{"type": "FeatureCollection", "features": [{"id": "10.3389/fmicb.2016.01446", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:20:32Z", "type": "Journal Article", "created": "2016-09-14", "description": "Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.", "keywords": ["Soil nutrients", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "long-term fertilization", "microbial biomass", "15. Life on land", "microbial activity", "Microbiology", "QR1-502", "03 medical and health sciences", "13. Climate action", "soil microbial communities", "soil nutrients", "454 pyrosequencing"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2016.01446"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2016.01446", "name": "item", "description": "10.3389/fmicb.2016.01446", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2016.01446"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-09-14T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2016.05.018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:15:26Z", "type": "Journal Article", "created": "2016-06-11", "title": "Interactive Effects Of Precipitation Manipulation And Nitrogen Addition On Soil Properties In California Grassland And Shrubland", "description": "Abstract Soil microbial communities and pools of carbon (C) and nitrogen (N) play an important role in ecosystem responses to precipitation variability and N deposition. In southern California, ecosystem vulnerability to these environmental change drivers may differ for grassland versus shrubland vegetation types. We hypothesized that (1) these vegetation types would differ in their responses to precipitation and N manipulation; (2) reduced precipitation (\u201cdrought treatment\u201d) would have a negative effect on soil microbial abundance and alter microbial community composition, (3) these changes would be associated with reductions in soil C and N pools, (4) N addition would increase microbial abundance as well as soil C and N pools, and (5) combined drought and N deposition would have offsetting effects on soil properties. We tested these hypotheses at the Loma Ridge Global Change Experiment in southern California. Across vegetation types, we found that microbial biomass based on phospholipid fatty acids declined with drought and N addition. Microbial composition differed more strongly by vegetation type than with environmental change treatments. Added precipitation had little effect on microbial biomass but reduced labile C and N pools; these reductions were mitigated by N addition. Drought reduced labile forms of soil C and N, whereas N addition increased labile soil C pools and all soil N pools. Negative effects of drought and N addition were additive for microbial biomass, which could inhibit soil C cycling if both of these environmental changes occur together. Drought interacted with N addition to significantly increase the most labile N pool under the drought\u00a0+\u00a0N treatment, which suggests a build-up of available N under these conditions. These results imply that multiple environmental changes may combine non-additively to affect below-ground microorganisms and soil C and N pools, which may have important consequences for ecosystem services such as productivity, biodiversity, and soil quality in Mediterranean climate regimes of North America.", "keywords": ["Veterinary and Food Sciences", "Soil Science", "Microbial communities", "Shrubland", "veterinary and food sciences", "Carbon and nitrogen cycle", "11. Sustainability", "Global change", "2. Zero hunger", "Agricultural", "Drought", "Agricultural and Veterinary Sciences", "Ecology", "Forestry Sciences", "Agronomy & Agriculture", "04 agricultural and veterinary sciences", "Biological Sciences", "15. Life on land", "Grassland", "Agricultural and Biological Sciences (miscellaneous)", "6. Clean water", "Environmental sciences", "Biological sciences", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Environmental Sciences"]}, "links": [{"href": "https://escholarship.org/content/qt1p4898qc/qt1p4898qc.pdf"}, {"href": "https://doi.org/10.1016/j.apsoil.2016.05.018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2016.05.018", "name": "item", "description": "10.1016/j.apsoil.2016.05.018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2016.05.018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-11-01T00:00:00Z"}}, {"id": "10.1007/s11104-012-1547-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:14:50Z", "type": "Journal Article", "created": "2012-12-14", "title": "Snow Cover Manipulation Effects On Microbial Community Structure And Soil Chemistry In A Mountain Bog", "description": "Background and Aims Alterations in snow cover driven by climate change may impact ecosystem functioning, including biogeochemistry and soil (microbial) processes. We elucidated the effects of snow cover manipulation (SCM) on above-and belowground processes in a temperate peatland.", "keywords": ["trends", "2. Zero hunger", "570", "biomass", "tundra soils", "variability", "[SDE.MCG]Environmental Sciences/Global Changes", "dynamics", "04 agricultural and veterinary sciences", "15. Life on land", "forest soil", "freeze-thaw cycles", "Microbial communities; peatland; phosphatase activity; Phospholipid fatty acids (PLFA); Snow cover manipulation; \uf020Winter Ecology", "01 natural sciences", "nitrogen", "13. Climate action", "[SDE]Environmental Sciences", "climate-change", "rv-coefficient", "0401 agriculture", " forestry", " and fisheries", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://eprints.soton.ac.uk/412453/2/Robroek_2013_Plant_and_Soil.pdf"}, {"href": "https://doi.org/10.1007/s11104-012-1547-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-012-1547-2", "name": "item", "description": "10.1007/s11104-012-1547-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-012-1547-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-12-16T00:00:00Z"}}, {"id": "10.1016/j.foodres.2022.112162", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:15:56Z", "type": "Journal Article", "created": "2022-11-19", "title": "High pressure processing at the early stages of ripening enhances the safety and quality of dry fermented sausages elaborated with or without starter culture", "description": "To study the quality of chorizo de Le\u00f3n dry fermented sausages (DFS), high pressure processing (HPP) applied at the early stages of ripening and the use of a functional starter culture were evaluated as additional safety measures. Furthermore, the ability to control the populations of artificially inoculated Listeria monocytogenes and Salmonella Typhimurium was investigated and the evolution of microbial communities was assessed by amplicon 16S rRNA metataxonomics. The use of HPP and the starter culture, independently or combined, induced a reduction of Listeria monocytogenes of 1.5, 4.3 and\u00a0>\u00a04.8 log CFU/g respectively, as compared to control. Salmonella Typhimurium counts were under the detection limit (<1 log) in all treated end-product samples. Both additional measures reduced the activity of undesirable microbiota, such as Serratia and Brochothrix, during the production of DFS. Moreover, the starter culture highly influencedthe taxonomic profile of samples.No adverse sensory effects were observed, and panelists showed preference for HPP treated DFS. In conclusion, this new approach of applying HPP at the early stages of ripening of DFS in combination with the use of a defined starter culture improved the safety and quality of the meat product.", "keywords": ["Salmonella typhimurium", "2. Zero hunger", "Tecnolog\u00eda de los alimentos", "Ripening", "Microbial communities", "04 agricultural and veterinary sciences", "Preservation", "Meat Products", "High Hydrostatic Pressure", "0404 agricultural biotechnology", "RNA", " Ribosomal", " 16S", "Fermentation", "Lactic acid bacteria", "Fermented meat", "0405 other agricultural sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.foodres.2022.112162"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Food%20Research%20International", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foodres.2022.112162", "name": "item", "description": "10.1016/j.foodres.2022.112162", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foodres.2022.112162"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2019.01.025", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:50Z", "type": "Journal Article", "created": "2018-10-29", "title": "Soil microbial communities with greater investment in resource acquisition have lower growth yield", "description": "Abstract

Resource acquisition and growth yield are fundamental traits of microorganisms that have consequences for ecosystem functioning. However, there is a lack of empirical observations linking these traits. Using a landscape-scale survey of temperate near-neutral pH soils, we show tradeoffs in key community-level parameters linked to these traits. Increased investment into extracellular enzymes was associated with reduced growth yield; this reduction was linked more to carbon than nitrogen acquisition enzymes suggesting smaller stoichiometric constraints on community metabolism in examined soils.Resource acquisition and growth yield are fundamental traits of microorganisms that have consequences for ecosystem functioning. However, there is a lack of empirical observations linking these traits. Using a landscape-scale survey of temperate near-neutral pH soils, we show tradeoffs in key community-level parameters linked to these traits. Increased investment into extracellular enzymes was associated with reduced growth yield; this reduction was linked more to carbon than nitrogen acquisition enzymes suggesting smaller stoichiometric constraints on community metabolism in examined soils.Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above\uffe2\uff80\uff90 and belowground linkages that regulate soil organic carbon dynamics and C\uffe2\uff80\uff90balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top\uffe2\uff80\uff90predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum\uffe2\uff80\uff90polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above\uffe2\uff80\uff90 and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands

", "keywords": ["0106 biological sciences", "2. Zero hunger", "570", "[SDE.MCG]Environmental Sciences/Global Changes", "water chemistry", "food chains", "15. Life on land", "Global Warming", "01 natural sciences", "[SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces", " environment", "microbial food web", "testate amoebae", "[SDE.MCG] Environmental Sciences/Global Changes", "plant and microbial communities", "13. Climate action", "Host-Pathogen Interactions", "Sphagnopsida", "[SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces", "environment", "polyphenols"]}, "links": [{"href": "https://doi.org/10.1111/gcb.12075"}, {"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.12075", "name": "item", "description": "10.1111/gcb.12075", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.12075"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-12-15T00:00:00Z"}}, {"id": "10.1111/gcb.12418", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:18:32Z", "type": "Journal Article", "created": "2013-10-12", "title": "Soil Microbial And Nutrient Responses To 7years Of Seasonally Altered Precipitation In A Chihuahuan Desert Grassland", "description": "Abstract

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": "10.1111/gcb.17516", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:18:36Z", "type": "Journal Article", "created": "2024-09-24", "title": "Phosphorus limitation promotes soil carbon storage in a boreal forest exposed to long\u2010term nitrogen fertilization", "description": "Abstract

Forests play a crucial role in global carbon cycling by absorbing and storing significant amounts of atmospheric carbon dioxide. Although boreal forests contribute to approximately 45% of the total forest carbon sink, tree growth and soil carbon sequestration are constrained by nutrient availability. Here, we examine if long\uffe2\uff80\uff90term nutrient input enhances tree productivity and whether this leads to carbon storage or whether stimulated microbial decomposition of organic matter limits soil carbon accumulation. Over six decades, nitrogen, phosphorus, and calcium were supplied to a Pinus sylvestris\uffe2\uff80\uff90dominated boreal forest. We found that nitrogen fertilization alone or together with calcium and/or phosphorus increased tree biomass production by 50% and soil carbon sequestration by 65% compared to unfertilized plots. However, the nonlinear relationship observed between tree productivity and soil carbon stock across treatments suggests microbial regulation. When phosphorus was co\uffe2\uff80\uff90applied with nitrogen, it acidified the soil, increased fungal biomass, altered microbial community composition, and enhanced biopolymer degradation capabilities. While no evidence of competition between ectomycorrhizal and saprotrophic fungi has been observed, key functional groups with the potential to reduce carbon stocks were identified. In contrast, when nitrogen was added without phosphorus, it increased soil carbon sequestration because microbial activity was likely limited by phosphorus availability. In conclusion, the addition of nitrogen to boreal forests may contribute to global warming mitigation, but this effect is context dependent. 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 .

", "keywords": ["aerobic respiration", "primary and secondary production", "0301 basic medicine", "Geologic Sediments", "hypersaline microbial mats", "microbial communities", "Sodium Chloride", "extremophiles/extremophily", "03 medical and health sciences", "CYANOBACTERIAL MATS", "REDUCING BACTERIA", "uncultured microbes", "BACTERIUM DESULFOVIBRIO-OXYCLINAE", "Environmental Microbiology", "14. Life underwater", "Photosynthesis", "Phylogeny", "DISSIMILATORY SULFATE REDUCTION", "106022 Mikrobiologie", "Bacteria", "Microbiota", "ANOXYGENIC PHOTOSYNTHESIS", "15. Life on land", "Archaea", "biofilm biology", "6. Clean water", "Oxygen", "sulfide microprofiles", "13. Climate action", "CHLOROFLEXUS-LIKE BACTERIA", "106022 Microbiology", "sulfate reduction rate", "GEN. NOV.", "sulfur cycling", "PHYSIOLOGICAL CHARACTERIZATION", "DUNALIELLA", "microbiology of unexplored habitats", "biofilm biology; element cycles and biogeochemical processes; extremophiles/extremophily; microbial communities; microbiology of unexplored habitats; primary and secondary production; uncultured microbes", "element cycles and biogeochemical processes", "key biogeochemical processes", "OXYGENIC PHOTOSYNTHESIS", "Sulfur"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.00698-21"}, {"href": "https://doi.org/10.1128/aem.00698-21"}, {"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.00698-21", "name": "item", "description": "10.1128/aem.00698-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.00698-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-11T00:00:00Z"}}, {"id": "10.1111/mec.15674", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:18:55Z", "type": "Journal Article", "created": "2020-10-09", "title": "Effects of soil preservation for biodiversity monitoring using environmental DNA", "description": "Abstract

Environmental DNA (eDNA) metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa such as soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guideline for best practices so far. Here, we assessed the impact of four methods of soil sample preservation that can be conveniently used also in metabarcoding studies targeting remote or difficult to access areas. Tested methods include: preservation at room temperature for 6\uffc2\uffa0hr, preservation at 4\uffc2\uffb0C for 3\uffc2\uffa0days, desiccation immediately after sampling and preservation for 21\uffc2\uffa0days, and desiccation after 6\uffc2\uffa0hr at room temperature and preservation for 21\uffc2\uffa0days. For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under ideal conditions (i.e., extraction of eDNA immediately after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in molecular operational taxonomic units (MOTU) richness of bacteria, fungi and eukaryotes across treatments, but MOTU richness was similar across preservation methods if rare taxa were not considered. All the approaches were able to identify differences in community structure among habitats, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.

", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "[SDV]Life Sciences [q-bio]", "Biodiversity", "Forests", "15. Life on land", "DNA", " Environmental", "Soil", "03 medical and health sciences", "eDNA metabarcoding; eukaryotes; microbial communities; MOTU richness; sample storage; \u03b1 and \u03b2 diversity", "13. Climate action", "DNA Barcoding", " Taxonomic", "Environmental Monitoring"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/791337/2/guerrieri%202020%20%20submitted.pdf"}, {"href": "https://air.unimi.it/bitstream/2434/791337/4/mec.15674.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.15674"}, {"href": "https://doi.org/10.1111/mec.15674"}, {"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.15674", "name": "item", "description": "10.1111/mec.15674", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/mec.15674"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-06T00:00:00Z"}}, {"id": "10.1111/nph.12333", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:18:56Z", "type": "Journal Article", "created": "2013-05-30", "title": "Cumulative Response Of Ecosystem Carbon And Nitrogen Stocks To Chronic Co2exposure In A Subtropical Oak Woodland", "description": "Summary

Rising atmospheric carbon dioxide (CO2) could alter the carbon (C) and nitrogen (N) content of ecosystems, yet the magnitude of these effects are not well known. We examined C and N budgets of a subtropical woodland after 11\uffc2\uffa0yr of exposure to elevated CO2.

We used open\uffe2\uff80\uff90top chambers to manipulate CO2 during regrowth after fire, and measured C, N and tracer 15N in ecosystem components throughout the experiment.

Elevated CO2 increased plant C and tended to increase plant N but did not significantly increase whole\uffe2\uff80\uff90system C or N. Elevated CO2 increased soil microbial activity and labile soil C, but more slowly cycling soil C pools tended to decline. Recovery of a long\uffe2\uff80\uff90term 15N tracer indicated that CO2 exposure increased N losses and altered N distribution, with no effect on N inputs.

Increased plant C accrual was accompanied by higher soil microbial activity and increased C losses from soil, yielding no statistically detectable effect of elevated CO2 on net ecosystem C uptake. These findings challenge the treatment of terrestrial ecosystems responses to elevated CO2 in current biogeochemical models, where the effect of elevated CO2 on ecosystem C balance is described as enhanced photosynthesis and plant growth with decomposition as a first\uffe2\uff80\uff90order response.

", "keywords": ["Soil organic matter", "Long term experiment", "Elevated atmospheric CO2", "Florida scrub oak", "Scrub oak", "Research", "Plant Sciences", "Aboveground biomass", "Plant Biology", "Microbial communities", "04 agricultural and veterinary sciences", "Carbon Cycling", "15. Life on land", "Forest productivity", "Soil carbon", "Rhizosphere processes", "Terrestrial ecosystems", "Dioxide enrichment", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Elevated CO2", "Climate feedbacks", "Global change", "Subtropical woodland", "Nitrogen cycling"]}, "links": [{"href": "https://digitalcommons.odu.edu/context/biology_fac_pubs/article/1264/viewcontent/Day2013CumulativeResponseofEcosystemCarbonandNitrogenOCR.pdf"}, {"href": "https://doi.org/10.1111/nph.12333"}, {"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.12333", "name": "item", "description": "10.1111/nph.12333", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.12333"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-05-30T00:00:00Z"}}, {"id": "10.1371/journal.pone.0200979", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:19:23Z", "type": "Journal Article", "created": "2019-04-11", "title": "Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR", "description": "Abstract

Soil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition.

To address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer\uffc2\uffae, marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers between 1.00 and 2.20 m below ground level.

Importantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition.

Finally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier.

These outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.

", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Science", "Microbial Consortia", "DIVERSITY", "SOFTWARE", "Real-Time Polymerase Chain Reaction", "BACILLUS-SUBTILIS", "BIOMASS", "03 medical and health sciences", "BIOAUGMENTATION", "DNA", " Bacterial/chemistry", "MICROBIAL COMMUNITIES", "Soil Microbiology", "2. Zero hunger", "0303 health sciences", "16S RIBOSOMAL-RNA", "Q", "R", "PROFILES", "ACIDS", "TRANSFORMATION", "6. Clean water", "Microbial Consortia/genetics", "Enhancer Elements", " Genetic", "13. Climate action", "Medicine", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/365395v1.full.pdf"}, {"href": "https://doi.org/10.1371/journal.pone.0200979"}, {"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.0200979", "name": "item", "description": "10.1371/journal.pone.0200979", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0200979"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-09T00:00:00Z"}}, {"id": "10.1186/s40793-025-00667-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:19:13Z", "type": "Journal Article", "created": "2025-01-18", "title": "Bioinoculant-induced plant resistance is modulated by interactions with resident soil microbes", "description": "BACKGROUND: Entomopathogenic fungi are increasingly used as bio-inoculants to enhance crop growth and resistance. When applied to rhizosphere soil, they interact with resident soil microbes, which can affect their ability to colonize and induce resistance in plants as well as modify the structure of the resident soil microbiome, either directly through interactions in the rhizosphere or indirectly, mediated by the plant. The extent to which such direct versus indirect interactions between bio-inoculants and soil microbes impact microbe-induced resistance in crops remains unclear. This study uses a split-root system to examine the effects of direct versus indirect (plant-mediated) interactions between an entomopathogenic fungus, Metarhizium brunneum, and resident soil microbes on induced resistance in tomato against two-spotted spider mites. Additionally, the study explores how these interactions influence the composition and diversity of soil fungal and bacterial communities. RESULTS: Resident soil microbes reduced the efficacy of M. brunneum to induce resistance against spider mites. This reduction occurred not only when resident microbes directly interacted with the bio-inoculant but also when they were spatially separated within the root system, indicating plant-mediated effects. M. brunneum inoculation did not affect rhizosphere microbial diversity but led to changes in fungal and bacterial community composition, even when these communities were not in direct contact with the inoculant. CONCLUSIONS: This research highlights the impact of both direct and plant-mediated interactions between bio-inoculants and resident soil microbes on bio-inoculant-induced pest resistance in crop plants and underscores the importance of assessing potential adverse effects of fungal bio-inoculants on native soil communities. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00667-9.", "keywords": ["Environmental sciences", "Entomopathogenic fungi", "Research", "Spider mites", "GE1-350", "Arthropod pests", "Soil microbial communities", "Microbiology", "Tomato", "QR1-502"], "contacts": [{"organization": "Rasool, Shumaila, Groos, Manon, Hannula, S. Emilia, Biere, Arjen,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1186/s40793-025-00667-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-025-00667-9", "name": "item", "description": "10.1186/s40793-025-00667-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-025-00667-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-01-18T00:00:00Z"}}, {"id": "10.1890/02-0433", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:19:44Z", "type": "Journal Article", "created": "2007-06-04", "title": "Plant Diversity, Soil Microbial Communities, And Ecosystem Function: Are There Any Links?", "description": "A current debate in ecology centers on the extent to which ecosystem function depends on biodiversity. Here, we provide evidence from a long-term field manipulation of plant diversity that soil microbial communities, and the key ecosystem processes that they mediate, are significantly altered by plant species richness. After seven years of plant growth, we determined the composition and function of soil microbial communities beneath experimental plant diversity treatments containing 1-16 species. Microbial community bio- mass, respiration, and fungal abundance significantly increased with greater plant diversity, as did N mineralization rates. However, changes in microbial community biomass, activity, and composition largely resulted from the higher levels of plant production associated with greater diversity, rather than from plant diversity per se. Nonetheless, greater plant pro- duction could not explain more rapid N mineralization, indicating that plant diversity affected this microbial process, which controls rates of ecosystem N cycling. Greater N availability probably contributed to the positive relationship between plant diversity and productivity in the N-limited soils of our experiment, suggesting that plant-microbe in- teractions in soil are an integral component of plant diversity's influence on ecosystem", "keywords": ["2. Zero hunger", "soil C and N cycling", "Science", "Ecology and Evolutionary Biology", "microbial communities", "phospholipid fatty acid analysis", "04 agricultural and veterinary sciences", "15. Life on land", "plant communities", "gross N mineralization", "soil microbes", "ecosystem function", "0401 agriculture", " forestry", " and fisheries", "species richness", "gross N immobilization", "biodiversity"], "contacts": [{"organization": "Zak, Donald R., Holmes, William E., White, David C., Peacock, Aaron D., Tilman, David,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1890/02-0433"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1890/02-0433", "name": "item", "description": "10.1890/02-0433", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1890/02-0433"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-08-01T00:00:00Z"}}, {"id": "10.3389/fmicb.2016.00376", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:20:32Z", "type": "Journal Article", "created": "2016-04-05", "description": "There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, Northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests) due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM) fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.", "keywords": ["0301 basic medicine", "0303 health sciences", "southeast asia", "microbial communities", "Biodiversity", "15. Life on land", "Southeast Asia", "Microbiology", "QR1-502", "soil pH", "03 medical and health sciences", "13. Climate action", "tropical rainforest", "biodiversity"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2016.00376"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2016.00376", "name": "item", "description": "10.3389/fmicb.2016.00376", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2016.00376"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-05T00:00:00Z"}}, {"id": "10.3389/fmicb.2019.01347", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:20:33Z", "type": "Journal Article", "created": "2019-06-25", "title": "Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture", "description": "Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that L. kefiranofaciens, a dominant organism in kefir, stands out among the Lactobacilli because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated L. plantarum in malolactic fermentation. We observed that L. plantarum thrives better on white than on red wine fermentations and has the largest number of phosphotransferase system among the bacteria observed in the wine communities. Also, L. plantarum together with Pantoea, Erwinia, Asaia, Gluconobacter, and Komagataeibacter genera had the highest number of genes involved in biosynthesis of amino acids.", "keywords": ["0301 basic medicine", "metagenomics", "0303 health sciences", "microbial communities", "Microbial communities", "Wine", "Microbiology", "QR1-502", "Computational biology", "lactic acid bacteria", "03 medical and health sciences", "Kefir", "computational biology", "Lactic acid bacteria", "Metagenomics", "Genomes", "wine", "genomes"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2019.01347"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2019.01347", "name": "item", "description": "10.3389/fmicb.2019.01347", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2019.01347"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-25T00:00:00Z"}}, {"id": "10.3389/fmicb.2023.1197770", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:20:35Z", "type": "Journal Article", "created": "2023-05-24", "title": "Effects of tomato inoculation with the entomopathogenic fungus Metarhizium brunneum on spider mite resistance and the rhizosphere microbial community", "description": "

Entomopathogenic fungi have been well exploited as biocontrol agents that can kill insects through direct contact. However, recent research has shown that they can also play an important role as plant endophytes, stimulating plant growth, and indirectly suppressing pest populations. In this study, we examined the indirect, plant-mediated, effects of a strain of entomopathogenic fungus, Metarhizium brunneum on plant growth and population growth of two-spotted spider mites (Tetranychus urticae) in tomato, using different inoculation methods (seed treatment, soil drenching and a combination of both). Furthermore, we investigated changes in tomato leaf metabolites (sugars and phenolics), and rhizosphere microbial communities in response to M. brunneum inoculation and spider mite feeding. A significant reduction in spider mite population growth was observed in response to M. brunneum inoculation. The reduction was strongest when the inoculum was supplied both as seed treatment and soil drench. This combination treatment also yielded the highest shoot and root biomass in both spider mite-infested and non-infested plants, while spider mite infestation increased shoot but reduced root biomass. Fungal treatments did not consistently affect leaf chlorogenic acid and rutin concentrations, but M. brunneum inoculation via a combination of seed treatment and soil drenching reinforced chlorogenic acid (CGA) induction in response to spider mites and under these conditions the strongest spider mite resistance was observed. However, it is unclear whether the M. brunneum-induced increase in CGA contributed to the observed spider mite resistance, as no general association between CGA levels and spider mite resistance was observed. Spider mite infestation resulted in up to two-fold increase in leaf sucrose concentrations and a three to five-fold increase in glucose and fructose concentrations, but these concentrations were not affected by fungal inoculation. Metarhizium, especially when applied as soil drench, impacted the fungal community composition but not the bacterial community composition which was only affected by the presence of spider mites. Our results suggest that in addition to directly killing spider mites, M. brunneum can indirectly suppress spider mite populations on tomato, although the underlying mechanism has not yet been resolved, and can also affect the composition of the soil microbial community.This study evaluated microbial communities of soil (0\uffe2\uff80\uff9310 cm) as affected by dryland cropping systems under different tillage practices after 5 years. The soil type was an Olton sandy loam with an average of 16.4% clay, 67.6% sand and 0.65 g kg\uffe2\uff88\uff921 of organic matter (OM). The cropping systems evaluated were grain sorghum (Sorghum bicolor L.)\uffe2\uff80\uff94cotton (Gossypium hirsutum) (Srg-Ct), cotton-winter rye (Secale cereale)-grain sorghum (Ct-Rye-Srg), and a rotation of forage (f) sorghum (Sorghum bicolor L. and Sorghum sudanense) with winter rye (Srf-Rye), which were under no-tillage (nt) and conventional tillage (ct) practices. Soil microbial communities under cotton based cropping systems (Srg-Ct and Ct-Rye-Srg) showed lower fungal:bacterial ratios compared to the soil under Srf-Rye. Soil under Srf-Rye showed higher population densities of Bacteroidetes and Proteobacteria while lower Actinobacteria compared to Srg-Ct and Ct-Rye-Srg. Chloroflexi, Gemmatimonadetes and Verrucomicrobiae were higher in tilled soil compared to the no-tilled plots. Regardless the limited irrigation available to sustain agricultural production within these dryland cropping systems, this study demonstrated that differences in microbial communities are more affected by crop rotation than tillage management history. Although soil fungal diversity was not analyzed in this study, pyrosequencing suggests that tillage practices can affect bacterial phyla distribution in this sandy soil.

", "keywords": ["FAME analysis", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "QH301-705.5", "bacterial diversity", "cropping systems", "pyrosequencing; soil microbial communities; bacterial diversity; FAME analysis; enzyme activities; cropping systems; tillage; GRACEnet", "15. Life on land", "6. Clean water", "GRACEnet", "03 medical and health sciences", "pyrosequencing", "enzyme activities", "soil microbial communities", "tillage", "Biology (General)"]}, "links": [{"href": "http://www.mdpi.com/1424-2818/2/6/910/pdf"}, {"href": "https://doi.org/10.3390/d2060910"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Diversity", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/d2060910", "name": "item", "description": "10.3390/d2060910", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/d2060910"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-06-07T00:00:00Z"}}, {"id": "10.3390/microorganisms13040848", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:20:51Z", "type": "Journal Article", "created": "2025-04-10", "title": "Assessing Microbial Activity and Rhizoremediation in Hydrocarbon and Heavy Metal-Impacted Soil", "description": "

Rhizodegradation enhances pollutant degradation through plant\u2013microbe interactions in the rhizosphere. Plant roots provide a colonisation surface and root exudates that promote microbial abundance and activity, facilitating organic pollutant breakdown via direct microbial degradation and co-metabolism. This study assessed the rhizodegradation of weathered petroleum hydrocarbons (PHCs) in heavy metal co-contaminated soil in a microcosm-scale pot trial. Treatments included Sinapis alba, Lolium perenne, a L. perenne + Trifolium repens mix, and Cichorium intybus, alongside a non-planted control. After 14 weeks, PHC concentrations were analysed via gas chromatography, and rhizosphere microbial communities were characterised through sequencing. Sinapis alba achieved the highest PHC degradation (68%), significantly exceeding the non-planted control (p < 0.05, Kruskal\u2013Wallis test). Hydrocarbon-degrading bacteria, including KCM-B-112, C1-B045, Hydrogenophaga, unclassified Saccharimonadales sp., and Pedobacter, were enriched in the rhizosphere, with the uncultured clade mle1-27 potentially contributing indirectly. Metals analysis of plant tissues showed that mustard could accumulate copper more than lead and zinc, despite higher concentrations of zinc and lead in the soil. These results highlight the potential of S. alba for rhizoremediation in PHC\u2013heavy metal co-contaminated soils.

", "keywords": ["petroleum hydrocarbons", "bioremediation", "QH301-705.5", "microbial communities", "phytoremediation", "Biology (General)", "heavy metals", "rhizodegradation", "Article"], "contacts": [{"organization": "Robert Conlon, David N. Dowling, Kieran J. Germaine,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3390/microorganisms13040848"}, {"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/microorganisms13040848", "name": "item", "description": "10.3390/microorganisms13040848", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms13040848"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-04-08T00:00:00Z"}}, {"id": "10.5061/dryad.gb5mkkwws", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:21:27Z", "type": "Dataset", "created": "2023-10-30", "title": "Biogeochemical cycles in holm oak dehesas", "description": "unspecified# Biogeochemical cycles in holm oak dehesas [https://doi.org/10.5061/dryad.gb5mkkwws](https://doi.org/10.5061/dryad.gb5mkkwws) ## Description of the data and file structure This dataset contains data from 9 holm oak dehesas (n=162 trees) in which holm oak leaf biochemistry (photosynthetic performance index, chlorophylls, VAZ and total tocopherols), root functional parameters (fine root branching, fine root length and fine root diameter), soil functional genes (carbon, nitrogen, phosphorus and sulfur cycling) and soil chemistry (mineral nitrogen, phosphate, potassium, organic carbon, organic nitrogen, organic phosphorus and pH) are related. The dataset includes: **Aboveground leaf parameters:** * Photosynthetic performance index (PiAbs), as a proxy of the photosynthetic energy conservation. * Chlorophylls (Chl a + b, \u03bcmol m-2), as a proxy of light harvesting regulation and plant acclimation. * Violaxanthin cycle pigment pool (VAZ, violaxanthin + zeaxanthin + antheraxanthin, mmol mol Chl-1), as proxy photoprotective compounds through thermal dissipation. * Total tocopherols (mmol mol Chl-1), as a proxy of antioxidant compounds. * Defoliation (%), as a proxy of crown transparency. * Crown health. Is the linear combination of the variables mentioned above. **Belowground root parameters:** * Fine root branching. * Fine root leghth (cm). Mean length of the fine roots. * Fine root diameter (cm). Mean diameter of the fine roots. **Soil chemical analyses** * Total organic carbon content (org. C), total organic nitrogen content (org. N) and total organic phosphorus content (org. P). These analyses were expressed as mg of organic C, N or P per 100 mg of soil (%). * Mineral N (ammonium+nitrate+nitrite) was expresed as ppm, \u03bcg per g. * Phosphate was expresed as ppm, \u03bcg per g. * Potassium was expresed as ppm, \u03bcg per g. * pH **Soil microbial functional genes** * Carbon hydrolysis genes (i.e., genes involved in starch, hemicellulose, cellulose, chitin, pectin and lignin degradation). abfA, manB, Xyl, cex, pgu, glx, lig, mnp, apu, iso-plu, ammiA, sga, chiA * Carbon fixation genes. aclB,accA, mcrA, pccA, korA, smtA, frdA, rbcL, acsB, acsA, acsE. * Methane oxidation. pmoA, mmoX, mxaF, pqq-mdh * Nitrogen cycling (i.e., genes involved in N fixation, nitrification, denitrification, ammonification, anaerobic ammonium oxidation, assimilatory and dissimilatory N reduction and organic N mineralization. nifH, amoA1, amoA2, amoB, ureC, gdhA, hao, nxrA, nirS, nirK, nosZ, hzsB. * Phosphorus cycling genes (i.e., mineralization, solubilization, biosynthesis and hydrolysis of phosphorus). gcd, pqqC, phoD, phoX, phnK, ppx, ppk. * Sulfur cycling genes. soxY, yedZ, dsrA, dsrB, apsA. These genes were expresed as the abundance, gene copy number relative to 16S. The primer pairs and the encoded enzymes of the analyzed soil microbial functional genes may be found in the electronic supplementary material published in Table S2 of the manuscript.", "keywords": ["2. Zero hunger", "Quercus ilex", "defoliation", "13. Climate action", "Dehesa", "FOS: Agricultural sciences", "soil microbial communities", "14. Life underwater", "biogeochemical cycles", "15. Life on land", "soil functional genes"], "contacts": [{"organization": "Encinas-Valero, Manuel, Esteban, Raquel, Here\u015f, Ana-Mar\u00eda, Vivas, Mar\u00eda, Solla, Alejandro, Moreno, Gerardo, Corcobado, Tamara, Odriozolacrobiology, I\u00f1aki, Garbisu, Carlos, Epelde, Lur, Curiel Yuste, Jorge,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.gb5mkkwws"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.gb5mkkwws", "name": "item", "description": "10.5061/dryad.gb5mkkwws", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.gb5mkkwws"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-11-06T00:00:00Z"}}, {"id": "1887/3631563", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:25:11Z", "type": "Journal Article", "created": "2023-05-24", "title": "Effects of tomato inoculation with the entomopathogenic fungus Metarhizium brunneum on spider mite resistance and the rhizosphere microbial community", "description": "

Entomopathogenic fungi have been well exploited as biocontrol agents that can kill insects through direct contact. However, recent research has shown that they can also play an important role as plant endophytes, stimulating plant growth, and indirectly suppressing pest populations. In this study, we examined the indirect, plant-mediated, effects of a strain of entomopathogenic fungus, Metarhizium brunneum on plant growth and population growth of two-spotted spider mites (Tetranychus urticae) in tomato, using different inoculation methods (seed treatment, soil drenching and a combination of both). Furthermore, we investigated changes in tomato leaf metabolites (sugars and phenolics), and rhizosphere microbial communities in response to M. brunneum inoculation and spider mite feeding. A significant reduction in spider mite population growth was observed in response to M. brunneum inoculation. The reduction was strongest when the inoculum was supplied both as seed treatment and soil drench. This combination treatment also yielded the highest shoot and root biomass in both spider mite-infested and non-infested plants, while spider mite infestation increased shoot but reduced root biomass. Fungal treatments did not consistently affect leaf chlorogenic acid and rutin concentrations, but M. brunneum inoculation via a combination of seed treatment and soil drenching reinforced chlorogenic acid (CGA) induction in response to spider mites and under these conditions the strongest spider mite resistance was observed. However, it is unclear whether the M. brunneum-induced increase in CGA contributed to the observed spider mite resistance, as no general association between CGA levels and spider mite resistance was observed. Spider mite infestation resulted in up to two-fold increase in leaf sucrose concentrations and a three to five-fold increase in glucose and fructose concentrations, but these concentrations were not affected by fungal inoculation. Metarhizium, especially when applied as soil drench, impacted the fungal community composition but not the bacterial community composition which was only affected by the presence of spider mites. Our results suggest that in addition to directly killing spider mites, M. brunneum can indirectly suppress spider mite populations on tomato, although the underlying mechanism has not yet been resolved, and can also affect the composition of the soil microbial community.Resource acquisition and growth yield are fundamental traits of microorganisms that have consequences for ecosystem functioning. However, there is a lack of empirical observations linking these traits. Using a landscape-scale survey of temperate near-neutral pH soils, we show tradeoffs in key community-level parameters linked to these traits. Increased investment into extracellular enzymes was associated with reduced growth yield; this reduction was linked more to carbon than nitrogen acquisition enzymes suggesting smaller stoichiometric constraints on community metabolism in examined soils.Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function. 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 .

Rhizodegradation enhances pollutant degradation through plant\u2013microbe interactions in the rhizosphere. Plant roots provide a colonisation surface and root exudates that promote microbial abundance and activity, facilitating organic pollutant breakdown via direct microbial degradation and co-metabolism. This study assessed the rhizodegradation of weathered petroleum hydrocarbons (PHCs) in heavy metal co-contaminated soil in a microcosm-scale pot trial. Treatments included Sinapis alba, Lolium perenne, a L. perenne + Trifolium repens mix, and Cichorium intybus, alongside a non-planted control. After 14 weeks, PHC concentrations were analysed via gas chromatography, and rhizosphere microbial communities were characterised through sequencing. Sinapis alba achieved the highest PHC degradation (68%), significantly exceeding the non-planted control (p < 0.05, Kruskal\u2013Wallis test). Hydrocarbon-degrading bacteria, including KCM-B-112, C1-B045, Hydrogenophaga, unclassified Saccharimonadales sp., and Pedobacter, were enriched in the rhizosphere, with the uncultured clade mle1-27 potentially contributing indirectly. Metals analysis of plant tissues showed that mustard could accumulate copper more than lead and zinc, despite higher concentrations of zinc and lead in the soil. These results highlight the potential of S. alba for rhizoremediation in PHC\u2013heavy metal co-contaminated soils.

", "keywords": ["petroleum hydrocarbons", "bioremediation", "QH301-705.5", "microbial communities", "phytoremediation", "Biology (General)", "heavy metals", "rhizodegradation", "Article"]}, "links": [{"href": "https://doi.org/PMC12029208"}, {"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": "PMC12029208", "name": "item", "description": "PMC12029208", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC12029208"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-04-08T00:00:00Z"}}, {"id": "b05d5d83-e03a-4eea-a705-853abcc7473d", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[9.24, 51.09], [9.24, 54.71], [11.22, 54.71], [11.22, 51.09], [9.24, 51.09]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "rhizosphere"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata"}, {"id": "Wheat microbial communities"}, {"id": "soil and root-associated microbiota"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the Rhizo4Bio - RhizoWheat's research activities.\" Although every care has been taken in preparing and testing the data, the Rhizo4Bio - RhizoWheat and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the Rhizo4Bio - RhizoWheat and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The Rhizo4Bio - RhizoWheat and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2023-08-16", "type": "Dataset", "created": "2023-07-17", "language": "eng", "title": "Influence of plant stage and cropping history on soil and root-associated prokaryotic community structure and composition in wheat", "description": "We conducted field studies at two locations in Germany in 2020 and 2021 to study the effect of plant developmental stage and wheat rotational position on the soil, rhizosphere and rhizoplane prokaryotic communities. Soil and root samples were taken from long-term field experiments in Hohenshulen (Kiel) and Harste (G\u00f6ttingen), Germany. \nExperimental design :\nThe crop rotational trial in Hohenschulen was established 1989 and included the factors a) cropping history, i.e. a first (W1) and a third wheat (W3) after a break crop (rapeseed), b) winter wheat cultivars (four levels), and c) N fertilization (four levels). Each field plot of 27 m\u00b2 was replicated four times in a split-plot design. Treatment samples were taken in W1 and W3 plots of the cultivar \u201cNordkap\u201d of the optimal N-level plots (240 kg N/ha). The crop rotational trial in Harste was established 2006 and included eight crop rotations, out of which two with winter wheat were included in this study, (1) a wheat monoculture and (2) a winter oilseed rape - winter wheat \u2013 winter wheat \u2013 grain pea \u2013 sugar beet \u2013 winter wheat rotation. Each crop rotational element is cultivated every year, which allowed us to sample three different crop rotational positions of winter wheat simultaneously per year. In Harste treatment samples were taken from the first wheat after winter oilseed rape grown as break crop (W1), from the second wheat after winter oilseed rape grown as break crop (W2), and from the long-term wheat monoculture (WM). Each plot of 110 m\u00b2 was replicated three times within a split-plot design containing incomplete blocks.\nFor each replicate, 9 -12 soil cores (0-30 cm depth), sampled randomly across the respective total field plot area, were combined. Soil samples were sieved (4 mm mesh-size) and all samples were split among project partners for enzymology testing, fungal microbiome and prokaryotic microbiome analyses. For the root-associated samples 9-12 wheat plants were picked per treatment (wheat rotational positions) across the field plot area and combined (composite sample). Samples were taken in 2020 at the plant developmental stages flowering (BBCH 59-65) and early ripening (BBCH 69-75) and in 2021 in addition at the end of tillering (BBCH 30). Root-associated samples were split at the field sites into the rhizosphere fraction by brushing off the soil particles from roots using sterile disposable toothbrushes and wearing gloves at all times. The remaining roots were put in clean plastic bags. All samples were transported to the laboratory on ice. At the lab the rhizoplane fraction was taken by washing off the tightly adhering soil particles from the roots using 0.3 % NaCl (5 g roots/45 ml buffer) and a Stomacher machine. \nThe prokaryotic community in bulk soils, rhizosphere and rhizoplane of different wheat rotational positions was analyzed analyzed by high-throughput Illumina sequencing of the 16S rRNA gene fragments (V3-V4 region) amplified from total community. A total of 289 samples was investigated over two years.", "formats": [{"name": "CSV"}], "keywords": ["Soil", "rhizosphere", "opendata", "Wheat microbial communities", "soil and root-associated microbiota", "Boden"], "contacts": [{"name": "Andrea Braun-Kiewnick", "organization": "Julius Kuehn-Institute, Braunschweig, Germany", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "andrea.braun-kiewnick@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "https://orcid.org/0009-0008-7369-8717", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Doreen Babin", "organization": "Julius K\u00fchn-Institut", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "doreen.babin@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "https://orcid.org/0000-0001-7144-8898", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": null, "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Adriana Giongo", "organization": "Julius Kuehn-Institute, Braunschweig, Germany", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "adriana.giongo@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "orcid.org/0000-0002-1412-7040", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Kornelia Smalla", "organization": "Julius K\u00fchn-Institut", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "kornelia.smalla@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "https://orcid.org/0000-0001-7653-5560", "name_url": "", "description": "ORCID:", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"organization": "Julius Kuehn-Institute, Braunschweig, Germany", "roles": ["contributor"]}]}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=b05d5d83-e03a-4eea-a705-853abcc7473d", "rel": "information"}, {"rel": "self", "type": "application/geo+json", "title": "b05d5d83-e03a-4eea-a705-853abcc7473d", "name": "item", "description": "b05d5d83-e03a-4eea-a705-853abcc7473d", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/b05d5d83-e03a-4eea-a705-853abcc7473d"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-08-16T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microbial+communities&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microbial+communities&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microbial+communities&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microbial+communities&offset=32", "hreflang": "en-US"}], "numberMatched": 32, "numberReturned": 32, "distributedFeatures": [], "timeStamp": "2026-07-27T04:00:07.699509Z"}