The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H 2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.
IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota , and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment\uffe2\uff80\uff94including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.
", "keywords": ["570", "Bacteria", "Fungi", "Antarctic Regions", "Chloroflexi", "15. Life on land", "Survival strategies", "Cold Temperature", "Extremophiles", "13. Climate action", "Antarctica", "Endolithic communities", "Metagenomics", "14. Life underwater", "Sugars", "Settore BIO/19 - MICROBIOLOGIA GENERALE"]}, "links": [{"href": "https://doi.org/10.1128/aem.02264-23"}, {"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.02264-23", "name": "item", "description": "10.1128/aem.02264-23", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02264-23"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-19T00:00:00Z"}}, {"id": "10.3389/fmicb.2021.758395", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:18:37Z", "type": "Journal Article", "created": "2022-01-12", "title": "Fresh rumen liquid inoculant enhances the rumen microbial community establishment in pre-weaned dairy calves", "description": "The development of the functional rumen in calves involves a complex interplay between the host and host-related microbiome. Attempts to modulate rumen microbial community establishment may therefore have an impact on weaning success, calf health, and animal performance later in life. In this experiment, we aimed to elucidate how rumen liquid inoculum from an adult cow, provided to calves during the pre-weaning period, influences the establishment of rumen bacterial, archaeal, fungal, and ciliate protozoan communities in monozygotic twin calves (n = 6 pairs). The calves were divided into treatment (T-group) and control (C-group) groups, where the T-group received fresh rumen liquid as an oral inoculum during a 2\uffe2\uff80\uff938-week period. The C-group was not inoculated. The rumen microbial community composition was determined using bacterial and archaeal 16S ribosomal RNA (rRNA) gene, protozoal 18S rRNA gene, and fungal ITS1 region amplicon sequencing. Animal weight gain and feed intake were monitored throughout the experiment. The T-group tended to have a higher concentrate intake (Treatment: p < 0.08) and had a significantly higher weekly weight gain (Treatment: p < 0.05), but no significant difference in volatile fatty acid concentrations between the groups was observed. In the T-group, the inoculum stimulated the earlier establishment of mature rumen-related bacterial taxa, affecting significant differences between the groups until 6 weeks of age. The inoculum also increased the archaeal operational taxonomic unit (OTU) diversity (Treatment: p < 0.05) but did not affect the archaeal quantity. Archaeal communities differed significantly between groups until week 4 (p = 0.02). Due to the inoculum, ciliate protozoa were detected in the T-group in week 2, while the C-group remained defaunated until 6 weeks of age. In week 8, Eremoplastron dilobum was the dominant ciliate protozoa in the C-group and Isotricha sp. in the T-group, respectively. The Shannon diversity of rumen anaerobic fungi reduced with age (Week: p < 0.01), and community establishment was influenced by a change of diet and potential interaction with other rumen microorganisms. Our results indicate that an adult cow rumen liquid inoculum enhanced the maturation of bacterial and archaeal communities in pre-weaning calves\uffe2\uff80\uff99 rumen, whereas its effect on eukaryotic communities was less clear and requires further investigation.
", "keywords": ["0301 basic medicine", "570", "Anaerobic fungi", "microbiome establishment", "archaea", "Rumen function", "Microbiome manipulation", "Microbiology", "630", "Microbiome establishment", "ciliate protozoa", "03 medical and health sciences", "Dairy calf", "anaerobic fungi", "bacteria", "[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology", "2. Zero hunger", "0303 health sciences", "ta412", "Bacteria", "dairy calf", "Animal science", " dairy science", "Archaea", "Ciliate protozoa", "QR1-502", "rumen function", "[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology", "microbiome manipulation"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2021.758395"}, {"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.2021.758395", "name": "item", "description": "10.3389/fmicb.2021.758395", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2021.758395"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-12T00:00:00Z"}}, {"id": "10.1016/j.ejsobi.2013.10.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:15:29Z", "type": "Journal Article", "created": "2013-11-02", "title": "Effect Of Biochar Addition On Soil Microbial Community In A Wheat Crop", "description": "Biochar is known to enhance soil fertility and C sequestration, but relatively little information is currently available about its effect on soil microbial community, a component of terrestrial ecosystems that plays a key role in nutrient cycling. This study tested the effects of soil amendment with two loads of wood-derived biochar (30 and 60 t ha(-1)) in a wheat crop in Tuscany (Italy). Soil samples were collected 3 and 14 months after treatments over two successive growing seasons, and analysed for pH, total organic C (C-org), extractable C (C-ext), microbial biomass-C (C-mic), 25 specific microbial activities, mean substrate-induced respiration (mSIR) for 25 substrates, functional microbial diversity and bacterial genetic diversity. No significant effect of biochar treatment was observed on C-org, C-ext, C-mic, microbial quotient (C-mic % C-org) or genetic diversity. An increase in mSIR, some specific microbial activities and soil pH, and a significant change in functional diversity were observed 3 months after treatment. In contrast, no effect of biochar was detected 14 months after treatment for the parameters considered, except for a small but significant increase in pH. Our data suggest that biochar addition stimulated soil microbial activity without causing any apparent disturbance, but this positive effect was very short-lived. (C) 2013 Published by Elsevier Masson SAS.", "keywords": ["2. Zero hunger", "Soil management", "Wood-derived biochar", "Soil bacterial diversity; Soil management; Soil microbial activity; Soil microbial functional diversity; Wheat crop; Wood-derived biochar;", "Soil microbial functional diversity", "Wheat crop", "Soil microbial activity", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "Soil bacterial diversity", "15. Life on land", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1016/j.ejsobi.2013.10.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/European%20Journal%20of%20Soil%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ejsobi.2013.10.007", "name": "item", "description": "10.1016/j.ejsobi.2013.10.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ejsobi.2013.10.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-01-01T00:00:00Z"}}, {"id": "10.1002/ecy.1513", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:14Z", "type": "Journal Article", "created": "2016-07-02", "title": "Land Use Intensification In The Humid Tropics Increased Both Alpha And Beta Diversity Of Soil Bacteria", "description": "AbstractAnthropogenic pressures on tropical forests are rapidly intensifying, but our understanding of their implications for biological diversity is still very limited, especially with regard to soil biota, and in particular soil bacterial communities. Here we evaluated bacterial community composition and diversity across a gradient of land use intensity in the eastern Amazon from undisturbed primary forest, through primary forests varyingly disturbed by fire, regenerating secondary forest, pasture, and mechanized agriculture. Soil bacteria were assessed by paired\uffe2\uff80\uff90end Illumina sequencing of 16S rRNA gene fragments (V4 region). The resulting sequences were clustered into operational taxonomic units (OTU) at a 97% similarity threshold. Land use intensification increased the observed bacterial diversity (both OTU richness and community heterogeneity across space) and this effect was strongly associated with changes in soil pH. Moreover, land use intensification and subsequent changes in soil fertility, especially pH, altered the bacterial community composition, with pastures and areas of mechanized agriculture displaying the most contrasting communities in relation to undisturbed primary forest. Together, these results indicate that tropical forest conversion impacts soil bacteria not through loss of diversity, as previously thought, but mainly by imposing marked shifts on bacterial community composition, with unknown yet potentially important implications for ecological functions and services performed by these communities.
", "keywords": ["Rios de composi\u00e7\u00e3o de comunidade bacteriana", "2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "550", "Bacteria", "Biodiversidade subterr\u00e2nea", "Agriculture", "Biodiversity", "Forests", "15. Life on land", "Below\u2010ground biodiversity", "High\u2010throughput sequencing", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Sequenciamento de alto rendimento", "Rivers of bacterial community composition", "Soil Microbiology"]}, "links": [{"href": "https://eprints.lancs.ac.uk/id/eprint/82660/1/de_Carvalho_et_al_2016_raw_pdf.pdf"}, {"href": "https://doi.org/10.1002/ecy.1513"}, {"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": "10.1002/ecy.1513", "name": "item", "description": "10.1002/ecy.1513", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecy.1513"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-09-09T00:00:00Z"}}, {"id": "10.1007/s10021-020-00497-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:37Z", "type": "Journal Article", "created": "2020-03-30", "title": "Biocrusts Modulate Responses of Nitrous Oxide and Methane Soil Fluxes to Simulated Climate Change in a Mediterranean Dryland", "description": "Little is known about the role of biocrusts in regulating the responses of N2O and CH4 fluxes to climate change in drylands. Here, we aim to help filling this knowledge gap by using an 8-year field experiment in central Spain where temperature and rainfall are being manipulated (~\u20091.9\u00b0C warming, 33% rainfall reduction and their combination) in areas with and without well-developed biocrust communities. Areas with initial high cover of well-developed biocrusts showed lower N2O emissions, enhanced CH4 uptake and higher abundances of functional genes linked to N2O and CH4 fluxes compared with areas with poorly developed biocrusts. Moreover, biocrusts modulated the responses of gases emissions and related functional genes to warming and rainfall reductions. Specifically, we found under rainfall exclusion and its combination with warming a sharp reduction in N2O fluxes (~\u200996% and ~\u2009197%, respectively) only under well-developed biocrust cover. Warming and its combination with rainfall exclusion reduced CH4 consumption in areas with initial low cover of well-developed biocrust, whereas rainfall exclusion enhanced CH4 uptake only in areas with high initial cover of well-developed biocrusts. Similarly, the combination of warming and rainfall exclusion increased the abundance of the nosZ gene compared to the rainfall exclusion treatment and increased the abundance of the pmoA gene compared to the control, but only in areas with low biocrust cover. Taken together, our results indicate that well-developed biocrust communities could counteract the impact of warming and altered rainfall patterns on soil N2O and CH4 fluxes, highlighting their importance and the need to preserve them to minimize climate change impacts on drylands. A. L. is supported by a FPI fellowship from the Spanish Ministry of Economy and Competitiveness (BES-2014-067831). M.D-B. acknowledges support from the Marie Sklodowska-Curie Actions of the Horizon 2020 Framework Programme H2020-MSCA-IF-2016 under REA Grant Agreement No. 702057 (CLIMIFUN) and the BES Grant Agreement No. LRA17 1193 (MUSGONET). J.D acknowledges support from the Funda\u00e7\u00e3o para Ci\u00eancia e Tecnologia (IF/00950/2014) and the FEDER, within the PT2020 Partnership Agreement and COMPETE 2020 (UID/BIA/04004/2013). This research was supported by the European Research Council (ERC Grant Agreements 242658 [BIOCOM] and 647038 [BIODESERT]), by the Spanish Ministry of Economy and Competitiveness (BIOMOD project, ref. CGL2013-44661-R and AGL2015-64582-C3-3-R project) and by the Comunidad de Madrid and European Structural and Investment Funds (AGRISOST-CM S2013/ABI-2717). F.T.M. acknowledges support from Generalitat Valenciana (BIOMORES project, ref. CIDEGENT/2018/041). B.K.S research on the topic of biodiversity and ecosystem functions is funded by Australian Research Council (DP170104634).", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "arid regions", "Nitrous oxide", "nitrous oxide", "Mediterranean Region", "methane", "Ecolog\u00eda", "15. Life on land", "climatic changes", "Dryland", "03 medical and health sciences", "Methanotrophs", "13. Climate action", "XXXXXX - Unknown", "Biocrust", "crust vegetation", "Denitrifiers", "denitrifying bacteria", "Methane"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s10021-020-00497-5.pdf"}, {"href": "https://doi.org/10.1007/s10021-020-00497-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecosystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10021-020-00497-5", "name": "item", "description": "10.1007/s10021-020-00497-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10021-020-00497-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-30T00:00:00Z"}}, {"id": "10.1016/j.cej.2022.135748", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:15:22Z", "type": "Journal Article", "created": "2022-03-19", "title": "Evaluating bioelectrochemically-assisted constructed wetland (METland\u00ae) for treating wastewater: Analysis of materials, performance and electroactive communities", "description": "METland\u00ae technology consists of a bioengineering strategy for treating wastewater by integrating microbial electrochemical concepts into constructed wetland systems to enhance pollutants removal. In this context, we have constructed planted (Iris sibirica) biofilters to assess the impact of different electrically conductive bed materials (electroconductive coke, electroconductive biochar, non-electroconductive biochar and gravel) by analyzing the (i) wastewater treatment efficiency (COD and nitrogen removal), (ii) bioelectrochemical response, and (iii) diversity of microbial communities. Electrically conductive materials outperformed non-conductive ones allowing removal rates as high as 175-180 gCOD/bed*m3 day capable to support footprint as low 0.4 m2/pe. In contrast, the highest nitrogen removal rates were achieved with non-conductive biochar in presence of plants (80 %) regardless the anoxic conditions of the assay. This was confirmed by the presence of annamox bacteria like Planctomycetes. Furthermore, the presence of a marked electric potential profile along the bed height in electroconductive materials together with redox pairs (cyclic voltammetry analysis) demonstrated an effective electron flow from bottom to uppermost layers of the bed (geoconductor mechanism). In electroconductive biochar, such effective conductivity-based model co-exists with a geobattery mechanism due to presence of electroactive phenolic and carbonyl/quinone groups and/or microporosity. Microbial biodiversity analysis revealed the impact of plants just at the upper layers of the biofilters where roots and Rhizobium predominate. Bacteria from genus Clostridium were dominant in gravel inert material; in contrast, bacteria from genus Geobacter (12%) and Trichococcus (30%) outcompete the rest of communities for an effective colonization of carbonaceous beds, suggesting their main role as part of the electrosyntrophies mechanism after METland\u00ae.", "keywords": ["Electroactive bacteria", "0301 basic medicine", "0303 health sciences", "Metland\u00ae", "Electroconductive biochar", "Wastewater treatment", "QD Chemistry", "6. Clean water", "Constructed wetland", "03 medical and health sciences", "13. Climate action", "Microbial electrochemistry", "TD Environmental technology. Sanitary engineering", "Qu\u00edmica F\u00edsica"]}, "links": [{"href": "https://doi.org/10.1016/j.cej.2022.135748"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemical%20Engineering%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.cej.2022.135748", "name": "item", "description": "10.1016/j.cej.2022.135748", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.cej.2022.135748"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2011.08.031", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:15:23Z", "type": "Journal Article", "created": "2011-09-22", "title": "Impact Of Biochar Application To A Mediterranean Wheat Crop On Soil Microbial Activity And Greenhouse Gas Fluxes", "description": "Biochar has been recently proposed as a management strategy to improve crop productivity and global warming mitigation. However, the effect of such approach on soil greenhouse gas fluxes is highly uncertain and few data from field experiments are available. In a field trial, cultivated with wheat, biochar was added to the soil (3 or 6 kg m(-2)) in two growing seasons (2008/2009 and 2009/2010) so to monitor the effect of treatments on microbial parameters 3 months and 14 months after char addition. N(2)O, CH(4) and CO(2) fluxes were measured in the field during the first year after char addition. Biochar incorporation into the soil increased soil pH (from 5.2 to 6.7) and the rates of net N mineralization, soil microbial respiration and denitrification activity in the first 3 months, but after 14 months treated and control plots did not differ significantly. No changes in total microbial biomass and net nitrification rate were observed. In char treated plots, soil N(2)O fluxes were from 26% to 79% lower than N(2)O fluxes in control plots, excluding four sampling dates after the last fertilization with urea, when N(2)O emissions were higher in char treated plots. However, due to the high spatial variability, the observed differences were rarely significant. No significant differences of CH(4) fluxes and field soil respiration were observed among different treatments, with just few exceptions. Overall the char treatments showed a minimal impact on microbial parameters and GHG fluxes over the first 14 months after biochar incorporation.", "keywords": ["Crops", " Agricultural", "Greenhouse Effect", "Nitrous Oxide", "Biochar; CH; 4; CO; 2; Denitrification; N; 2; O; Nitrification;", "630", "12. Responsible consumption", "Fertilizers", "Soil Microbiology", "Triticum", "2. Zero hunger", "CH4", "Bacteria", "N2O", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "Nitrification", "6. Clean water", "Biochar", "13. Climate action", "Charcoal", "Denitrification", "0401 agriculture", " forestry", " and fisheries", "CO2", "Gases", "Methane", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2011.08.031"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2011.08.031", "name": "item", "description": "10.1016/j.chemosphere.2011.08.031", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2011.08.031"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-11-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2022.137472", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:15:23Z", "type": "Journal Article", "created": "2022-12-07", "title": "Assembled mixed co-cultures for emerging pollutant removal using native microorganisms from sewage sludge", "description": "The global pharmaceutical pollution caused by drug consumption (>100,000 tonnes) and its disposal into the environment is an issue which is currently being addressed by bioremediation techniques, using single or multiple microorganisms. Nevertheless, the low efficiency and the selection of non-compatible species interfere with the success of this methodology. This paper proposes a novel way of obtaining an effective multi-domain co-culture, with the capacity to degrade multi-pharmaceutical compounds simultaneously. To this end, seven microorganisms (fungi and bacteria) previously isolated from sewage sludge were investigated to enhance their degradation performance. All seven strains were factorially mixed and used to assemble different artificial co-cultures. Consequently, 127 artificial co-cultures were established and ranked, based on their fitness performance, by using the BSocial analysis web tool. The individual strains were categorized according to their social behaviour, whose net effect over the remaining strains was defined as 'Positive', 'Negative' or 'Neutral'. To evaluate the emerging-pollutant degradation rate, the best 10 co-cultures, and those which contained the social strains were then challenged with three different Pharmaceutical Active compounds (PhACs): diclofenac, carbamazepine and ketoprofen. The co-cultures with the fungi Penicillium oxalicum XD-3.1 and Penicillium rastrickii were able to degrade PhACs. However, the highest performance (>80% degradation) was obtained by the minimal active microbial consortia consisting of both Penicillium spp., Cladosporium cladosporoides and co-existing bacteria. These consortia transformed the PhACs to derivate molecules through hydroxylation and were released to the media, resulting in a low ecotoxicity effect. High-throughput screening of co-cultures provides a quick, reliable and efficient method to narrow down suitable degradation co-cultures for emerging PhAC contaminants while avoiding toxic metabolic derivatives.", "keywords": ["Sewage", "Bacteria", "Fungi", "HTGrowth", "Waste Disposal", " Fluid", "01 natural sciences", "Coculture Techniques", "6. Clean water", "12. Responsible consumption", "Biodegradation", " Environmental", "Pharmaceutical Preparations", "13. Climate action", "Environmental Pollutants", "BSocial", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2022.137472"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2022.137472", "name": "item", "description": "10.1016/j.chemosphere.2022.137472", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2022.137472"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2016.03.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:16:08Z", "type": "Journal Article", "created": "2016-03-26", "title": "Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland", "description": "Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA. Microbial respiration was 28-37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland.
", "keywords": ["FUNGAL", "2. Zero hunger", "106022 Mikrobiologie", "Nitrogen addition", "BACTERIAL", "NITROGEN DEPOSITION", "GROWTH EFFICIENCY", "FOREST FLOOR", "Nutrients", "04 agricultural and veterinary sciences", "15. Life on land", "Stoichiometry", "ORGANIC-MATTER", "RESPIRATION", "106026 \u00d6kosystemforschung", "13. Climate action", "Nutrient limitation", "Microbial growth yield", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Mean residence time", "STOICHIOMETRIC CONTROLS", "ENZYME-ACTIVITY", "106026 Ecosystem research", "COMMUNITY STRUCTURE"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2016.03.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2016.03.008", "name": "item", "description": "10.1016/j.soilbio.2016.03.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2016.03.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2023.161600", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:16:00Z", "type": "Journal Article", "created": "2023-01-18", "title": "Risk reductions during pyrene biotransformation and mobilization in a model plant-bacteria-biochar system", "description": "The productive application of motile microorganisms for degrading hydrophobic contaminants in soil is one of the most promising processes in modern remediation due to its sustainability and low cost. However, the incomplete biodegradation of the contaminants and the formation of the intermediary metabolites in the process may increase the toxicity in soil during bioremediation, and motile inoculants may mobilize the pollutants through biosorption. Therefore, controlling these factors should be a fundamental part of soil remediation approaches. The aim of this study was to evaluate the sources of risk associated with the cometabolism-based transformation of 14C-labeled pyrene by inoculated Pseudomonas putida G7 and identify ways to minimize risk. Our model scenario examined the increase in bioaccessibility to a distant source of contamination facilitated by sunflower (Helianthus annuus L.) roots. A biochar trap for mobilized pollutant metabolites and bacteria has also been employed. The experimental design consisted of pots filled with a layer of sand with 14C-labeled pyrene (88 mg kg-1) as a contamination focus located several centimeters from the inoculation point. Half of the pots included a biochar layer at the bottom. The pots were incubated in a greenhouse with sunflower plants and P. putida G7 bacteria. Pots with sunflower plants showed a higher biodegradation of pyrene, its mobilization as metabolites through the percolate and the roots, and bacterial mobilization toward the source of contamination, also resulting in increased pyrene transformation. In addition, the biochar layer efficiently reduced the concentrations of pyrene metabolites collected in the leachates. Therefore, the combination of plants, motile bacteria and biochar safely reduced the risk caused by the biological transformation of pyrene.", "keywords": ["Risk", "2. Zero hunger", "570", "Pyrenes", "Bacteria", "04 agricultural and veterinary sciences", "Plants", "01 natural sciences", "Polycyclic aromatic hydrocarbons", "6. Clean water", "Sunflower", "Soil", "Biodegradation", " Environmental", "13. Climate action", "Biodegradation", "Soil Pollutants", "0401 agriculture", " forestry", " and fisheries", "Polycyclic Aromatic Hydrocarbons", "Bioremediation", "Biotransformation", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2023.161600"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2023.161600", "name": "item", "description": "10.1016/j.scitotenv.2023.161600", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2023.161600"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2018.09.128", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:15:32Z", "type": "Journal Article", "created": "2018-09-28", "title": "A rationale for the high limits of quantification of antibiotic resistance genes in soil", "description": "The determination of values of abundance of antibiotic resistance genes (ARGs) per mass of soil is extremely useful to assess the potential impacts of relevant sources of antibiotic resistance, such as irrigation with treated wastewater or manure application. Culture-independent methods and, in particular, quantitative PCR (qPCR), have been regarded as suitable approaches for such a purpose. However, it is arguable if these methods are sensitive enough to measure ARGs abundance at levels that may represent a risk for environmental and human health. This study aimed at demonstrating the range of values of ARGs quantification that can be expected based on currently used procedures of DNA extraction and qPCR analyses. The demonstration was based on the use of soil samples spiked with known amounts of wastewater antibiotic resistant bacteria (ARB) (Enterococcus faecalis, Escherichia coli, Acinetobacter johnsonii, or Pseudomonas aeruginosa), harbouring known ARGs, and also on the calculation of expected values determined based on qPCR. The limits of quantification (LOQ) of the ARGs (vanA, qnrS, blaTEM, blaOXA, blaIMP, blaVIM) were observed to be approximately 4 log-units per gram of soil dry weight, irrespective of the type of soil tested. These values were close to the theoretical LOQ values calculated based on currently used DNA extraction methods and qPCR procedures. The observed LOQ values can be considered extremely high to perform an accurate assessment of the impacts of ARGs discharges in soils. A key message is that ARGs accumulation will be noticeable only at very high doses. The assessment of the impacts of ARGs discharges in soils, of associated risks of propagation and potential transmission to humans, must take into consideration this type of evidence, and avoid the simplistic assumption that no detection corresponds to risk absence.", "keywords": ["0301 basic medicine", "2. Zero hunger", "LOD - Limit of detection", "0303 health sciences", "Acinetobacter", "Drug Resistance", " Microbial", "Wastewater", "Real-Time Polymerase Chain Reaction", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "Manure", "Quantitative PCR", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "13. Climate action", "Pseudomonas aeruginosa", "Enterococcus faecalis", "Escherichia coli", "LOQ - Limit of quantification", "Soil Microbiology", "Risk assessment"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2018.09.128"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envpol.2018.09.128", "name": "item", "description": "10.1016/j.envpol.2018.09.128", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2018.09.128"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2020.114002", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:15:32Z", "type": "Journal Article", "created": "2020-01-21", "title": "Elucidating biotransformation pathways of ofloxacin in lettuce (Lactuca sativa L)", "description": "Antibiotics can be uptaken by plants from soil desorption or directly from irrigation water, but their metabolization pathways in plants are largely unknown. In this paper, an analytical workflow based on high-resolution mass spectrometry was applied for the systematic identification of biotransformation products of ofloxacin in lettuce. The targeted metabolites were selected by comparing the mass chromatograms of exposed with control samples using an advanced spectra-processing method (Fragment Ion Search). The innovative methodology presented allowed us to identify a total of 11 metabolites, including 5 ofloxacin metabolites that are being reported for the first time in plants. Accordingly, major transformation pathways were proposed revealing insight into how ofloxacin and related chemicals are metabolized in lettuce. Furthermore, the influence of biotransformation on potential residual antimicrobial activity of identified compounds was discussed. Human exposure to antibiotics at doses below the minimum inhibitory concentrations is crucial in human risk assessment, including food ingestion; however, in the case of ofloxacin presented results reveal that plant metabolites should also be considered so as not to underestimate their risk.", "keywords": ["High-resolution mass spectrometry", "Ofloxacin", "0211 other engineering and technologies", "02 engineering and technology", "Biotransformation pathways", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Antibiotics", "Humans", "Plant metabolites", "Biotransformation", "Lactuca", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2020.114002"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envpol.2020.114002", "name": "item", "description": "10.1016/j.envpol.2020.114002", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2020.114002"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-01T00:00:00Z"}}, {"id": "10.1016/j.orggeochem.2021.104346", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:15:53Z", "type": "Journal Article", "created": "2021-11-27", "title": "Soil chemistry, temperature and bacterial community composition drive brGDGT distributions along a subarctic elevation gradient", "description": "Open AccessOrganic Geochemistry, 163", "keywords": ["2. Zero hunger", "Chemistry", "Soil biomarkers", "13. Climate action", "Physics", "brGDGT", "Bacterial community", "brGDGT; Biomarker proxy; Bacterial community; Soil biomarkers", "15. Life on land", "Biomarker proxy", "01 natural sciences", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.orggeochem.2021.104346"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Organic%20Geochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.orggeochem.2021.104346", "name": "item", "description": "10.1016/j.orggeochem.2021.104346", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.orggeochem.2021.104346"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "0e018dea-ab53-461f-b454-2eaaca8c765c", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[6.67, 47.98], [6.67, 51.27], [10.81, 51.27], [10.81, 47.98], [6.67, 47.98]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "winter wheat"}, {"id": "spring barley"}, {"id": "organic fertilizers"}, {"id": "ammonium"}, {"id": "nitrates"}, {"id": "protein quality"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata; Wheat"}, {"id": "barley"}, {"id": "organic agriculture"}, {"id": "Rhizosphere soil"}, {"id": "bulk soil"}, {"id": "microbial biomass"}, {"id": "microrespiration"}, {"id": "meta-barcode sequencing of bacterial community"}, {"id": "quantification of bacterial inoculant"}, {"id": "gluten"}, {"id": "HMW"}, {"id": "hordein"}, {"id": "ProteinZ"}, {"id": "bread quality"}, {"id": "grain storage protein"}], "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 - bread and beer's research activities.\" Although every care has been taken in preparing and testing the data, the Rhizo4Bio - bread and beer and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the Rhizo4Bio - bread and beer 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 - bread and beer and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2024-08-22", "type": "Dataset", "created": "2024-07-18", "language": "eng", "title": "Production of wheat and barley under reduced input in organic farming - Soil parameters for season I and II", "description": "During the last decades, organic farming has undergone a notable expansion as a common agricultural practice throughout the world. This, together with an increasing demand for fertilizer and pesticide reduction has led to consider different and new approaches. We investigate the effect of Hartmannibacter diazotrophicus strain E19, a plant growth promoting rhizobacterium, in order to enhance the production of wheat and barley under low energy input. For that, we analyze the effect of three factors: organic fertilizer (with and without, only wheat), row distance (15 cm and 50 cm), and bacterial inoculation (E19 and control) at two different organic experimental field stations (Gladbacherhof and Kleinhohenheim). The dataset provides information about different parameter determined from rhizosphere soil and root samples collected at two different developmental stages (flowering and milk/fully ripe), as well as, the grain yield, straw yield, 1000 kernel mass, and seed quality during the seasons 2020-2021 and 2021-2022. The following soil parameter were evaluated: ammonium, nitrate, carbon-nitrogen ratio, microbial biomass, the respiration activity using different carbon sources (glucose, galactose, N-acetylglucosamine, arginine). These data sets are currently under evaluation and complemented with the quantification from root samples through quantitative PCR (qPCR) of strain E19 and the metabarcoding sequencing of the bacterial communities based on 16S rRNA genes obtained from rhizosphere soil samples during the two seasons. Soil parameter data\n\nRelated datasets are listed in the metadata element 'Related Identifier'.\nDataset version 1.0", "formats": [{"name": "CSV"}], "keywords": ["Soil", "winter wheat", "spring barley", "organic fertilizers", "ammonium", "nitrates", "protein quality", "opendata; Wheat", "barley", "organic agriculture", "Rhizosphere soil", "bulk soil", "microbial biomass", "microrespiration", "meta-barcode sequencing of bacterial community", "quantification of bacterial inoculant", "gluten", "HMW", "hordein", "ProteinZ", "bread quality", "grain storage protein", "Boden"], "contacts": [{"name": "Santiago Quiroga", "organization": "Justus-Liebig University Giessen", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "Santiago.Quiroga@umwelt.uni-giessen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0009-0001-1392-8241", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Sylvia Schnell", "organization": "Justus-Liebig University Giessen", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "sylvia.schnell@umwelt.uni-giessen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-3903-6089", "name_url": "", "description": "orcid", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "ZALF", "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": "Stefan Ratering", "organization": "Justus-Liebig University Giessen", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "Stefan.Ratering@umwelt.uni-giessen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0001-7572-6306", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Azin Rekowski", "organization": "University of Hohenheim", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "azin.ghabelrahmat@uni-hohenheim.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-0179-663X", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Christian Z\u00f6rb", "organization": "University of Hohenheim", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "Christian.zoerb@uni-hohenheim.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-0000-5138", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Sylvia Schnell", "organization": "Justus-Liebig University Giessen", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "sylvia.schnell@umwelt.uni-giessen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-3903-6089", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"organization": "Justus-Liebig University Giessen;University of Hohenheim", "roles": ["contributor"]}], "title_alternate": "LTE: Part 1/5, table: Soil parameters for season I and II"}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=0e018dea-ab53-461f-b454-2eaaca8c7gmd:65c", "rel": "download"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/0e018dea-ab53-461f-b454-2eaaca8c765c", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "0e018dea-ab53-461f-b454-2eaaca8c765c", "name": "item", "description": "0e018dea-ab53-461f-b454-2eaaca8c765c", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/0e018dea-ab53-461f-b454-2eaaca8c765c"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-22T00:00:00Z"}}, {"id": "10.1002/advs.201901408", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:12Z", "type": "Journal Article", "created": "2019-09-19", "title": "Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms", "description": "AbstractBiofouling proceeds in successive steps where the primary colonizers affect the phylogenetic and functional structure of a future microbial consortium. Using microbiologically influenced corrosion (MIC) as a study case, a novel approach for material surface protection is described, which does not prevent biofouling, but rather shapes the process of natural biofilm development to exclude MIC\uffe2\uff80\uff90related microorganisms. This approach interferes with the early steps of natural biofilm formation affecting how the community is finally developed. It is based on a multilayer artificial biofilm, composed of electrostatically modified bacterial cells, producing antimicrobial compounds, extracellular antimicrobial polyelectrolyte matrix, and a water\uffe2\uff80\uff90proof rubber elastomer barrier. The artificial biofilm is constructed layer\uffe2\uff80\uff90by\uffe2\uff80\uff90layer (LBL) by manipulating the electrostatic interactions between microbial cells and material surfaces. Field testing on standard steel coupons exposed in the sea for more than 30 days followed by laboratory analyses using molecular\uffe2\uff80\uff90biology tools demonstrate that the preapplied artificial biofilm affects the phylogenetic structure of the developing natural biofilm, reducing phylogenetic diversity and excluding MIC\uffe2\uff80\uff90related bacteria. This sustainable solution for material protection showcases the usefulness of artificially guiding microbial evolutionary processes via the electrostatic modification and controlled delivery of bacterial cells and extracellular matrix to the exposed material surfaces.Selectively fluorinated compounds are found frequently in pharmaceutical and agrochemical products where currently 25\uffe2\uff80\uff9330\uffe2\uff80\uff89% of optimised compounds emerge from development containing at least one fluorine atom. There are many methods for the site\uffe2\uff80\uff90specific introduction of fluorine, but all are chemical and they often use environmentally challenging reagents. Biochemical processes for C\uffe2\uff88\uff92F bond formation are attractive, but they are extremely rare. In this work, the fluorinase enzyme, originally identified from the actinomycete bacterium Streptomyces cattleya, is engineered into Escherichia coli in such a manner that the organism is able to produce 5\uffe2\uff80\uffb2\uffe2\uff80\uff90fluorodeoxyadenosine (5\uffe2\uff80\uffb2\uffe2\uff80\uff90FDA) from S\uffe2\uff80\uff90adenosyl\uffe2\uff80\uff90l\uffe2\uff80\uff90methionine (SAM) and fluoride in live E.\uffe2\uff80\uff85coli cells. Success required the introduction of a SAM transporter and deletion of the endogenous fluoride efflux capacity in order to generate an E.\uffe2\uff80\uff85coli host that has the potential for future engineering of more elaborate fluorometabolites.
", "keywords": ["SAM transporters", "0301 basic medicine", "570", "S-Adenosylmethionine", "0303 health sciences", "Deoxyadenosines", "Halogenation", "DAS", "Fluorine", "Halogenations", "540", "QD Chemistry", "Streptomyces", "3. Good health", "03 medical and health sciences", "Bacterial Proteins", "Isomerism", "Escherichia coli", "QD", "Fluoride channels", "Genetic Engineering", "Oxidoreductases", "Fluorinases"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/cbic.202000051"}, {"href": "https://doi.org/10.1002/cbic.202000051"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/ChemBioChem", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/cbic.202000051", "name": "item", "description": "10.1002/cbic.202000051", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/cbic.202000051"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-03T00:00:00Z"}}, {"id": "10.1002/ecy.2137", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:14Z", "type": "Journal Article", "created": "2018-01-10", "title": "Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere", "description": "AbstractThe ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co\uffe2\uff80\uff90occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co\uffe2\uff80\uff90occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.Meeting the energy and nitrogen (N) requirements of high\uffe2\uff80\uff90performing ruminants at the same time as avoiding digestive disturbances (i.e. rumen acidosis) is a key priority in ruminant nutrition. The present study evaluated the effect of a cereal ammoniation treatment, in which barley grains are combined with urea and enzymes that catalyze the conversion of urea to ammonia to optimize rumen function. Twelve rumen cannulated sheep were randomly divided into two groups and fed a diet containing 60% of ammoniated barley (AMM) or untreated barley supplemented with urea (CTL) to investigate the impact on rumen fermentation and feed utilization.
RESULTSAMM had higher total N content and effective rumen degradable N than untreated barely. AMM sheep had a consistently higher rumen pH throughout the day (6.31 versus 6.03) and tended to have a lower post\uffe2\uff80\uff90prandial ammonia peak and higher acetate molar proportion (+5.1%) than CTL sheep. The rumen environment in AMM sheep favored the colonization and utilization of agro\uffe2\uff80\uff90industrial by\uffe2\uff80\uff90products (i.e. orange pulp) by the rumen microbes leading to a higher feed degradability. AMM sheep also had higher total tract apparent N digestibility (+21.7%) and urinary excretion of purine derivatives (+34%), suggesting a higher N uptake and microbial protein synthesis than CTL sheep.
CONCLUSIONThe inclusion of AMM in the diet of ruminants represents a valid strategy for maintaining rumen pH within a physiological range and improving N utilization by the rumen microbes, which could have positive effects on the health and productivity of animals in intensive production systems. These findings warrant further studies under conventional farm conditions. \uffc2\uffa9 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
", "keywords": ["2. Zero hunger", "Rumen", "Sheep", "Bacteria", "Food Handling", "0402 animal and dairy science", "Hordeum", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Animal Feed", "Diet", "Gastrointestinal Microbiome", "Bacterial Proteins", "Ammonia", "Barley", "Rumen fermentation", "Animals", "Urea", "Ammoniation", "Digestion", "Feed utilization", "Research Articles"]}, "links": [{"href": "https://eprints.gla.ac.uk/235892/1/235892.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/jsfa.11205"}, {"href": "https://doi.org/10.1002/jsfa.11205"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.11205", "name": "item", "description": "10.1002/jsfa.11205", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.11205"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-24T00:00:00Z"}}, {"id": "10.1002/jsfa.4533", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:17Z", "type": "Journal Article", "created": "2011-07-27", "title": "Influence Of Fertilisation Regimes On A Nosz-Containing Denitrifying Community In A Rice Paddy Soil", "description": "AbstractBACKGROUND: Denitrification is a microbial process that has received considerable attention during the past decade since it can result in losses of added nitrogen fertilisers from agricultural soils. Paddy soil has been known to have strong denitrifying activity, but the denitrifying microorganisms responsible for fertilisers in paddy soil are not well known. The objective of this study was to explore the impacts of 17\uffe2\uff80\uff90year application of inorganic and organic fertiliser (rice straw) on the abundance and composition of a nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Soil samples were collected from CK plots (no fertiliser), N (nitrogen fertiliser), NPK (nitrogen, phosphorus and potassium fertilisers) and NPK + OM (NPK plus organic matter). The nitrous oxide reductase gene (nosZ) community composition was analysed using terminal restriction fragment length polymorphism, and the abundance was determined by quantitative PCR.
RESULTS: Both the largest abundance of nosZ\uffe2\uff80\uff90denitrifier and the highest potential denitrifying activity (PDA) occurred in the NPK + OM treatment with about four times higher than that in the CK and two times higher than that in the N and NPK treatments (no significant difference). Denitrifying community composition differed significantly among fertilisation treatments except for the comparison between CK and N treatments. Of the measured abiotic factors, total organic carbon was significantly correlated with the observed differences in community composition and abundance (P < 0.01 by Monte Carlo permutation).
CONCLUSION: This study shows that the addition of different fertilisers affects the size and composition of the nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Copyright \uffc2\uffa9 2011 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Nitrogen", "0402 animal and dairy science", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Carbon", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "Denitrification", "0405 other agricultural sciences", "Fertilizers", "Oxidoreductases", "Monte Carlo Method", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.4533"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.4533", "name": "item", "description": "10.1002/jsfa.4533", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.4533"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-27T00:00:00Z"}}, {"id": "10.1002/jsfa.6206", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:17Z", "type": "Journal Article", "created": "2013-05-01", "title": "Effect Of Organic, Conventional And Mixed Cultivation Practices On Soil Microbial Community Structure And Nematode Abundance In A Cultivated Onion Crop", "description": "AbstractBACKGROUNDResponses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long\uffe2\uff80\uff90term field experiment which divides conventional and organic agriculture into component pest\uffe2\uff80\uff90control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles, microbial and nematode counts, and denaturing gradient gel electrophoresis (DGGE) to characterise soil microbial communities in plots used for onion (Allium cepa L.) cultivation.
RESULTSMicrobial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest\uffe2\uff80\uff90control treatment plots.
CONCLUSIONOrganic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. \uffc2\uffa9 2013 Society of Chemical Industry
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Microbial diversity", "Nematoda", "Soil", "03 medical and health sciences", "Onions", "Animals", "DNA", " Fungal", "Ecosystem", "Soil Microbiology", "2. Zero hunger", "Organic Agriculture", "0303 health sciences", "Bacteria", "Denaturing Gradient Gel Electrophoresis", "0402 animal and dairy science", "Fungi", "Denaturing gradient gel electrophoresis", "Agriculture", "Biolog Eco-plates", "04 agricultural and veterinary sciences", "15. Life on land", "Community level physiological profile", "Organic agriculture", "0405 other agricultural sciences"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.6206"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.6206", "name": "item", "description": "10.1002/jsfa.6206", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.6206"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-06-07T00:00:00Z"}}, {"id": "10.1002/ldr.3453", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:18Z", "type": "Journal Article", "created": "2019-10-15", "title": "Increases in aridity lead to drastic shifts in the assembly of dryland complex microbial networks", "description": "AbstractWe have little information on how and why soil microbial community assembly will respond to predicted increases in aridity by the end of this century. Here, we used correlation networks and structural equation modeling to assess the changes in the abundance of the ecological clusters including potential winner and loser microbial taxa associated with predicted increases in aridity. To do this, we conducted a field survey in an environmental gradient from eastern Australia and obtained information on bacterial and fungal community composition for 120 soil samples and multiple abiotic and biotic factors. Overall, our structural equation model explained 83% of the variance in the two mesic modules. Increases in aridity led to marked shifts in the abundance of the two major microbial modules found in our network, which accounted for >99% of all phylotypes. In particular, the relative abundance of one of these modules, the Mesic Module #1, which was positively related to multiple soil properties and plant productivity, declined strongly with aridity. Conversely, the relative abundance of a second dominant module (Xeric Module #2) was positively correlated with increases in aridity. Our study provides evidence that network analysis is a useful tool to identify microbial taxa that are either winners or losers under increasing aridity and therefore potentially under changing climates. Our work further suggests that climate change, and associated land degradation, could potentially lead to extensive microbial phylotypes exchange and local extinctions, as demonstrated by the reductions of up to 97% in the relative abundance of microbial taxa within Mesic Module #1.Natural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off\uffe2\uff80\uff90target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co\uffe2\uff80\uff90operation and Development, which is a key international standard\uffe2\uff80\uff90setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5\uffe2\uff80\uff90dichloraniline). We determined the following in three different soils: (i) ammonium (NH4+) and nitrate (NO3\uffe2\uff88\uff92) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q\uffe2\uff80\uff90PCR).
RESULTSAll pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose\uffe2\uff80\uff90dependent effects on NH4+ and NO3\uffe2\uff88\uff92 levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q\uffe2\uff80\uff90PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5\uffe2\uff80\uff90dichloraniline.
CONCLUSIONOur findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well\uffe2\uff80\uff90standardized tools. \uffc2\uffa9 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.Antibiotics are some of the most widely used drugs. Their release in the environment is of great concern since their consumption is a major factor for antibiotic resistance, one of the most important threats to human health. Their occurrence and fate in agricultural systems have been extensively investigated in recent years. Yet whilst their biotic and abiotic degradation pathways have been thoroughly researched, their biotransformation pathways in plants are less understood, such as in case of trimethoprim. Although trimethoprim has been reported in the environment, its fate in higher plants still remains unknown. A bench-scale experiment was performed and 30 trimethoprim metabolites were identified in lettuce (Lactuca sativa L.), of which 5 belong to phase I and 25 to phase II. Data mining yielded a list of 1018 ions as possible metabolite candidates, which was filtered to a final list of 87 candidates. Molecular structures were assigned for 19 compounds, including 14 TMP metabolites reported for the first time. Alongside well-known biotransformation pathways in plants, additional novel pathways were suggested, namely, conjugation with sesquiterpene lactones, and abscisic acid as a part of phase II of plant metabolism. The results obtained offer insight into the variety of phase II conjugates and may serve as a guideline for studying the metabolization of other chemicals that share a similar molecular structure or functional groups with trimethoprim. Finally, the toxicity and potential contribution of the identified metabolites to the selective pressure on antibiotic resistance genes and bacterial communities via residual antimicrobial activity were evaluated.
", "keywords": ["2. Zero hunger", "High-resolution mass spectrometry", "Phytochemicals", "0211 other engineering and technologies", "02 engineering and technology", "01 natural sciences", "Trimethoprim", "Anti-Bacterial Agents", "3. Good health", "Conjugates", "Antibiotics", "Non-target screening", "Humans", "Plant metabolites", "Biotransformation", "Research Paper", "Lactuca", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Tadi\u0107, \u0110or\u0111e, Gramblicka, Michal, Mistrik, Robert, Bayona, Josep Maria,", "roles": ["creator"]}]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00216-022-03943-6.pdf"}, {"href": "https://doi.org/10.1007/s00216-022-03943-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Analytical%20and%20Bioanalytical%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00216-022-03943-6", "name": "item", "description": "10.1007/s00216-022-03943-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00216-022-03943-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-09T00:00:00Z"}}, {"id": "10.1007/s00253-012-4173-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:28Z", "type": "Journal Article", "created": "2012-06-20", "title": "Pectin-Rich Biomass As Feedstock For Fuel Ethanol Production", "description": "The USA has proposed that 30\u00a0% of liquid transportation fuel be produced from renewable resources by 2030 (Perlack and Stokes 2011). It will be impossible to reach this goal using corn kernel-based ethanol alone. Pectin-rich biomass, an under-utilized waste product of the sugar and juice industry, can augment US ethanol supplies by capitalizing on this already established feedstock. Currently, pectin-rich biomass is sold (at low value) as animal feed. This review focuses on the three most studied types of pectin-rich biomass: sugar beet pulp, citrus waste and apple pomace. Fermentations of these materials have been conducted with a variety of ethanologens, including yeasts and bacteria. Escherichia coli can ferment a wide range of sugars including galacturonic acid, the primary component of pectin. However, the mixed acid metabolism of E. coli can produce unwanted side products. Saccharomyces cerevisiae cannot naturally ferment galacturonic acid nor pentose sugars but has a homoethanol pathway. Erwinia chrysanthemi is capable of degrading many of the cell wall components of pectin-rich materials, including pectin. Klebsiella oxytoca can metabolize a diverse array of sugars including cellobiose, one degradation product of cellulose. However, both E. chrysanthemi and K. oxytoca produce side products during fermentation, similar to E. coli. Using pectin-rich residues from industrial processes is beneficial because the material is already collected and partially pretreated to facilitate enzymatic deconstruction of the plant cell walls. Using biomass already produced for other purposes is an attractive practice because fewer greenhouse gases (GHG) will be anticipated from land-use changes.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Ethanol", "Fungi", "Industrial Waste", "Mini-Review", "15. Life on land", "Applied Microbiology and Biotechnology", "7. Clean energy", "12. Responsible consumption", "03 medical and health sciences", "13. Climate action", "Fermentation", "Food Industry", "Pectins", "Biomass", "Biotechnology"], "contacts": [{"organization": "Joy Doran-Peterson, Meredith C. Edwards,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s00253-012-4173-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-012-4173-2", "name": "item", "description": "10.1007/s00253-012-4173-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-012-4173-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-06-14T00:00:00Z"}}, {"id": "10.1007/s00248-003-0229-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:27Z", "type": "Journal Article", "created": "2005-06-17", "title": "Methanogen Communities In A Drained Bog: Effect Of Ash Fertilization", "description": "Forestry practises such has drainage have been shown to decrease emissions of the greenhouse gas methane (CH(4)) from peatlands. The aim of the study was to examine the methanogen populations in a drained bog in northern Finland, and to assess the possible effect of ash fertilization on potential methane production and methanogen communities. Peat samples were collected from control and ash fertilized (15,000 kg/ha) plots 5 years after ash application, and potential CH(4) production was measured. The methanogen community structure was studied by DNA isolation, PCR amplification of the methyl coenzyme-M reductase (mcr) gene, denaturing gradient gel electrophoresis (DGGE), and restriction fragment length polymorphism (RFLP) analysis. The drained peatland showed low potential methane production and methanogen diversity in both control and ash-fertilized plots. Samples from both upper and deeper layers of peat were dominated by three groups of sequences related to Rice cluster-I hydrogenotroph methanogens. Even though pH was marginally greater in the ash-treated site, the occurrence of those sequences was not affected by ash fertilization. Interestingly, a less common group of sequences, related to the Fen cluster, were found only in the fertilized plots. The study confirmed the depth related change of methanogen populations in peatland.", "keywords": ["0301 basic medicine", "0303 health sciences", "Bacteria", "tuhkalannoitus", "metanogeeniset mikrobit", "Biodiversity", "15. Life on land", "03 medical and health sciences", "Genes", " Bacterial", "ojitetut suot", "Fertilizers", "Methane", "Ecosystem", "Phylogeny", "Polymorphism", " Restriction Fragment Length"]}, "links": [{"href": "https://doi.org/10.1007/s00248-003-0229-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-003-0229-2", "name": "item", "description": "10.1007/s00248-003-0229-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-003-0229-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-02-01T00:00:00Z"}}, {"id": "10.1007/s00248-007-9276-4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:27Z", "type": "Journal Article", "created": "2007-07-17", "title": "Comparison Of Soil Bacterial Communities Under Diverse Agricultural Land Management And Crop Production Practices", "description": "The composition and structure of bacterial communities were examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Five land management programs were initiated in July 2000: conventional, organic, continuous removal of vegetation (disk fallow), undisturbed (weed fallow), and bahiagrass pasture (Paspalum notatum var Argentine). Similar levels in the diversity of bacterial 16S rDNA amplicons were detected in soil samples collected from organically and conventionally managed plots 3 and 4 years after initiation of land management programs, whereas significantly lower levels of diversity were observed in samples collected from bahiagrass pasture. Differences in diversity were attributed to effects on how the relative abundance of individual amplicons were distributed (evenness) and not on the total numbers of bacterial 16S rDNA amplicons detected (richness). Similar levels of diversity were detected among all land management programs in soil samples collected after successive years of tomato (Lycopersicon esculentum) cultivation. A different trend was observed after a multivariate examination of the similarities in genetic composition among soil bacterial communities. After 3 years of land management, similarities in genetic composition of soil bacterial communities were observed in plots where disturbance was minimized (bahiagrass and weed fallow). The genetic compositions in plots managed organically were similar to each other and distinct from bacterial communities in other land management programs. After successive years of tomato cultivation and damage from two major hurricanes, only the composition of soil bacterial communities within organically managed plots continued to maintain a high degree of similarity to each other and remain distinct from other bacterial communities. This study reveals the effects of agricultural land management practices on soil bacterial community composition and diversity in a large-scale, long-term replicated study where the effect of soil type on community attributes was removed.", "keywords": ["Crops", " Agricultural", "DNA", " Bacterial", "2. Zero hunger", "Analysis of Variance", "Conservation of Natural Resources", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "DNA", " Ribosomal", "Polymerase Chain Reaction", "Solanum lycopersicum", "RNA", " Ribosomal", " 16S", "0401 agriculture", " forestry", " and fisheries", "Cloning", " Molecular", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-007-9276-4"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-007-9276-4", "name": "item", "description": "10.1007/s00248-007-9276-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-007-9276-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-07-07T00:00:00Z"}}, {"id": "10.1007/s00248-007-9295-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:27Z", "type": "Journal Article", "created": "2007-08-31", "title": "Plfa Profiling Of Microbial Community Structure And Seasonal Shifts In Soils Of A Douglas-Fir Chronosequence", "description": "The impact and frequency of forest harvesting could significantly affect soil microbial community (SMC) structure and functioning. The ability of soil microorganisms to perform biogeochemical processes is critical for sustaining forest productivity and has a direct impact on decomposition dynamics and carbon storage potential. The Wind River Canopy Crane Research Forest in SW, WA, provided a unique opportunity to study a forest chronosequence and the residual effects of harvesting on the SMC in comparison to old-growth forests. The objective of this study was to determine the effect of clear-cutting and stand age on temporal dynamics of SMC and physiological stress markers using phospholipid fatty acid (PLFA) profiling. Soil microbial PLFA profiles were determined seven times over 22 months (Nov. 02 to Sep. 04) in old-growth coniferous forest stands (300-500 years) and 8 (CC8)- or 25 (CC25)-year-old replanted clear-cuts. PLFA patterns of the SMC shifted because of clear-cutting, but seasonal temporal changes had greater shifts than differences among stand age. The microbial biomass (total PLFA) and bacterial, fungal, and selected other PLFAs were significantly reduced in CC8 but not in CC25 sites relative to the old-growth sites. An increase in stress indicators [PLFA ratios of saturated/monsaturated and (cy17:0 + cy19:0)/(16:1omega7 + 18:1omega7)] in late summer was related to water stress. Although the canopy and litter input are quite different for a 25-year clear-cut compared to virgin old-growth forest, we conclude that the composition of the microbial communities, 25 years after clear-cutting, has recovered sufficiently to be much more similar to old-growth forests than a recent clear-cut at this Pacific Northwest forest site. The study shows the potential of PLFA analysis for profiling microbial communities and their stress status under field conditions, but wide temporal shifts emphasize the need for sampling over seasons to fully interpret ecosystem management impacts on microbial populations.", "keywords": ["Washington", "Time Factors", "Bacteria", "Fatty Acids", "Fungi", "Temperature", "Eukaryota", "Water", "04 agricultural and veterinary sciences", "15. Life on land", "Pseudotsuga", "Trees", "Soil", "13. Climate action", "Animals", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Seasons", "Phospholipids", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-007-9295-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-007-9295-1", "name": "item", "description": "10.1007/s00248-007-9295-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-007-9295-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-08-31T00:00:00Z"}}, {"id": "10.1007/s00248-007-9308-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:27Z", "type": "Journal Article", "created": "2007-09-01", "title": "Long-Term Effect Of Municipal Solid Waste Amendment On Microbial Abundance And Humus-Associated Enzyme Activities Under Semiarid Conditions", "description": "Microbial ecology is the key to understanding the function of soil biota for organic matter cycling after a single amendment of organic waste in semiarid soils. Therefore, in this paper, the long-term effect (17 years) of adding different doses of a solid municipal waste to an arid soil on humus-enzyme complexes, a very stable and long-lasting fraction of soil enzymes, as well as on microbial and plant abundance, was studied. Humic substances were extracted by 0.1 M pH 7 sodium pyrophosphate from soil samples collected in experimental plots amended with different doses of a solid municipal waste (0, 65, 130, 195, and 260 t/ha) 17 years before. The activity of different hydrolases related with the C (beta-glucosidase), N (urease), and P (alkaline phosphatase) cycles and with the formation of humic substances (o-diphenol oxidase) were determined in this extract. The density and diversity of plant cover in the plots, as well as the fungal and bacterial biomass (by analyzing phopholipid fatty acids) were also determined. In general, the amended plots showed greater humic substance-related enzymatic activity than the unamended plots. This activity increased with the dose but only up to a certain level, above which it leveled off or even diminished. Plant diversity and cover density followed the same trend. Fungal and bacterial biomass also benefited in a dose-dependent manner. Different signature molecules representing gram+ and gram- bacteria, and those corresponding to monounsaturated and saturated fatty acids showed a similar behavior. The results demonstrate that organic amendment had a noticeable long-term effect on the vegetal development, humic substances-related enzyme activity and on the development of bacteria and fungi in semiarid conditions.", "keywords": ["2. Zero hunger", "Analysis of Variance", "Time Factors", "Bacteria", "Fatty Acids", "Fungi", "04 agricultural and veterinary sciences", "15. Life on land", "01 natural sciences", "6. Clean water", "Enzymes", "Refuse Disposal", "12. Responsible consumption", "Soil", "Ergosterol", "11. Sustainability", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Humic Substances", "Phospholipids", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1007/s00248-007-9308-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-007-9308-0", "name": "item", "description": "10.1007/s00248-007-9308-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-007-9308-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-09-02T00:00:00Z"}}, {"id": "10.1007/s00248-008-9467-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:27Z", "type": "Journal Article", "created": "2008-11-21", "title": "Molecular And Functional Assessment Of Bacterial Community Convergence In Metal-Amended Soils", "description": "Species diversity and the structure of microbial communities in soils are thought to be a function of the cumulative selective pressures within the local environment. Shifts in microbial community structure, as a result of metal stress, may have lasting negative effects on soil ecosystem dynamics if critical microbial community functions are compromised. Three soils in the vicinity of a copper smelter, previously contaminated with background, low and high levels of aerially deposited metals, were amended with metal-salts to determine the potential for metal contamination to shape the structural and functional diversity of microbial communities in soils. We hypothesized that the microbial communities native to the three soils would initially be unique to each site, but would converge on a microbial community with similar structure and function, as a result of metal stress. Initially, the three different sites supported microbial communities with unique structural and functional diversity, and the nonimpacted site supported inherently higher levels of microbial activity and biomass, relative to the metal-contaminated sites. Amendment of the soils with metal-salts resulted in a decrease in microbial activity and biomass, as well as shifts in microbial community structure and function at each site. Soil microbial communities from each site were also observed to be sensitive to changes in soil pH as a result of metal-salt amendment; however, the magnitude of these pH-associated effects varied between soils. Microbial communities from each site did not converge on a structurally or functionally similar community following metal-salt amendment, indicating that other factors may be equally important in shaping microbial communities in soils. Among these factors, soil physiochemical parameters like organic matter and soil pH, which can both influence the bioavailability and toxicity of metals in soils, may be critical.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "0303 health sciences", "Bacteria", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Soil", "03 medical and health sciences", "13. Climate action", "Metals", " Heavy", "Soil Pollutants", "Biomass", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-008-9467-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-008-9467-7", "name": "item", "description": "10.1007/s00248-008-9467-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-008-9467-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-11-22T00:00:00Z"}}, {"id": "10.1007/s00248-010-9727-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:27Z", "type": "Journal Article", "created": "2010-08-03", "title": "Soil Microbial Abundance And Diversity Along A Low Precipitation Gradient", "description": "The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while \u223c2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (\u223c9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem.", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "0301 basic medicine", "Salinity", "0303 health sciences", "Bacteria", "Mediterranean Region", "Climate", "Rain", "Water", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Soil", "03 medical and health sciences", "Phospholipids", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-010-9727-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-010-9727-1", "name": "item", "description": "10.1007/s00248-010-9727-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-010-9727-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-08-01T00:00:00Z"}}, {"id": "10.1007/s00248-011-9897-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:27Z", "type": "Journal Article", "created": "2011-06-29", "title": "Impacts Of Organic And Inorganic Fertilizers On Nitrification In A Cold Climate Soil Are Linked To The Bacterial Ammonia Oxidizer Community", "description": "The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38\u00b0C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification.", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "China", "Bacteria", "04 agricultural and veterinary sciences", "15. Life on land", "Cold Climate", "Archaea", "Nitrification", "6. Clean water", "Genes", " Archaeal", "Soil", "DNA", " Archaeal", "Ammonia", "Genes", " Bacterial", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidoreductases", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-011-9897-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-011-9897-5", "name": "item", "description": "10.1007/s00248-011-9897-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-011-9897-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-29T00:00:00Z"}}, {"id": "10.1007/s00248-013-0225-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:28Z", "type": "Journal Article", "created": "2013-04-15", "title": "Agricultural Management And Labile Carbon Additions Affect Soil Microbial Community Structure And Interact With Carbon And Nitrogen Cycling", "description": "We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 \u03bcg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Environmental Microbiology and Microbial Ecology", "Bacteria", "Nitrogen", "Fungal Community Structure", "Agriculture", "Nitrogen Cycle", "15. Life on land", "Microbiology", "630", "Carbon", "Carbon Cycle", "Soil", "03 medical and health sciences", "rRNA Gene Copy", "Soil Microbial Community Structure", "fungal community", "Biology", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-013-0225-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-013-0225-0", "name": "item", "description": "10.1007/s00248-013-0225-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-013-0225-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-04-16T00:00:00Z"}}, {"id": "10.1007/s00248-013-0235-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:28Z", "type": "Journal Article", "created": "2013-05-01", "title": "Changes In Diversity, Abundance, And Structure Of Soil Bacterial Communities In Brazilian Savanna Under Different Land Use Systems", "description": "The Brazilian Savanna, also known as 'Cerrado', is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "03 medical and health sciences", "Bacteria", "Molecular Sequence Data", "Agriculture", "Biodiversity", "15. Life on land", "Brazil", "Ecosystem", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-013-0235-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-013-0235-y", "name": "item", "description": "10.1007/s00248-013-0235-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-013-0235-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-04-27T00:00:00Z"}}, {"id": "10.1007/s00248-013-0322-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:28Z", "type": "Journal Article", "created": "2013-11-25", "title": "Pyrosequencing Reveals Contrasting Soil Bacterial Diversity And Community Structure Of Two Main Winter Wheat Cropping Systems In China", "description": "Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems.", "keywords": ["Crops", " Agricultural", "DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "China", "0303 health sciences", "Agriculture", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "Zea mays", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Microbiology", "Triticum"]}, "links": [{"href": "https://doi.org/10.1007/s00248-013-0322-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-013-0322-0", "name": "item", "description": "10.1007/s00248-013-0322-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-013-0322-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-26T00:00:00Z"}}, {"id": "10.1007/s00248-016-0730-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:28Z", "type": "Journal Article", "created": "2016-02-02", "title": "Responses Of Soil Bacterial Communities To Nitrogen Deposition And Precipitation Increment Are Closely Linked With Aboveground Community Variation", "description": "It has been predicted that precipitation and atmospheric nitrogen (N) deposition will increase in northern China; yet, ecosystem responses to the interactive effects of water and N remain largely unknown. In particular, responses of belowground microbial community to projected global change and their potential linkages to aboveground macro-organisms are rarely studied. In this study, we examined the responses of soil bacterial diversity and community composition to increased precipitation and multi-level N deposition in a temperate steppe in Inner Mongolia, China, and explored the diversity linkages between aboveground and belowground communities. It was observed that N addition caused the significant decrease in bacterial alpha-diversity and dramatic changes in community composition. In addition, we documented strong correlations of alpha- and beta-diversity between plant and bacterial communities in response to N addition. It was found that N enriched the so-called copiotrophic bacteria, but reduced the oligotrophic groups, primarily by increasing the soil inorganic N content and carbon availability and decreasing soil pH. We still highlighted that increased precipitation tended to alleviate the effects of N on bacterial diversity and dampen the plant-microbe connections induced by N. The counteractive effects of N addition and increased precipitation imply that even though the ecosystem diversity and function are predicted to be negatively affected by N deposition in the coming decades; the combination with increased precipitation may partially offset this detrimental effect.", "keywords": ["0301 basic medicine", "2. Zero hunger", "China", "0303 health sciences", "Bacteria", "Nitrogen", "Climate", "Microbial Consortia", "Water", "Biodiversity", "Plants", "15. Life on land", "Carbon", "6. Clean water", "Soil", "03 medical and health sciences", "13. Climate action", "Chemical Precipitation", "Ecosystem", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-016-0730-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-016-0730-z", "name": "item", "description": "10.1007/s00248-016-0730-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-016-0730-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-02-02T00:00:00Z"}}, {"id": "10.1007/s00248-018-1305-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:28Z", "type": "Journal Article", "created": "2018-12-08", "title": "Soil Type and Cyanobacteria Species Influence the Macromolecular and Chemical Characteristics of the Polysaccharidic Matrix in Induced Biocrusts", "description": "Inoculation of soils with cyanobacteria is proposed as a sustainable biotechnological technique for restoration of degraded areas in drylands due to the important role that cyanobacteria and their exopolysaccharides (EPS) play in the environment. So far, few studies have analyzed the macromolecular and chemical characteristics of the polysaccharidic matrix in induced cyanobacterial biocrusts and the scarce existing studies have mainly focused on sandy soil textures. However, the characteristics of the cyanobacterial polysaccharidic matrix may greatly depend on soil type. The objective of this study was to examine the macromolecular distribution and monosaccharidic composition of the polysaccharidic matrix induced by inoculation of two cyanobacterial species common in arid environments, Phormidium ambiguum (non N-fixing) and Scytonema javanicum (N-fixing) in different soil types. S. javanicum promoted a higher release in the soil of the more soluble and less condensed EPS fraction (i.e., the loosely bound EPS fraction, LB-EPS), while P. ambiguum showed a higher release of the less soluble and more condensed EPS fraction (i.e., the tightly bound EPS fraction, TB-EPS). LB-EPSs were mainly composed of low MW molecules (<\u200950\u00a0kDa), while TB-EPSs were mainly composed of high MW molecules (1100-2000\u00a0kDa). The two EPS fractions showed a complex monosaccharidic composition (from 11 to 12 different types of monosaccharides), with glucose as the most abundant monosaccharide, in particular in the poorer soils characterized by lower organic C contents. In more C-rich soils, high abundances of galactose, mannose, and xylose were also found. Low abundance of uronic acids and hydrophobic monosaccharides, such as fucose and rhamnose, was found in the EPS extracted from the inoculated soils. Our results point to the influence of soil type on the macromolecular distribution and monosaccharide composition of the polysaccharidic matrix in induced biocrusts, which is likely to affect biocrust development and their role in soil structure and nutrient cycling in restored dryland soils.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Cyanobacteria inoculation", "Tightly bound EPS", "Polysaccharides", " Bacterial", "Biological soil crust; Cyanobacteria inoculation; Loosely bound EPS; Molecular weight; Monosaccharide composition; Tightly bound EPS; Ecology; Evolution; Behavior and Systematics; Ecology; Soil Science", "Biological soil crust", "Monosaccharide composition", "15. Life on land", "Cyanobacteria", "Molecular weight", "Biological soil crust; Cyanobacteria inoculation; Loosely bound EPS; Molecular weight; Monosaccharide composition; Tightly bound EPS; Ecology", " Evolution", " Behavior and Systematics; Ecology; Soil Science", "Soil", "03 medical and health sciences", "13. Climate action", "Loosely bound EPS", "Desert Climate", "Soil Microbiology"]}, "links": [{"href": "https://iris.unive.it/bitstream/10278/5089943/1/s00248-018-1305-y.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1007/s00248-018-1305-y.pdf"}, {"href": "https://doi.org/10.1007/s00248-018-1305-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-018-1305-y", "name": "item", "description": "10.1007/s00248-018-1305-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-018-1305-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-08T00:00:00Z"}}, {"id": "10.1007/s00253-020-10811-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:28Z", "type": "Journal Article", "created": "2020-08-13", "title": "Industrial biotechnology of Pseudomonas putida: advances and prospects", "description": "AbstractPseudomonas putidais a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications ofP. putidaas a cell factory.
Key points\uffe2\uff80\uffa2 Pseudomonas putida advances to a global industrial cell factory.
\uffe2\uff80\uffa2 Novel tools enable system-wide understanding and streamlined genomic engineering.
\uffe2\uff80\uffa2 Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
", "keywords": ["0301 basic medicine", "ddc:500", "0303 health sciences", "Pseudomonas putida", "EDEMP cycle", "PHA", "Systems Biology", "500", "Genomics", "Mini-Review", "Bioeconomy", "Bacterial chassis", "Lignin", "03 medical and health sciences", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "Microbial cell factory", "13. Climate action", "Biocatalysis", "Synthetic Biology", "KT2440", "Metabolic engineering", "Biotransformation", "Synthetic biology", "Biotechnology"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00253-020-10811-9.pdf"}, {"href": "https://doi.org/10.1007/s00253-020-10811-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-020-10811-9", "name": "item", "description": "10.1007/s00253-020-10811-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-020-10811-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-13T00:00:00Z"}}, {"id": "10.1007/s00248-024-02363-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-19T16:14:28Z", "type": "Journal Article", "created": "2024-03-01", "title": "The Feather Moss Hylocomium splendens Affects the Transcriptional Profile of a Symbiotic Cyanobacterium in Relation to Acquisition and Turnover of Key Nutrients", "description": "AbstractMoss-cyanobacteria symbioses were proposed to be based on nutrient exchange, with hosts providing C and S while bacteria provide N, but we still lack understanding of the underlying molecular mechanisms of their interactions. We investigated how contact between the ubiquitous moss Hylocomium splendens and its cyanobiont affects nutrient-related gene expression of both partners. We isolated a cyanobacterium from H. splendens and co-incubated it with washed H. splendens shoots. Cyanobacterium and moss were also incubated separately. After 1\uffc2\uffa0week, we performed acetylene reduction assays to estimate N2 fixation and RNAseq to evaluate metatranscriptomes. Genes related to N2 fixation and the biosynthesis of several amino acids were up-regulated in the cyanobiont when hosted by the moss. However, S-uptake and the biosynthesis of the S-containing amino acids methionine and cysteine were down-regulated in the cyanobiont while the degradation of selenocysteine was up-regulated. In contrast, the number of differentially expressed genes in the moss was much lower, and almost no transcripts related to nutrient metabolism were affected. It is possible that, at least during the early stage of this symbiosis, the cyanobiont receives few if any nutrients from the host in return for N, suggesting that moss\uffe2\uff80\uff93cyanobacteria symbioses encompass relationships that are more plastic than a constant mutualist flow of nutrients.