant attributes explain the distribution of soil microbial communities in two contrasting regions of the globe", "description": "Summary
We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales.
Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities.
Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation.
Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres.
Microplastic effects in terrestrial ecosystems have recently moved into focus, after about a decade of research being limited to aquatic systems. While effects on soil physical properties and soil biota are starting to become apparent, there is not much information on the consequences for plant performance. We here propose and discuss mechanistic pathways through which microplastics could impact plant growth, either positively or negatively. These effects will vary as a function of plant species, and plastic type, and thus are likely to translate to changes in plant community composition and perhaps primary production. Our mechanistic framework serves to guide ongoing and future research on this important topic.", "keywords": ["2. Zero hunger", "Soil", "Food Safety", "Microbiota", "Microplastics", "0211 other engineering and technologies", "02 engineering and technology", "Plants", "15. Life on land", "Plant Roots", "01 natural sciences", "Ecosystem", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15794"}, {"href": "https://doi.org/10.1111/nph.15794"}, {"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.15794", "name": "item", "description": "10.1111/nph.15794", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.15794"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-29T00:00:00Z"}}, {"id": "10.1111/nph.18118", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:45Z", "type": "Journal Article", "created": "2022-03-26", "title": "Deciphering the role of specialist and generalist plant\u2013microbial interactions as drivers of plant\u2013soil feedback", "description": "SummaryFeedback between plants and soil microbial communities can be a powerful driver of vegetation dynamics. Plants elicit changes in the soil microbiome that either promote or suppress conspecifics at the same location, thereby regulating population density\uffe2\uff80\uff90dependence and species co\uffe2\uff80\uff90existence. Such effects are often attributed to the accumulation of host\uffe2\uff80\uff90specific antagonistic or beneficial microbiota in the rhizosphere. However, the identity and host\uffe2\uff80\uff90specificity of the microbial taxa involved are rarely empirically assessed. Here we review the evidence for host\uffe2\uff80\uff90specificity in plant\uffe2\uff80\uff90associated microbes and propose that specific plant\uffe2\uff80\uff93soil feedbacks can also be driven by generalists. We outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plant\uffe2\uff80\uff93soil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities. Identifying factors that promote specialization or generalism in plant\uffe2\uff80\uff93microbial interactions and thereby modulate the impact of microbiota on plant performance will advance our understanding of the mechanisms underlying plant\uffe2\uff80\uff93soil feedback and the ways it contributes to plant co\uffe2\uff80\uff90existence. Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s V = 0.857, and Theil\uffe2\uff80\uff99s U = 0.316). For species-level community profiling, we found strong correlations ( r s > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average r s = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.
IMPORTANCEA quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.
", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/10.1128/msystems.00859-24"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00859-24", "name": "item", "description": "10.1128/msystems.00859-24", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00859-24"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "10.1126/sciadv.aax8787", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:48Z", "type": "Journal Article", "created": "2020-01-25", "title": "The global-scale distributions of soil protists and their contributions to belowground systems", "description": "We studied the dominant protists found in soils across the globe and their contributions to belowground food webs.
Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even on Earth, the limitations imposed on microbial processes by saturation-level salinity have rarely been studied in situ . The microbiota of raw milk is affected by many factors that can control or promote the introduction of undesirable microorganisms. Chlorine-based cleaning agents have been commonly used due to their effectiveness in controlling undesirable microorganisms, but they have been associated with the formation of chlorine residues that are detrimental to product quality and may impact consumer health.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Geography", "Microbiota", "Dairy", "Dairying", "03 medical and health sciences", "Milk", "Food Microbiology", "Animals", "Equipment Contamination", "DNA sequencing", "Metagenomics", "Seasons", "Chlorine", "Ireland", "Disinfectants"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.01081-21"}, {"href": "https://doi.org/10.1128/aem.01081-21"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.01081-21", "name": "item", "description": "10.1128/aem.01081-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01081-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-28T00:00:00Z"}}, {"id": "10.1128/aem.02209-19", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:50Z", "type": "Journal Article", "created": "2019-12-04", "title": "Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous \u201cMost-Wanted\u201d Core Bacterial Taxon from Municipal Wastewater Treatment Plants", "description": "The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.
", "keywords": ["0301 basic medicine", "activated sludge microbiome", "DATABASE", "DIVERSITY", "nitrogen and phosphorus removal", "GENOME ANNOTATION", "POLYPHOSPHATE-ACCUMULATING ORGANISMS", "12. Responsible consumption", "ACTIVATED-SLUDGE", "03 medical and health sciences", "SEARCH", "RNA", " Ribosomal", " 16S", "11. Sustainability", "microbial network", "Phylogeny", "WWTP", "0303 health sciences", "IDENTIFICATION", "Sewage", "Microbiota", "Betaproteobacteria", "core taxa", "15. Life on land", "6. Clean water", "COMMUNITY", "RNA", " Bacterial", "Casimicrobium huifangae", "13. Climate action", "Earth and Environmental Sciences", "BIOLOGICAL PHOSPHORUS REMOVAL", "municipal wastewater treatment plant", "CARBON SOURCE"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.02209-19"}, {"href": "https://doi.org/10.1128/aem.02209-19"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.02209-19", "name": "item", "description": "10.1128/aem.02209-19", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02209-19"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-03T00:00:00Z"}}, {"id": "10.1128/aem.02218-17", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:50Z", "type": "Journal Article", "created": "2017-11-27", "title": "Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog", "description": "ABSTRACTOmbrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA -based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities.
IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects.
", "keywords": ["0301 basic medicine", "570", "oxidation", "hiili", "ta1172", "Euryarchaeota", "630", "Mining", "Soil", "03 medical and health sciences", "Sphagnum", "Bacterial Proteins", "Nitrogen Fixation", "Sphagnopsida", "14. Life underwater", "ennallistaminen", "turvemaat", "Ecosystem", "Phylogeny", "Soil Microbiology", "0303 health sciences", "nifH", "methane", "Microbiota", "ta1182", "land use", "methanogenesis", "15. Life on land", "Carbon", "kasvihuonekaasup\u00e4\u00e4st\u00f6t", "nitrogen fixation", "13. Climate action", "international", "Wetlands", "Oxygenases", "ta1181", "Methane", "Oxidation-Reduction"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.02218-17"}, {"href": "https://doi.org/10.1128/aem.02218-17"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.02218-17", "name": "item", "description": "10.1128/aem.02218-17", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02218-17"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-01T00:00:00Z"}}, {"id": "10.1128/msphere.00130-21", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:50Z", "type": "Journal Article", "created": "2021-08-11", "title": "Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield", "description": "Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield.
", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "Biological Products", "0303 health sciences", "Bacteria", "Microbiota", "Fungi", "High-Throughput Nucleotide Sequencing", "Agriculture", "Agricultural Inoculants", "15. Life on land", "Microbiology", "QR1-502", "United States", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Soil Microbiology", "Research Article", "Solanum tuberosum"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSphere.00130-21"}, {"href": "https://doi.org/10.1128/msphere.00130-21"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msphere.00130-21", "name": "item", "description": "10.1128/msphere.00130-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msphere.00130-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-25T00:00:00Z"}}, {"id": "10.1128/msystems.00226-20", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:50Z", "type": "Journal Article", "created": "2020-04-06", "title": "Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder", "description": "Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from raw milk to the end product. Routine implementation of high-throughput sequencing would elucidate the factors that influence population dynamics. This will enable a manufacturer to adopt control measures specific to each stage of processing and respond in an effective manner, which would ultimately lead to increased food safety and quality.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "metagenomics", "0303 health sciences", "whole-milk silo", "collection tanker", "bulk tank milk", "Microbiology", "QR1-502", "3. Good health", "03 medical and health sciences", "skimmed milk silo", "skimmed milk powder", "microbiota", "dairy", "processing", "16S rRNA gene amplicon sequencing", "Research Article"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSystems.00226-20"}, {"href": "https://doi.org/10.1128/msystems.00226-20"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00226-20", "name": "item", "description": "10.1128/msystems.00226-20", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00226-20"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-28T00:00:00Z"}}, {"id": "10.1146/annurev-food-052720-010751", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:55Z", "type": "Journal Article", "created": "2021-10-22", "title": "Next-generation food research: Use of meta-omic approaches for characterizing microbial communities along the food chain", "description": "Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread ofantimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "High-throughput sequencing", "Food Chain", "Food microbiome", "Microbiota", "high-throughput sequencing", "Meta-omic approaches", "food processing environment", "3. Good health", "meta-omic approaches", "03 medical and health sciences", "food-processing environment", "food microbiome; food-processing environment; high-throughput sequencing; meta-omic approaches; Fermentation; Food Industry; Food Chain; Microbiota", "food microbiome", "Fermentation", "Food Industry", "Food-processing environment"]}, "links": [{"href": "https://www.annualreviews.org/doi/pdf/10.1146/annurev-food-052720-010751"}, {"href": "https://doi.org/10.1146/annurev-food-052720-010751"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Annual%20Review%20of%20Food%20Science%20and%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1146/annurev-food-052720-010751", "name": "item", "description": "10.1146/annurev-food-052720-010751", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1146/annurev-food-052720-010751"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-25T00:00:00Z"}}, {"id": "10.1155/2019/1751783", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:19:56Z", "type": "Journal Article", "created": "2019-05-02", "title": "Acetotrophic Activity Facilitates Methanogenesis from LCFA at Low Temperatures: Screening from Mesophilic Inocula", "description": "The inoculum source plays a crucial role in the anaerobic treatment of wastewaters. Lipids are present in various wastewaters and have a high methanogenic potential, but their hydrolysis results in the production of long chain fatty acids (LCFAs) that are inhibitory to anaerobic microorganisms. Screening of inoculum for the anaerobic treatment of LCFA-containing wastewaters has been performed at mesophilic and thermophilic conditions. However, an evaluation of inocula for producing methane from LCFA-containing wastewater has not yet been conducted at low temperatures and needs to be undertaken. In this study, three inocula (one granular sludge and two municipal digester sludges) were assessed for methane production from LCFA-containing synthetic dairy wastewater (SDW) at low temperatures (10 and 20\uffc2\uffb0C). A methane yield (based on mL-CH4/g-CODadded) of 86-65% with acetate and 45-20% with SDW was achieved within 10 days using unacclimated granular sludge, whereas the municipal digester sludges produced methane only at 20\uffc2\uffb0C but not at 10\uffc2\uffb0C even after 200 days of incubation. The acetotrophic activity in the inoculum was found to be crucial for methane production from LCFA at low temperatures, highlighting the role ofMethanosaeta(acetoclastic archaea) at low temperatures. The presence of bacterial taxa from the familySyntrophaceae(Syntrophusand uncultured taxa) in the inoculum was found to be important for methane production from SDW at 10\uffc2\uffb0C. This study suggests the evaluation of acetotrophic activity and the initial microbial community characteristics by high-throughput amplicon sequencing for selecting the inoculum for producing methane at low temperatures (up to 10\uffc2\uffb0C) from lipid-containing wastewaters.
", "keywords": ["Deltaproteobacteria", "0301 basic medicine", "570", "0303 health sciences", "Sewage", "218 Environmental engineering", "Microbiota", "116 Chemical sciences", "Fatty Acids", "Temperature", "116", "Acetates", "Methanosarcinales", "6. Clean water", "03 medical and health sciences", "218", "13. Climate action", "11. Sustainability", "Anaerobiosis", "Methane", "Research Article"]}, "links": [{"href": "https://doi.org/10.1155/2019/1751783"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Archaea", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1155/2019/1751783", "name": "item", "description": "10.1155/2019/1751783", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1155/2019/1751783"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-02T00:00:00Z"}}, {"id": "10.1186/s40168-021-01144-4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:20:00Z", "type": "Journal Article", "created": "2021-09-20", "title": "Trophic level drives the host microbiome of soil invertebrates at a continental scale", "description": "Abstract BackgroundIncreasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China.
ResultsDifferent soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web.
ConclusionsOur findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates.
", "keywords": ["0301 basic medicine", "0303 health sciences", "Microbial dark matter", "Trophic dynamics", "Research", "Microbiota", "QR100-130", "Biodiversity", "15. Life on land", "Microbiology", "Invertebrates", "Microbial ecology", "Soil", "03 medical and health sciences", "Soil food web", "13. Climate action", "XXXXXX - Unknown", "Host microbiome", "Animals", "Network analysis", "Continental-scale survey", "Deterministic process", "Unique microbial taxa", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1186/s40168-021-01144-4"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-021-01144-4", "name": "item", "description": "10.1186/s40168-021-01144-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-021-01144-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-20T00:00:00Z"}}, {"id": "10.1371/journal.pone.0076500", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:20:08Z", "type": "Journal Article", "created": "2013-10-04", "title": "Response Of The Abundance Of Key Soil Microbial Nitrogen-Cycling Genes To Multi-Factorial Global Changes", "description": "Multiple co-occurring environmental changes are affecting soil nitrogen cycling processes, which are mainly mediated by microbes. While it is likely that various nitrogen-cycling functional groups will respond differently to such environmental changes, very little is known about their relative responsiveness. Here we conducted four long-term experiments in a steppe ecosystem by removing plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and manipulating some of their combinations. We quantified the abundance of seven nitrogen-cycling genes, including those for fixation (nifH), mineralization (chiA), nitrification (amoA of ammonia-oxidizing bacteria (AOB) or archaea (AOA)), and denitrification (nirS, nirK and nosZ). First, for each gene, we compared its sensitivities to different environmental changes and found that the abundances of various genes were sensitive to distinct and different factors. Overall, the abundances of nearly all genes were sensitive to nitrogen enrichment. In addition, the abundances of the chiA and nosZ genes were sensitive to plant functional group removal, the AOB-amoA gene abundance to phosphorus enrichment when nitrogen was added simultaneously, and the nirS and nirK gene abundances responded to watering. Second, for each single- or multi-factorial environmental change, we compared the sensitivities of the abundances of different genes and found that different environmental changes primarily affected different gene abundances. Overall, AOB-amoA gene abundance was most responsive, followed by the two denitrifying genes nosZ and nirS, while the other genes were less sensitive. These results provide, for the first time, systematic insights into how the abundance of each type of nitrogen-cycling gene and the equilibrium state of all these nitrogen-cycling gene abundances would shift under each single- or multi-factorial global change.", "keywords": ["2. Zero hunger", "Bacteria", "Science", "Microbiota", "Q", "R", "04 agricultural and veterinary sciences", "Environment", "Nitrogen Cycle", "15. Life on land", "Archaea", "Soil", "13. Climate action", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Gene-Environment Interaction", "Ecosystem", "Soil Microbiology", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0076500"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0076500", "name": "item", "description": "10.1371/journal.pone.0076500", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0076500"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-10-04T00:00:00Z"}}, {"id": "10.1371/journal.pone.0180442", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-24T16:20:10Z", "type": "Journal Article", "created": "2017-07-13", "title": "Organic farming enhances soil microbial abundance and activity\u2014A meta-analysis and meta-regression", "description": "Population growth and climate change challenge our food and farming systems and provide arguments for an increased intensification of agriculture. A promising option is eco-functional intensification through organic farming, an approach based on using and enhancing internal natural resources and processes to secure and improve agricultural productivity, while minimizing negative environmental impacts. In this concept an active soil microbiota plays an important role for various soil based ecosystem services such as nutrient cycling, erosion control and pest and disease regulation. Several studies have reported a positive effect of organic farming on soil health and quality including microbial community traits. However, so far no systematic quantification of whether organic farming systems comprise larger and more active soil microbial communities compared to conventional farming systems was performed on a global scale. Therefore, we conducted a meta-analysis on current literature to quantify possible differences in key indicators for soil microbial abundance and activity in organic and conventional cropping systems. All together we integrated data from 56 mainly peer-reviewed papers into our analysis, including 149 pairwise comparisons originating from different climatic zones and experimental duration ranging from 3 to more than 100 years. Overall, we found that organic systems had 32% to 84% greater microbial biomass carbon, microbial biomass nitrogen, total phospholipid fatty-acids, and dehydrogenase, urease and protease activities than conventional systems. Exclusively the metabolic quotient as an indicator for stresses on microbial communities remained unaffected by the farming systems. Categorical subgroup analysis revealed that crop rotation, the inclusion of legumes in the crop rotation and organic inputs are important farming practices affecting soil microbial community size and activity. Furthermore, we show that differences in microbial size and activity between organic and conventional farming systems vary as a function of land use (arable, orchards, and grassland), plant life cycle (annual and perennial) and climatic zone. In summary, this study shows that overall organic farming enhances total microbial abundance and activity in agricultural soils on a global scale.", "keywords": ["Crops", " Agricultural", "2. Zero hunger", "Organic Agriculture", "Science", "Climate", "Microbiota", "Environmental aspects", "Q", "R", "Fabaceae", "04 agricultural and veterinary sciences", "15. Life on land", "Soil quality", "Systems research and participatory research", "13. Climate action", "Life Science", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Soil Microbiology", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0180442"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0180442", "name": "item", "description": "10.1371/journal.pone.0180442", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0180442"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-12T00:00:00Z"}}, {"id": "10.5061/dryad.v9s4mw6zf", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:22:15Z", "type": "Dataset", "title": "Abandoned pastures and restored savannahs have distinct patterns of plant-soil feedback and nutrient cycling compared with native Brazilian savannahs.", "description": "Around 40% of the original Brazilian savannah territory is occupied by pastures dominated by fast-growing exotic C4 grasses, which impact ecosystem nutrient cycling. The restoration of these areas depends on the re-establishment of soil processes. We assessed how restoration of abandoned pastures through direct seeding of native species and land-management practices (burning and ploughing) affect soil nutrient cycling dynamics compared to native savannahs. We compared the activity of soil enzymes related to carbon (C), nitrogen (N) and phosphorus (P) cycling, as well as soil microbial biomass and soil chemical properties, such as pH and the concentration of N, P, potassium (K) and soil organic matter, among abandoned pastures, native savannah and restored areas. Abandoned pastures had faster nutrient turnover than native savannah, dominated by slow-growing native species. This pattern was evident from the overall higher biomass-specific enzyme activity in abandoned pastures than in native savannah. Compared with native savannah, restored areas had similar levels of soil enzyme activity, but lower microbial biomass and soil organic matter. Synthesis and application: The low enzyme activity in restored areas was likely related to a reduced soil organic carbon concentration due to practices such as burning and ploughing, rather than plant-soil feedback. The lower immobilization of nutrients in microbial biomass and lower retention of nutrients in restored areas, compared with native savannah, is expected to favour the re-establishment of fast-growing exotic species. Furthermore, the modifications of soil chemical and microbial properties related to abandonment of pastures did not influence restoration outcomes, because land-management practices applied prior to direct seedling had a major impact on the soil microbial community and soil fertility. Therefore, restoration of abandoned pastures should consider a greater focus on restoring soil carbon and nutrient cycling.", "keywords": ["2. Zero hunger", "soil enzyme activity", "13. Climate action", "Nutrient cycling dynamics", "Brazilian savannah", "FOS: Biological sciences", "Cerrado", "Tropical grassland", "15. Life on land", "soil microbiota", "ecosystem restoration"], "contacts": [{"organization": "D'Angioli, Andr\u00e9, Giles, Andr\u00e9, Costa, Patr\u00edcia, Wolfsdorf, Gabriel, Pecoral, Lu\u00edsa, Verona, Larissa, Piccolo, Fernanda, Sampaio, Alexandre, Schmidt, Isabel, Rowland, Lucy, Lambers, Hans, Kandeler, Ellen, Oliveira, Rafael, Abrah\u00e3o, Anna,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.v9s4mw6zf"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.v9s4mw6zf", "name": "item", "description": "10.5061/dryad.v9s4mw6zf", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.v9s4mw6zf"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-04-25T00:00:00Z"}}, {"id": "10.24072/pcjournal.11", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:21:14Z", "type": "Journal Article", "created": "2020-11-10", "title": "Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production", "description": "AbstractBackgroundThe red macroalgae Asparagopsis taxiformis is a potent natural supplement for reducing methane production from cattle. A. taxiformis contains several anti-methanogenic compounds including bromoform that inhibits directly methanogenesis. The positive and adverse effects of A. taxiformis on the rumen microbiota are dose-dependent and operate in a dynamic fashion. It is therefore key to characterize the dynamic response of the rumen microbial fermentation for identifying optimal conditions on the use of A. taxiformis as a dietary supplement for methane mitigation. Accordingly, the objective of this work was to model the effect of A. taxiformis supplementation on the rumen microbial fermentation under in vitro conditions. We adapted a published mathematical model of rumen microbial fermentation to account for A. taxiformis supplementation. We modelled the impact of A. taxiformis on the fermentation and methane production by two mechanisms, namely (i) direct inhibition of the growth rate of methanogens by bromoform and (ii) hydrogen control on sugars utilization and on the flux allocation towards volatile fatty acids production. We calibrated our model using a multi-experiment estimation approach that integrated experimental data with six macroalgae supplementation levels from a published in vitro study assessing the dose-response impact of A. taxiformis on rumen fermentation.
Resultsour model captured satisfactorily the effect of A. taxiformis on the dynamic profile of rumen microbial fermentation for the six supplementation levels of A. taxiformis with an average determination coefficient of 0.88 and an average coefficient of variation of the root mean squared error of 15.2% for acetate, butyrate, propionate, ammonia and methane.
Conclusionsour results indicated the potential of our model as prediction tool for assessing the impact of additives such as seaweeds on the rumen microbial fermentation and methane production in vitro. Additional dynamic data on hydrogen and bromoform are required to validate our model structure and look for model structure improvements. We expect this model development can be useful to help the design of sustainable nutritional strategies promoting healthy rumen function and low environmental footprint.
", "keywords": ["570", "Asparagopsis taxiformis", "[SDV.BIO]Life Sciences [q-bio]/Biotechnology", "methane inhibitors", "Science", "rumen model", "630", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "[INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering", "rumen microbiota", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "greenhouse gas mitigation", " hydrogen control", " methane inhibitors", " methane mitigation", " red seaweed", " rumen fermentation", " rumen microbiota", " rumen model.", "[SDV.SA.SPA] Life Sciences [q-bio]/Agricultural sciences/Animal production studies", "2. Zero hunger", "methane mitigation", "Q", "greenhouse gas mitigation", "0402 animal and dairy science", "04 agricultural and veterinary sciences", "15. Life on land", "[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation", "[SDV.BIO] Life Sciences [q-bio]/Biotechnology", "rumen fermentation", "Archaeology", "hydrogen control", "13. Climate action", "[SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "red seaweed", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation", "environment/Ecosystems", "[INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering", "CC1-960"]}, "links": [{"href": "https://peercommunityjournal.org/item/10.24072/pcjournal.11.pdf"}, {"href": "https://doi.org/10.24072/pcjournal.11"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Peer%20Community%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.24072/pcjournal.11", "name": "item", "description": "10.24072/pcjournal.11", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.24072/pcjournal.11"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-09T00:00:00Z"}}, {"id": "10.3389/fmicb.2023.1158130", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:21:26Z", "type": "Journal Article", "created": "2023-04-21", "title": "Field scale biodegradation of total petroleum hydrocarbons and soil restoration by Ecopiles: microbiological analysis of the process", "description": "Ecopiling is a method for biodegradation of hydrocarbons in soils. It derives from Biopiles, but phytoremediation is added to biostimulation with nitrogen fertilization and bioaugmentation with local bacteria. We have constructed seven Ecopiles with soil heavily polluted with hydrocarbons in Carlow (Ireland). The aim of the study was to analyze changes in the microbial community during ecopiling. In the course of 18\u2009months of remediation, total petroleum hydrocarbons values decreased in 99 and 88% on average for aliphatics and aromatics, respectively, indicating a successful biodegradation. Community analysis showed that bacterial alfa diversity (Shannon Index), increased with the degradation of hydrocarbons, starting at an average value of 7.59 and ending at an average value of 9.38. Beta-diversity analysis, was performed using Bray-Curtis distances and PCoA ordination, where the two first principal components (PCs) explain the 17 and 14% of the observed variance, respectively. The results show that samples tend to cluster by sampling time instead of by Ecopile. This pattern is supported by the hierarchical clustering analysis, where most samples from the same timepoint clustered together. We used DSeq2 to determine the differential abundance of bacterial populations in Ecopiles at the beginning and the end of the treatment. While TPHs degraders are more abundant at the start of the experiment, these populations are substituted by bacterial populations typical of clean soils by the end of the biodegradation process. Similar results are found for the fungal community, indicating that the microbial community follows a succession along the process. This succession starts with a TPH degraders or tolerant enriched community, and finish with a microbial community typical of clean soils.
Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3\uffe2\uff80\uff934 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%\uffe2\uff80\uff9330% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils. We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community\u2019s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 \u00b0C + 50% water holding capacity (WHC)); increased air temperature (15\u201325 \u00b0C or 20\u201330 \u00b0C + 50% WHC); flood (20 \u00b0C + 75% WHC); drought (20 \u00b0C + 25% WHC); and ultraviolet radiation (UV) (20 \u00b0C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community\u2019s physiological profile and the bacterial community\u2019s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20\u201330 \u00b0C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome\u2013invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed. Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.
Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early \uffe2\uff80\uff9comics\uffe2\uff80\uff9d experiments focused mainly on the species composition of microbial communities, new \uffe2\uff80\uff9cmeta-omics\uffe2\uff80\uff9d approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "QH301-705.5", "tomato", "RNA-seq; fungi; holobiont; meta-transcriptome; microbiota; tomato", "Article", "03 medical and health sciences", "rna-seq", "microbiota", "fungi", "Biology (General)", "RNA-seq", "meta-transcriptome", "holobiont"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/1/38/pdf"}, {"href": "https://iris.unito.it/bitstream/2318/1720787/1/Chialva%20et%20al.%2c%202020_tomato_meta-transcriptome.pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/1/38/pdf"}, {"href": "https://doi.org/10.3390/microorganisms8010038"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms8010038", "name": "item", "description": "10.3390/microorganisms8010038", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms8010038"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-24T00:00:00Z"}}, {"id": "10.5061/dryad.t4b8gtj8d", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:22:14Z", "type": "Dataset", "created": "2024-02-07", "title": "Data for: Male, female and mixed-sex poplar plantations support divergent soil microbial communities", "description": "unspecifiedMixed-species forests are often more productive than monocultures because of a lower niche overlap and higher taxonomic and functional diversity of soil microbial communities. Males and females of dioecious plants have sex-specific adaptations to diverse habitats. The potential of using sexual differences in establishing more diverse poplar plantations has not been explored in degraded areas. We conducted a series of greenhouse and field experiments to investigate how belowground competition, soil microbial communities and seasonal variation nitrogen content differ among female, male and mixed-sex Populus cathayana plantations. In the greenhouse experiment, female neighbors suppressed the growth of males under optimal nitrogen conditions. However, male neighbors enhanced \u03b415N of females under inter-sexual competition. In the field, the root length density, root area density and biomass of fine roots were lower in female plantations than in male or mixed-sex plantations. Bacterial networks of female, male and mixed-sex plantations were characterized by different composition of hub nodes, including connectors, module and network hubs. The sex composition of plantations altered bacterial and fungal community structures according to Bray-Curtis distances, with 44% and 65% of variance explained by the root biomass, respectively. The total soil nitrogen content of mixed-sex plantation was higher than that in female plantation in spring and summer. The mixed-sex plantation also had a higher \u03b2-1,4-N-acetyl-glucosaminidase activity in summer and a higher nitrification rate in autumn than the other two plantations. The seasonal soil N content, nitrification rate and root distribution traits demonstrated spatiotemporal niche separation in the mixed-sex plantation. We argue that a strong female-female competition and limited nitrogen content could strongly impede plant growth and reduce the resistance of monosex plantations to climate change and the mixed-sex plantations constitutes a promising way to restore degraded land.", "keywords": ["belowground competition", "plant-microbe interactions", "neighbor sexual identity", "FOS: Earth and related environmental sciences", "microbiota assembly", "dioecious species"], "contacts": [{"organization": "Guo, Qingxue", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.t4b8gtj8d"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.t4b8gtj8d", "name": "item", "description": "10.5061/dryad.t4b8gtj8d", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.t4b8gtj8d"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-23T00:00:00Z"}}, {"id": "20.500.11850/424423", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:26:20Z", "type": "Journal Article", "created": "2020-06-07", "title": "The physical structure of soil: Determinant and consequence of trophic interactions", "description": "Open AccessSoil Biology and Biochemistry, 148", "keywords": ["2. Zero hunger", "0301 basic medicine", "Matric potential", "Soil pores", "Microbiota", "04 agricultural and veterinary sciences", "15. Life on land", "Mesofauna", "03 medical and health sciences", "Soil microhabitat", "Soil food web", "13. Climate action", "Soil pores; Soil microhabitat; Microbiota; Mesofauna; Soil food web; Matric potential", "0401 agriculture", " forestry", " and fisheries"], "contacts": [{"organization": "Erktan, Amandine, Or, Dani, Scheu, Stefan,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/20.500.11850/424423"}, {"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": "20.500.11850/424423", "name": "item", "description": "20.500.11850/424423", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.11850/424423"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-01T00:00:00Z"}}, {"id": "10.5281/zenodo.15019338", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-24T16:23:39Z", "type": "Dataset", "title": "Soil sampling, pre-treatment, storage and shipment procedure for soil health monitoring", "description": "Soil sampling, pre-treatment, storage and shipment procedure for soil health monitoring used in BIOservicES project, agreed under a paticipatory approach with international projects, organisations and initiatives. Soil sampling strategy defined to collect, store and ship soil to assess different types of soil properties: i) physicochemical, related to soil fertility, carbon sequestration, pollution; ii) soil structure, by measures of soil aggregate stability, porosity and bulk density; iii) soil microorganisms; iv) microfauna; v) mesofauna; and vi) macrofauna.", "keywords": ["Fauna", "soil shipment", "soil health", "Microbiota", "soil sampling", "Methods", "soil storage", "Analysis", "biodiversity"], "contacts": [{"organization": "Universidad Polit\u00e9cnica de Cartagena, University of Vigo, LGI Sustainable Innovation, Instituut voor Landbouw en Visserijonderzoek, Johann Heinrich von Th\u00fcnen-Institut, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Zabala Innovation Consulting (Spain), CMCC Foundation - Euro-Mediterranean Center on Climate Change, CSIC, Central Organisation, Frauenklinik der Technischen Universit\u00e4t M\u00fcnchen, Wageningen University & Research, Latvian State Forest Research Institute 'Silava ', Universit\u00e0 degli Studi della Tuscia, JUNE COMMUNICATIONS SRL, SOLUCIONES AGRICOLAS CULTIVATE, FUNDACION JUANA DE VEGA, FLACHENAGENTUR RHEINLAND GMBH, SIA RIGAS MEZI, Forschungsinstitut f\u00fcr Biologischen Landbau, Scotland's Rural College, University of Sussex, Northern Arizona University,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.15019338"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.15019338", "name": "item", "description": "10.5281/zenodo.15019338", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.15019338"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-03-13T00:00:00Z"}}, {"id": "10.5281/zenodo.15720421", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:23:55Z", "type": "Dataset", "title": "Dataset for paper: Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic", "description": "Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic. New collected data at HIS below.Corresponding author: Speranza Panico - speranza.panico@uniud.it", "keywords": ["climate change", "Soil organic carbon", "space-for-time approach", "soil microbiota", "alpha-diversity", "DNA metabarcoding"], "contacts": [{"organization": "Panico, Speranza Claudia, Alberti, Giorgio, Foscari, Alessandro, Tomao, Antonio, Incerti, Guido, Sciabbarrasi, Giovanni Luca,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.15720421"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.15720421", "name": "item", "description": "10.5281/zenodo.15720421", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.15720421"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-06-23T00:00:00Z"}}, {"id": "PMC9314937", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-24T16:29:49Z", "type": "Journal Article", "created": "2022-03-14", "title": "Reduced methane emissions in former permafrost soils driven by vegetation and microbial changes following drainage", "description": "AbstractIn Arctic regions, thawing permafrost soils are projected to release 50 to 250 Gt of carbon by 2100. This data is mostly derived from carbon\uffe2\uff80\uff90rich wetlands, although 71% of this carbon pool is stored in faster\uffe2\uff80\uff90thawing mineral soils, where ecosystems close to the outer boundaries of permafrost regions are especially vulnerable. Although extensive data exists from currently thawing sites and short\uffe2\uff80\uff90term thawing experiments, investigations of the long\uffe2\uff80\uff90term changes following final thaw and co\uffe2\uff80\uff90occurring drainage are scarce. Here we show ecosystem changes at two comparable tussock tundra sites with distinct permafrost thaw histories, representing 15 and 25\uffc2\uffa0years of natural drainage, that resulted in a 10\uffe2\uff80\uff90fold decrease in CH4 emissions (3.2\uffc2\uffa0\uffc2\uffb1\uffc2\uffa02.2 vs. 0.3\uffc2\uffa0\uffc2\uffb1\uffc2\uffa00.4\uffc2\uffa0mg C\uffe2\uff80\uff90CH4\uffc2\uffa0m\uffe2\uff88\uff922\uffc2\uffa0day\uffe2\uff88\uff921), while CO2 emissions were comparable. These data extend the time perspective from earlier studies based on short\uffe2\uff80\uff90term experimental drainage. The overall microbial community structures did not differ significantly between sites, although the drier top soils at the most advanced site led to a loss of methanogens and their syntrophic partners in surface layers while the abundance of methanotrophs remained unchanged. The resulting deeper aeration zones likely increased CH4 oxidation due to the longer residence time of CH4 in the oxidation zone, while the observed loss of aerenchyma plants reduced CH4 diffusion from deeper soil layers directly to the atmosphere. Our findings highlight the importance of including hydrological, vegetation and microbial specific responses when studying long\uffe2\uff80\uff90term effects of climate change on CH4 emissions and underscores the need for data from different soil types and thaw histories.