{"type": "FeatureCollection", "features": [{"id": "10.1007/s00248-011-9897-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-31T06:55:22Z", "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": "10.1016/j.vaccine.2004.03.053", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-31T06:58:04Z", "type": "Journal Article", "created": "2004-04-28", "title": "Reducing Methane Emissions In Sheep By Immunization Against Rumen Methanogens", "description": "This work was conducted to determine if methane emissions from sheep immunized with an anti-methanogen vaccine were significantly lower than methane emissions from non-immunized sheep, to test the effectiveness of two different vaccine formulations (VF) on methane abatement, and to compare methane emissions measured using a closed-circuit respiration chamber and the sulphur-hexafluoride (SF6) tracer technique. Thirty mature wether sheep were randomly allocated to three treatment groups (n = 10). One group received an immunization of adjuvant only on days 0 and 153 (control), a second group received an immunization with a 3-methanogen mix on days 0 and 153 (VF3 + 3), and a third group received an immunization of a 7-methanogen mix on day 0 followed by a 3-methanogen mix on day 153 (VF7 + 3). Four weeks post-secondary immunization, there was a significant 7.7% reduction in methane production per kg dry matter intake in the VF7 + 3 group compared to the controls (P = 0.051). However, methane emissions from sheep immunized with VF7 + 3 were not significantly different when compared to the sheep in the control group (P = 0.883). The average IgG and IgA antibody titres in both plasma and saliva of the VF3 + 3 immunized sheep were four to nine times higher than those immunized with VF7 + 3 (P< 0.001) at both 3 and 6 weeks post-secondary immunization. Data also revealed that SF6 methane estimates were consistently higher than the respiration chamber estimates and that there was no significant correlation between the SF6 methane estimates and the respiration chamber methane estimates (R2 = 0.11).", "keywords": ["2. Zero hunger", "Vaccines", "Rumen", "Sheep", "Time Factors", "Methanobacterium", "Immunization", " Secondary", "0402 animal and dairy science", "04 agricultural and veterinary sciences", "Methanobrevibacter", "Archaea", "Immunoglobulin A", "3. Good health", "Antibodies", " Archaeal", "Kinetics", "Adjuvants", " Immunologic", "13. Climate action", "Immunoglobulin G", "Methanosarcina", "Animals", "Methanomicrobiaceae", "Saliva", "Methane"]}, "links": [{"href": "https://doi.org/10.1016/j.vaccine.2004.03.053"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Vaccine", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.vaccine.2004.03.053", "name": "item", "description": "10.1016/j.vaccine.2004.03.053", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.vaccine.2004.03.053"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2004-09-01T00:00:00Z"}}, {"id": "10.1038/ismej.2009.136", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-31T06:58:26Z", "type": "Journal Article", "created": "2009-12-24", "title": "Biogeography Of Soil Archaea And Bacteria Along A Steep Precipitation Gradient", "description": "Abstract                <p>For centuries, biodiversity has spellbound biologists focusing mainly on macroorganism's diversity and almost neglecting the geographic mediated dynamics of microbial communities. We surveyed the diversity of soil bacteria and archaea along a steep precipitation gradient ranging from the Negev Desert in the south of Israel (&amp;lt;100\uffe2\uff80\uff89mm annual rain) to the Mediterranean forests in the north (&amp;gt;900\uffe2\uff80\uff89mm annual rain). Soil samples were retrieved from triplicate plots at five long-term ecological research stations, collected from two types of patches: plant interspaces and underneath the predominant perennial at each site. The molecular fingerprint of each soil sample was taken using terminal restriction length polymorphism of the 16S rRNA gene to evaluate the bacterial and archaeal community composition and diversity within and across sites. The difference in community compositions was not statistically significant within sites (P=0.33 and 0.77 for bacteria and archaea, respectively), but it differed profoundly by ecosystem type. These differences could largely be explained by the precipitation gradient combined with the vegetation cover: the archaeal and bacterial operational taxonomic units were unique to each climatic region, that is, arid, semiarid and Mediterranean (P=0.0001, for both domains), as well as patch type (P=0.009 and 0.02 for bacteria and archaea, respectively). Our results suggest that unlike macroorganisms that are more diverse in the Mediterranean ecosystems compared with the desert sites, archaeal and bacterial diversities are not constrained by precipitation. However, the community composition is unique to the climate and vegetation cover that delineates each ecosystem.</p>", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Geography", "Biodiversity", "15. Life on land", "Archaea", "DNA Fingerprinting", "DNA", " Ribosomal", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Cluster Analysis", "Israel", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2009.136"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2009.136", "name": "item", "description": "10.1038/ismej.2009.136", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2009.136"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-12-24T00:00:00Z"}}, {"id": "10.1038/ismej.2010.3", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-31T06:58:26Z", "type": "Journal Article", "created": "2010-02-04", "title": "Shifts In Microbial Community Structure Along An Ecological Gradient Of Hypersaline Soils And Sediments", "description": "Abstract<p>Studies of hypersaline ecosystems often yield novel organisms and contribute to our understanding of extreme environments. Soils and sediments from La Sal del Rey, a previously uncharacterized, hypersaline lake located in southern Texas, USA, were surveyed to characterize the structure and diversity of their microbial communities. Samples were collected along a transect that spanned vegetated uplands, exposed lakebed sediments, and water-logged locations, capturing a wide range of environments and physical and chemical gradients. Community quantitative PCR (qPCR) was used in combination with tag-encoded pyrosequencing, 16S rRNA gene cloning, and Sanger sequencing to characterize the lake's soil and sediment microbial communities. Further, we used multivariate statistics to identify the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa, and sharing significant correlations with site water content, phosphorus and total organic carbon concentrations, and pH. Some individual populations, especially of Archaea, also correlated with sodium concentration and electrical conductivity salinity. Across the transect, Bacteria were numerically dominant relative to Archaea, and among them, three phyla\uffe2\uff80\uff94the Proteobacteria, Bacteroidetes, and Firmicutes\uffe2\uff80\uff94accounted for the majority of taxa detected. Although these taxa were detected with similar abundances to those described in other hypersaline ecosystems, the greater depth of sequencing achieved here resulted in the detection of taxa not described previously in hypersaline sediments. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems.</p>", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Geologic Sediments", "Salinity", "0303 health sciences", "Bacteria", "Genes", " rRNA", "Sequence Analysis", " DNA", "15. Life on land", "Archaea", "Polymerase Chain Reaction", "Texas", "6. Clean water", "Soil", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Water Microbiology", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2010.3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2010.3", "name": "item", "description": "10.1038/ismej.2010.3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2010.3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-02-04T00:00:00Z"}}, {"id": "10.1038/srep28981", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-31T06:58:36Z", "type": "Journal Article", "created": "2016-06-30", "title": "Quantitative And Compositional Responses Of Ammonia-Oxidizing Archaea And Bacteria To Long-Term Field Fertilization", "description": "Abstract<p>Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM) and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.</p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Biota", "Article", "6. Clean water", "Genes", " Archaeal", "03 medical and health sciences", "Ammonia", "Genes", " Bacterial", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep28981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep28981", "name": "item", "description": "10.1038/srep28981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep28981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-30T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2007.00394.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-31T06:59:47Z", "type": "Journal Article", "created": "2007-10-19", "title": "Quantitation And Diversity Analysis Of Ruminal Methanogenic Populations In Response To The Antimethanogenic Compound Bromochloromethane", "description": "Methyl coenzyme-M reductase A (mcrA) clone libraries were generated from microbial DNA extracted from the rumen of cattle fed a roughage diet with and without supplementation of the antimethanogenic compound bromochloromethane. Bromochloromethane reduced total methane emissions by c. 30%, with a resultant increase in propionate and branched chain fatty acids. The mcrA clone libraries revealed that Methanobrevibacter spp. were the dominant species identified. A decrease in the incidence of Methanobrevibacter spp. from the clone library generated from bromochloromethane treatment was observed. In addition, a more diverse methanogenic population with representatives from Methanococcales, Methanomicrobiales and Methanosacinales orders was observed for the bromochloromethane library. Sequence data generated from these libraries aided in the design of an mcrA-targeted quantitative PCR (qPCR) assay. The reduction in methane production by bromochloromethane was associated with an average decrease of 34% in the number of methanogenic Archaea when monitored with this qPCR assay. Dissociation curve analysis of mcrA amplicons showed a clear difference in melting temperatures for Methanobrevibacter spp. (80-82 degrees C) and all other methanongens (84-86 degrees C). A decrease in the intensity of the Methanobrevibacter spp. specific peak and an increase for the other peak in the bromochloromethane-treated animals corresponded with the changes within the clone libraries.", "keywords": ["Male", "0301 basic medicine", "Rumen", "Bromochloromethane", "Methanogens", "Molecular Sequence Data", "Euryarchaeota", "Methanobrevibacter", "Polymerase Chain Reaction", "630", "03 medical and health sciences", "2402 Applied Microbiology and Biotechnology", "Animals", "Methyl coenzyme-M reductase", "Phylogeny", "Gene Library", "2. Zero hunger", "0303 health sciences", "Hydrocarbons", " Halogenated", "2404 Microbiology", "Sequence Analysis", " DNA", "mcrA", "qPCR", "DNA", " Archaeal", "Cattle", "Oxidoreductases", "2303 Ecology", "Methane"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2007.00394.x", "name": "item", "description": "10.1111/j.1574-6941.2007.00394.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-12-01T00:00:00Z"}}, {"id": "10.1128/aem.02453-08", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-31T06:59:58Z", "type": "Journal Article", "created": "2009-02-07", "title": "A Vaccine Against Rumen Methanogens Can Alter The Composition Of Archaeal Populations", "description": "ABSTRACT           <p>             The objectives of this study were to formulate a vaccine based upon the different species/strains of methanogens present in sheep intended to be immunized and to determine if a targeted vaccine could be used to decrease the methane output of the sheep. Two 16S rRNA gene libraries were used to survey the methanogenic archaea in sheep prior to vaccination, and methanogens representing five phylotypes were found to account for &gt;52% of the different species/strains of methanogens detected. A vaccine based on a mixture of these five methanogens was then formulated, and 32 sheep were vaccinated on days 0, 28, and 103 with either a control or the anti-methanogen vaccine. Enzyme-linked immunosorbent assay analysis revealed that each vaccination with the anti-methanogen formulation resulted in higher specific immunoglobulin G titers in plasma, saliva, and rumen fluid. Methane output levels corrected for dry-matter intake for the control and treatment groups were not significantly different, and real-time PCR data also indicated that methanogen numbers were not significantly different for the two groups after the second vaccination. However, clone library data indicated that methanogen diversity was significantly greater in sheep receiving the anti-methanogen vaccine and that the vaccine may have altered the composition of the methanogen population. A correlation between 16S rRNA gene sequence relatedness and cross-reactivity for the methanogens (             R             2             = 0.90) also exists, which suggests that a highly specific vaccine can be made to target specific strains of methanogens and that a more broad-spectrum approach is needed for success in the rumen. Our data also suggest that methanogens take longer than 4 weeks to adapt to dietary changes and call into question the validity of experimental results based upon a 2- to 4-week acclimatization period normally observed for bacteria.           </p>", "keywords": ["Rumen", "Molecular Sequence Data", "DNA", " Ribosomal", "630", "Antibodies", "Plasma", "RNA", " Ribosomal", " 16S", "2402 Applied Microbiology and Biotechnology", "Animals", "Saliva", "1106 Food Science", "2. Zero hunger", "Vaccines", "Gastric Juice", "Sheep", "0402 animal and dairy science", "Biodiversity", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Archaea", "3. Good health", "DNA", " Archaeal", "Immunoglobulin G", "1305 Biotechnology", "2303 Ecology", "Methane"]}, "links": [{"href": "https://doi.org/10.1128/aem.02453-08"}, {"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.02453-08", "name": "item", "description": "10.1128/aem.02453-08", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02453-08"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-04-01T00:00:00Z"}}, {"id": "10.13145/bacdive11415.20170425.1", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-31T07:00:14Z", "type": "Dataset", "title": "Brevibacillus parabrevis (Takagi et al. 1993) Shida et al. 1996", "description": "The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.", "keywords": ["Strain-linked information about bacterial and archaeal biodiversity", "15. Life on land"], "contacts": [{"organization": "Reimer, L.C., Vetcininova, A., Soehngen, C., Podstawka, A., Gleim, D., Overmann, J.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.13145/bacdive11415.20170425.1"}, {"rel": "self", "type": "application/geo+json", "title": "10.13145/bacdive11415.20170425.1", "name": "item", "description": "10.13145/bacdive11415.20170425.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.13145/bacdive11415.20170425.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-04-25T00:00:00Z"}}, {"id": "10.13145/bacdive109630.20190402.4", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-31T07:00:14Z", "type": "Dataset", "title": "Streptomyces sp.", "description": "The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.", "keywords": ["Strain-linked information about bacterial and archaeal biodiversity"], "contacts": [{"organization": "Reimer, L.C., Sarda Carbasse, J., Podstawka, A., Overmann, J.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.13145/bacdive109630.20190402.4"}, {"rel": "self", "type": "application/geo+json", "title": "10.13145/bacdive109630.20190402.4", "name": "item", "description": "10.13145/bacdive109630.20190402.4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.13145/bacdive109630.20190402.4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-02T00:00:00Z"}}, {"id": "10.13145/bacdive113332.20170425.1", "type": "Feature", "geometry": null, 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"https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-04-25T00:00:00Z"}}, {"id": "10.13145/bacdive114128.20230509.8.1", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-31T07:00:14Z", "type": "Dataset", "title": "Streptomyces sp.", "description": "The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.", "keywords": ["Strain-linked information about bacterial and archaeal biodiversity"], "contacts": [{"organization": "Reimer, L.C., Sarda Carbasse, J., Schober, I., Koblitz, J., Podstawka, A., Overmann, J.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.13145/bacdive114128.20230509.8.1"}, {"rel": "self", "type": "application/geo+json", "title": "10.13145/bacdive114128.20230509.8.1", "name": "item", "description": "10.13145/bacdive114128.20230509.8.1", "href": 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