{"type": "FeatureCollection", "features": [{"id": "10.1186/s40793-020-00354-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:20:06Z", "type": "Journal Article", "created": "2020-03-02", "title": "Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics", "description": "Abstract                 Background                 <p>Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37\uffe2\uff80\uff89\uffc2\uffb0C) and thermophilic (55\uffe2\uff80\uff89\uffc2\uffb0C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.</p>                                Results                 <p>In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or\uffc2\uffa0acetogenesis.</p>                                Conclusions                 <p>An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.</p>", "keywords": ["Integrated -omics", "Bioconversion", "0301 basic medicine", "570", "Polyomics", "Integrated-omics", "Biogas", "Microbiology", "7. Clean energy", "03 medical and health sciences", "Anaerobic digestion", "GE1-350", "2. Zero hunger", "0303 health sciences", "Metagenome assembled genomes", "Microbial community structure", "15. Life on land", "QR1-502", "6. Clean water", "3. Good health", "Environmental sciences", "Metagenome assembled genomes", " Integrated -omics", " Polyomics", " Anaerobic digestion", " Biogas", " Bioconversion", " Microbial community structure", " Methane", " Metabolic activity", "13. Climate action", "Metabolic activity", "Methane", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40793-020-00354-x.pdf"}, {"href": "https://doi.org/10.1186/s40793-020-00354-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-020-00354-x", "name": "item", "description": "10.1186/s40793-020-00354-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-020-00354-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-02T00:00:00Z"}}, {"id": "10.20944/preprints202106.0434.v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:20:46Z", "type": "Journal Article", "created": "2021-06-16", "title": "Going beyond Soil Conservation with the Use of Cover Crops in Mediterranean Sloping Olive Orchards", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Among the agricultural practices promoted by the Common Agricultural Policy to increase soil functions, the use of cover crops is a recommended tool to improve the sustainability of Mediter-ranean woody crops such as olive orchards. However, there is a broad range of cover crop ty-pologies in relation to its implementation, control and species composition. In that sense, the in-fluence of different plant species on soil quality indicators in olive orchards remains unknown yet. This study describes the effects of four treatments based on the implementation of different ground covers (CC-NAT, CC-GRA and CC-MIX) and conventional tillage (TILL) on soil erosion, soil physicochemical and biological properties, and soil microbial communities after 8 years of cover crop establishment. Our results have demonstrated that the presence of a temporary cover crop (CC), compared to a soil under tillage (TILL), can reduce soil losses and maintain good soil physicochemical properties and modify greatly the structure and diversity of soil bacterial com-munities and its functioning. The presence of a homogeneous CC of gramineous (Lolium rigidum or Lolilum multiflorum) (CC-GR) for 8 years significantly increased the functional properties of the soil as compared to TILL; although the most significant change was a modification on the bacte-rial community composition that was clearly different from the rest of treatments. On the other hand, the use of a mixture of plant species (CC-MIX) as a CC for only two years although did not modify greatly the structure and diversity of soil bacterial communities compared to the TILL soil, induced significant changes on the functional properties of the soil, and reverted those properties to a level similar to that of an undisturbed soil that had maintained a natural cover of spontaneous vegetation for decades (CC-NAT).</p></article>", "keywords": ["0301 basic medicine", "2. Zero hunger", "Microbial diversity", "soil erosion", "S", "Agriculture", "04 agricultural and veterinary sciences", "metabolic activity", "15. Life on land", "Soil quality", "6. Clean water", "bacterial community composition", "03 medical and health sciences", "13. Climate action", "microbial diversity", "Bacterial community composition", "Metabolic activity", "11. Sustainability", "Soil erosion", "biochemistry", "0401 agriculture", " forestry", " and fisheries", "soil quality"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://doi.org/10.20944/preprints202106.0434.v1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.20944/preprints202106.0434.v1", "name": "item", "description": "10.20944/preprints202106.0434.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.20944/preprints202106.0434.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-16T00:00:00Z"}}, {"id": "10.3390/agronomy11071387", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:21:38Z", "type": "Journal Article", "created": "2021-06-16", "title": "Going beyond Soil Conservation with the Use of Cover Crops in Mediterranean Sloping Olive Orchards", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Among the agricultural practices promoted by the Common Agricultural Policy to increase soil functions, the use of cover crops is a recommended tool to improve the sustainability of Mediter-ranean woody crops such as olive orchards. However, there is a broad range of cover crop ty-pologies in relation to its implementation, control and species composition. In that sense, the in-fluence of different plant species on soil quality indicators in olive orchards remains unknown yet. This study describes the effects of four treatments based on the implementation of different ground covers (CC-NAT, CC-GRA and CC-MIX) and conventional tillage (TILL) on soil erosion, soil physicochemical and biological properties, and soil microbial communities after 8 years of cover crop establishment. Our results have demonstrated that the presence of a temporary cover crop (CC), compared to a soil under tillage (TILL), can reduce soil losses and maintain good soil physicochemical properties and modify greatly the structure and diversity of soil bacterial com-munities and its functioning. The presence of a homogeneous CC of gramineous (Lolium rigidum or Lolilum multiflorum) (CC-GR) for 8 years significantly increased the functional properties of the soil as compared to TILL; although the most significant change was a modification on the bacte-rial community composition that was clearly different from the rest of treatments. On the other hand, the use of a mixture of plant species (CC-MIX) as a CC for only two years although did not modify greatly the structure and diversity of soil bacterial communities compared to the TILL soil, induced significant changes on the functional properties of the soil, and reverted those properties to a level similar to that of an undisturbed soil that had maintained a natural cover of spontaneous vegetation for decades (CC-NAT).</p></article>", "keywords": ["2. Zero hunger", "0301 basic medicine", "Microbial diversity", "soil erosion", "S", "Agriculture", "04 agricultural and veterinary sciences", "metabolic activity", "15. Life on land", "Soil quality", "6. Clean water", "bacterial community composition", "03 medical and health sciences", "13. Climate action", "microbial diversity", "Bacterial community composition", "Metabolic activity", "11. Sustainability", "Soil erosion", "biochemistry", "0401 agriculture", " forestry", " and fisheries", "soil quality"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://doi.org/10.3390/agronomy11071387"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agronomy11071387", "name": "item", "description": "10.3390/agronomy11071387", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agronomy11071387"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-16T00:00:00Z"}}, {"id": "10.5281/zenodo.14626839", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-06-23T16:23:35Z", "type": "Dataset", "title": "Data set of soil microbial components in response to extreme spring events at variable temperatures", "description": "The soil microbial response to prolonged soil drought (20% field capacity FC), wetness (above FC) and moderate drought (common at 50% FC) was simulated in pots at two spring temperatures - 2\u00b0C and +2.5\u00b0C colder and warmer, respectively, compared to the average in the central-eastern Po Valley, Italy (decade 2014-2024).\u00a0   Two soils (a ploughed soil and an adjacent renatured soil) were subjected to two 60-day cycles (cold and warm spring) at three levels of soil water content. The climate simulation started after the wheat seedlings had reached the two-leaf stage in all pots. Soil samples were taken from the wheat rhizome at the end of each experiment.  The response of microbial biomass was evaluated in terms of double-stranded DNA (dsDNA), total bacteria quantified as 16S gene copy number using Real Time PCR and total fungi quantified as 18S gene copy number using Digital PCR.   Three major bacterial groups, Pseudomonas, Actinomycetes and Bacillus, were quantified by real-time PCR using specific primers of the 16S region (F968/Ps-r; F243/518r; BacF/518).   Twenty-two enzyme activities were also quantified in soil samples. The data set contains a total of twenty-eight variables.", "keywords": ["climate change", "microbial biomass", "soil bacteria", "Pseudomonas", "actinomycetes", "estreme events", "soil fungi", "microrganisms", "Bacillus", "metabolic activity", "soil"], "contacts": [{"organization": "Manici, Luisa M.", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.14626839"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.14626839", "name": "item", "description": "10.5281/zenodo.14626839", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.14626839"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2026-01-10T00:00:00Z"}}, {"id": "10033/622632", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-23T16:25:32Z", "type": "Journal Article", "created": "2020-03-02", "title": "Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics", "description": "Abstract                 Background                 <p>Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37\uffe2\uff80\uff89\uffc2\uffb0C) and thermophilic (55\uffe2\uff80\uff89\uffc2\uffb0C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.</p>                                Results                 <p>In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or\uffc2\uffa0acetogenesis.</p>                                Conclusions                 <p>An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.</p>", "keywords": ["Integrated -omics", "Bioconversion", "0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "Polyomics", "Integrated-omics", "Metagenome assembled genomes", "Biogas", "Microbial community structure", "15. Life on land", "Microbiology", "7. Clean energy", "QR1-502", "6. Clean water", "3. Good health", "Environmental sciences", "03 medical and health sciences", "13. Climate action", "Anaerobic digestion", "Metabolic activity", "GE1-350", "Methane", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40793-020-00354-x.pdf"}, {"href": "https://doi.org/10033/622632"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10033/622632", "name": "item", "description": "10033/622632", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10033/622632"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-02T00:00:00Z"}}, {"id": "3177787314", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:27:22Z", "type": "Journal Article", "created": "2021-06-16", "title": "Going beyond Soil Conservation with the Use of Cover Crops in Mediterranean Sloping Olive Orchards", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Among the agricultural practices promoted by the Common Agricultural Policy to increase soil functions, the use of cover crops is a recommended tool to improve the sustainability of Mediter-ranean woody crops such as olive orchards. However, there is a broad range of cover crop ty-pologies in relation to its implementation, control and species composition. In that sense, the in-fluence of different plant species on soil quality indicators in olive orchards remains unknown yet. This study describes the effects of four treatments based on the implementation of different ground covers (CC-NAT, CC-GRA and CC-MIX) and conventional tillage (TILL) on soil erosion, soil physicochemical and biological properties, and soil microbial communities after 8 years of cover crop establishment. Our results have demonstrated that the presence of a temporary cover crop (CC), compared to a soil under tillage (TILL), can reduce soil losses and maintain good soil physicochemical properties and modify greatly the structure and diversity of soil bacterial com-munities and its functioning. The presence of a homogeneous CC of gramineous (Lolium rigidum or Lolilum multiflorum) (CC-GR) for 8 years significantly increased the functional properties of the soil as compared to TILL; although the most significant change was a modification on the bacte-rial community composition that was clearly different from the rest of treatments. On the other hand, the use of a mixture of plant species (CC-MIX) as a CC for only two years although did not modify greatly the structure and diversity of soil bacterial communities compared to the TILL soil, induced significant changes on the functional properties of the soil, and reverted those properties to a level similar to that of an undisturbed soil that had maintained a natural cover of spontaneous vegetation for decades (CC-NAT).</p></article>", "keywords": ["0301 basic medicine", "2. Zero hunger", "Microbial diversity", "soil erosion", "S", "Agriculture", "04 agricultural and veterinary sciences", "metabolic activity", "15. Life on land", "Soil quality", "6. Clean water", "bacterial community composition", "03 medical and health sciences", "13. Climate action", "microbial diversity", "Bacterial community composition", "Metabolic activity", "11. Sustainability", "Soil erosion", "biochemistry", "0401 agriculture", " forestry", " and fisheries", "soil quality"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://doi.org/3177787314"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3177787314", "name": "item", "description": "3177787314", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3177787314"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-16T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metabolic+activity&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metabolic+activity&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metabolic+activity&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metabolic+activity&offset=6", "hreflang": "en-US"}], "numberMatched": 6, "numberReturned": 6, "distributedFeatures": [], "timeStamp": "2026-06-24T13:20:47.879911Z"}