{"type": "FeatureCollection", "features": [{"id": "10.1038/s41598-023-49194-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:18:27Z", "type": "Journal Article", "created": "2023-12-13", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "description": "Abstract<p>Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.</p", "keywords": ["0301 basic medicine", "Bacillus", "Gene", "Agricultural and Biological Sciences", "https://purl.org/becyt/ford/1.6", "Phylogeny", "GC-content", "2. Zero hunger", "0303 health sciences", "Genome", "Acinetobacter", "soil bacteria", "Q", "Probiotics and Prebiotics", "R", "Life Sciences", "Anti-Bacterial Agents", "3. Good health", "Ribosomal RNA", "Medicine", "Microbial genetics", "metagenomics assembly", "Biotechnology", "Bacteriocin", "Science", ".", "Synteny", "Microbiology", "Article", "Applied microbiology", "Lipopeptides", "03 medical and health sciences", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "https://purl.org/becyt/ford/1", "Molecular Biology", "Biology", "genetic engineering", "Bacteria", "Secondary metabolites", "In silico", "bacterial genomes", "Whole genome sequencing", "FOS: Biological sciences", "Microbial Enzymes and Biotechnological Applications", "Antibacterial activity", "Genome", " Bacterial", "Food Science", "Phylogenetic tree"]}, "links": [{"href": "https://www.nature.com/articles/s41598-023-49194-y.pdf"}, {"href": "https://doi.org/10.1038/s41598-023-49194-y"}, {"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/s41598-023-49194-y", "name": "item", "description": "10.1038/s41598-023-49194-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-023-49194-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-13T00:00:00Z"}}, {"id": "10.1371/journal.pone.0038858", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:20:12Z", "type": "Journal Article", "created": "2012-06-11", "title": "Decline In Topsoil Microbial Quotient, Fungal Abundance And C Utilization Efficiency Of Rice Paddies Under Heavy Metal Pollution Across South China", "description": "Open AccessLos suelos agr\u00edcolas han estado cada vez m\u00e1s sujetos a la contaminaci\u00f3n por metales pesados en todo el mundo. Sin embargo, los impactos en la estructura y actividad de la comunidad microbiana del suelo de los suelos de campo a\u00fan no se han caracterizado bien. En 2009 se recolectaron muestras de tierra vegetal de campos de arroz contaminados con metales pesados (PS) y sus campos de fondo (BGS) en cuatro sitios del sur de China. Los cambios con la contaminaci\u00f3n met\u00e1lica en relaci\u00f3n con el BGS en el tama\u00f1o y la estructura de la comunidad de los microorganismos del suelo se examinaron con m\u00faltiples ensayos microbiol\u00f3gicos de medici\u00f3n de carbono de biomasa (MBC) y nitr\u00f3geno (MBN), recuento en placa de colonias cultivables y an\u00e1lisis de \u00e1cidos grasos fosfol\u00edpidos (PLFA) junto con el perfil de electroforesis en gel de gradiente desnaturalizante (DGGE) del gen de ARNr 16S y ARNr 18S y ensayo de PCR en tiempo real. Adem\u00e1s, se llev\u00f3 a cabo una incubaci\u00f3n de laboratorio de 7 d\u00edas a una temperatura constante de 25 \u00b0C para realizar un seguimiento adicional de los cambios en la actividad metab\u00f3lica. Si bien la disminuci\u00f3n de la contaminaci\u00f3n por metales en MBC y MBN, as\u00ed como en el tama\u00f1o de la poblaci\u00f3n cultivable, el contenido total de PLFA y el n\u00famero de bandas DGGE de bacterias no se observaron de manera significativa y consistente, de hecho se observ\u00f3 una reducci\u00f3n significativa de la contaminaci\u00f3n por metales en el cociente microbiano, en el tama\u00f1o de la poblaci\u00f3n f\u00fangica cultivable y en la proporci\u00f3n de PLFA f\u00fangicos a bacterianos de manera consistente en todos los sitios en una medida que var\u00eda de 6% a 74%. Adem\u00e1s, se observ\u00f3 un aumento consistentemente significativo en el cociente metab\u00f3lico de hasta un 68% bajo contaminaci\u00f3n en todos los sitios. Estas observaciones apoyaron un cambio de la comunidad microbiana con disminuci\u00f3n en su abundancia, disminuci\u00f3n en la proporci\u00f3n de hongos y, por lo tanto, en la eficiencia de utilizaci\u00f3n de C bajo contaminaci\u00f3n en los suelos. Adem\u00e1s, las proporciones de cociente microbiano, de hongos a bacterias y qCO2 son mejores indicativas de los impactos de los metales pesados en la estructura y actividad de la comunidad microbiana. Los efectos potenciales de estos cambios en el ciclo del carbono y la producci\u00f3n de CO2 en los arrozales contaminados merecen m\u00e1s estudios de campo.", "keywords": ["Microbial population biology", "Colony Count", " Microbial", "Agricultural and Biological Sciences", "Sociology", "Soil water", "Soil Pollutants", "Soil Microbiology", "2. Zero hunger", "Principal Component Analysis", "Temperature gradient gel electrophoresis", "Ecology", "Q", "Fatty Acids", "R", "Life Sciences", "Agriculture", "04 agricultural and veterinary sciences", "Biota", "Pollution", "6. Clean water", "FOS: Sociology", "Chemistry", "Physical Sciences", "Environmental chemistry", "Medicine", "Research Article", "Environmental Monitoring", "16S ribosomal RNA", "China", "Microorganism", "Environmental Impact of Heavy Metal Contamination", "Nitrogen", "Science", "Population", "Soil Science", "Real-Time Polymerase Chain Reaction", "Environmental science", "Microbial Ecology", "12. Responsible consumption", "Metals", " Heavy", "Genetics", "Biology", "Demography", "Bacteria", "Denaturing Gradient Gel Electrophoresis", "Marine Microbial Diversity and Biogeography", "Oryza", "15. Life on land", "Topsoil", "Carbon", "Agronomy", "RNA", " Ribosomal", "13. Climate action", "FOS: Biological sciences", "Environmental Science", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0038858"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0038858", "name": "item", "description": "10.1371/journal.pone.0038858", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0038858"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-06-11T00:00:00Z"}}, {"id": "10.1371/journal.pone.0124096", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:20:15Z", "type": "Journal Article", "created": "2015-04-16", "title": "Effects Of Different Organic Manures On The Biochemical And Microbial Characteristics Of Albic Paddy Soil In A Short-Term Experiment", "description": "Open AccessCette \u00e9tude visait \u00e0 \u00e9valuer les effets des engrais chimiques (NPK), NPK avec du fumier de b\u00e9tail (NPK+M), NPK avec de la paille (NPK+S) et NPK avec du fumier vert (NPK+G) sur les activit\u00e9s enzymatiques du sol et les caract\u00e9ristiques microbiennes du sol de paddy albique, qui est un sol typique avec une faible productivit\u00e9 en Chine. Les r\u00e9ponses des activit\u00e9s enzymatiques extracellulaires et de la diversit\u00e9 des communaut\u00e9s microbiennes (d\u00e9termin\u00e9es par analyse des acides gras phospholipidiques [PLFA] et \u00e9lectrophor\u00e8se sur gel \u00e0 gradient d\u00e9naturant [DGGE]) ont \u00e9t\u00e9 mesur\u00e9es. Les r\u00e9sultats ont montr\u00e9 que NPK+M et NPK+S augmentaient significativement le rendement du riz, NPK+M \u00e9tant sup\u00e9rieur d'environ 24\u00a0% \u00e0 NPK. Le NPK+M a significativement augment\u00e9 le carbone organique du sol (SOC) et les phosphates disponibles (P) et am\u00e9lior\u00e9 les activit\u00e9s de la phosphatase, de la \u03b2-cellobiosidase, de la L-leucine aminopeptidase et de l'ur\u00e9ase. Le NPK+S a significativement augment\u00e9 le COS et le potassium disponible (K) et significativement augment\u00e9 les activit\u00e9s de la N-ac\u00e9tyl-glucosamidase, de la \u03b2-xylosidase, de l'ur\u00e9ase et de la ph\u00e9nol oxydase. Le NPK+G a significativement am\u00e9lior\u00e9 l'azote total (N), l'ammonium N, le P disponible et l'activit\u00e9 de la N-ac\u00e9tyl-glucosamidase. La biomasse de PLFA \u00e9tait la plus \u00e9lev\u00e9e sous NPK+S, suivie des traitements NPK+M et NPK+G. L'analyse en composantes principales (ACP) du PLFA a indiqu\u00e9 que les sols avec NPK+M et NPK+S contenaient des proportions plus \u00e9lev\u00e9es d'acides gras insatur\u00e9s et de cyclopropane (biomarqueurs de champignons et de bact\u00e9ries \u00e0 Gram n\u00e9gatif) et que les sols sous NPK+G contenaient plus d'acides gras satur\u00e9s \u00e0 cha\u00eene droite (repr\u00e9sentant des bact\u00e9ries \u00e0 Gram positif). La PCA des patrons DGGE a montr\u00e9 que les amendements organiques avaient une plus grande influence sur la communaut\u00e9 fongique. L'analyse en grappes des profils DGGE fongiques a r\u00e9v\u00e9l\u00e9 que NPK+G \u00e9tait clairement s\u00e9par\u00e9. Pendant ce temps, la communaut\u00e9 bact\u00e9rienne du traitement NPK+M \u00e9tait la plus distincte. L'analyse RDA a r\u00e9v\u00e9l\u00e9 que les changements dans la composition de la communaut\u00e9 microbienne d\u00e9pendaient principalement de la \u03b2-xylosidase, des activit\u00e9s de la \u03b2-cellobiosidase, de l'azote total et des teneurs en K disponibles. Les abondances de PLFA bact\u00e9riens et fongiques gram-n\u00e9gatifs probablement efficaces pour am\u00e9liorer la fertilit\u00e9 des sols de paddy albique \u00e0 faible rendement en raison de leur influence significative sur le profil DGGE.", "keywords": ["China", "Mechanics and Transport in Unsaturated Soils", "Microbial population biology", "Science", "Materials Science", "Soil Science", "Organic chemistry", "Thermal Effects on Soil", "Biochemistry", "Gene", "Agricultural and Biological Sciences", "Biomaterials", "Food science", "Soil", "Engineering", "Genetics", "Biology", "Soil Microbiology", "Civil and Structural Engineering", "Applications of Clay Nanotubes in Various Fields", "2. Zero hunger", "Temperature gradient gel electrophoresis", "Bacteria", "Q", "R", "Fungi", "Life Sciences", "Straw", "Oryza", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Urease", "Agronomy", "6. Clean water", "Manure", "Chemistry", "Enzyme", "FOS: Biological sciences", "Physical Sciences", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Animal science", "Research Article", "16S ribosomal RNA"], "contacts": [{"organization": "Qian Zhang, Wei Zhou, Gaofeng Liang, Xiu\u2010Bin Wang, Jingwen Sun, Ping He, LI Lu-jiu,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0124096"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0124096", "name": "item", "description": "10.1371/journal.pone.0124096", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0124096"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-04-16T00:00:00Z"}}, {"id": "10.3389/fmicb.2015.00891", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:35Z", "type": "Journal Article", "created": "2015-09-04", "title": "Soil Bacterial And Fungal Community Responses To Nitrogen Addition Across Soil Depth And Microhabitat In An Arid Shrubland", "description": "Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0-0.5 or 0-10 cm) across the N-amendment gradient (0, 7, and 15 kg ha(-1) yr(-1)). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.", "keywords": ["2. Zero hunger", "0301 basic medicine", "biological soil crusts", "0303 health sciences", "microhabitat", "soil bacterial community", "dryland", "15. Life on land", "soil fungal community", "Microbiology", "Shrubland", "QR1-502", "6. Clean water", "03 medical and health sciences", "Soil bacterial community", "shrubland", "ribosomal RNA", "global change"], "contacts": [{"organization": "Cheryl R. Kuske, Jayne Belnap, Rebecca C. Mueller,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2015.00891"}, {"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.2015.00891", "name": "item", "description": "10.3389/fmicb.2015.00891", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2015.00891"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-09-04T00:00:00Z"}}, {"id": "11336/226991", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:26:12Z", "type": "Journal Article", "created": "2023-12-13", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "description": "Abstract<p>Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.</p", "keywords": ["0301 basic medicine", "Bacteriocin", "Science", "Bacillus", ".", "Gene", "Synteny", "Microbiology", "Article", "Agricultural and Biological Sciences", "Lipopeptides", "03 medical and health sciences", "https://purl.org/becyt/ford/1.6", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "https://purl.org/becyt/ford/1", "Molecular Biology", "Biology", "Phylogeny", "GC-content", "2. Zero hunger", "0303 health sciences", "Genome", "Acinetobacter", "Bacteria", "Secondary metabolites", "Q", "Probiotics and Prebiotics", "In silico", "R", "Life Sciences", "Anti-Bacterial Agents", "3. 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