{"type": "FeatureCollection", "features": [{"id": "10.1128/aem.02541-13", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:18:02Z", "type": "Journal Article", "created": "2013-09-21", "title": "Impact Of Logging And Forest Conversion To Oil Palm Plantations On Soil Bacterial Communities In Borneo", "description": "ABSTRACT

Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale \uffce\uffb1-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true \uffce\uffb2-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of \uffce\uffb2-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall \uffce\uffb3-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.

", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Tropical Climate", "0303 health sciences", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "15. Life on land", "Biota", "DNA", " Ribosomal", "333", "Trees", "03 medical and health sciences", "Borneo", "13. Climate action", "RNA", " Ribosomal", " 16S", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1128/aem.02541-13"}, {"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.02541-13", "name": "item", "description": "10.1128/aem.02541-13", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02541-13"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-12-01T00:00:00Z"}}, {"id": "10.1128/aem.04040-14", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:18:02Z", "type": "Journal Article", "created": "2015-01-24", "title": "Fungal Communities Respond To Long-Term Co2 Elevation By Community Reassembly", "description": "ABSTRACT

Fungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO 2 (eCO 2 ), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON (biodiversity, CO 2 , and N deposition) experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO 2 for 12 years. Long-term eCO 2 did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. The relative abundances of 119 operational taxonomic units (OTU; \uffe2\uff88\uffbc27% of the total captured sequences) were changed significantly. Significantly changed OTU under eCO 2 were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Co-occurrence ecological network analysis indicated that eCO 2 increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO 2 network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO 2 , especially with increased plant biomass and NH 4 + availability. This study provided novel insights into how eCO 2 shapes soil fungal communities in grassland ecosystems.

", "keywords": ["580", "0301 basic medicine", "0303 health sciences", "electric network topology", "Minnesota", "Molecular Sequence Data", "Fungi", "carbon dioxide", "Sequence Analysis", " DNA", "Carbon Dioxide", "15. Life on land", "Biota", "DNA", " Ribosomal", "333", "03 medical and health sciences", "13. Climate action", "XXXXXX - Unknown", "RNA", " Ribosomal", " 28S", "11. Sustainability", "fungi", "ecology", "DNA", " Fungal", "Soil Microbiology", "biodiversity"]}, "links": [{"href": "https://doi.org/10.1128/aem.04040-14"}, {"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.04040-14", "name": "item", "description": "10.1128/aem.04040-14", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.04040-14"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-04-01T00:00:00Z"}}, {"id": "10.1128/aem.69.3.1800-1809.2003", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:18:02Z", "type": "Journal Article", "created": "2003-03-06", "title": "Soil Type Is The Primary Determinant Of The Composition Of The Total And Active Bacterial Communities In Arable Soils", "description": "ABSTRACT

Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.

", "keywords": ["Polymerase Chain Reaction", "geography", "630", "1000 Technology", "Soil", "soil type", "RNA", " Ribosomal", " 16S", "C500 - Microbiology", "genetic polymorphism", "soil analysis", "Bacteria (microorganisms)", "Soil Microbiology", "2. Zero hunger", "article", "Agriculture", "Fabaceae", "Biodiversity", "legume", "04 agricultural and veterinary sciences", "Bacterial Typing Techniques", "microbial community", "Polymorphism", " Restriction Fragment Length", "0605 Microbiology", "Electrophoresis", "16S", "570", "Conservation of Natural Resources", "productivity", "RNA 16S", "soil microorganism", "0600 Biological Sciences", "DNA", " Ribosomal", "0700 Agricultural And Veterinary Sciences", "controlled study", "community composition", "Polymorphism", "Pisum sativum", "Ecosystem", "Ribosomal", "nonhuman", "Bacteria", "bacterial flora", "land use", "DNA", "15. Life on land", "bacterial disease", "Restriction Fragment Length", "C180 - Ecology", "physiology", "RNA", "Soils", "0401 agriculture", " forestry", " and fisheries", "bioavailability"]}, "links": [{"href": "https://doi.org/10.1128/aem.69.3.1800-1809.2003"}, {"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.69.3.1800-1809.2003", "name": "item", "description": "10.1128/aem.69.3.1800-1809.2003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.69.3.1800-1809.2003"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-03-01T00:00:00Z"}}, {"id": "10.1128/msphere.00130-21", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:18:02Z", "type": "Journal Article", "created": "2021-08-11", "title": "Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield", "description": "

Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield.

", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "Biological Products", "0303 health sciences", "Bacteria", "Microbiota", "Fungi", "High-Throughput Nucleotide Sequencing", "Agriculture", "Agricultural Inoculants", "15. Life on land", "Microbiology", "QR1-502", "United States", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Soil Microbiology", "Research Article", "Solanum tuberosum"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSphere.00130-21"}, {"href": "https://doi.org/10.1128/msphere.00130-21"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msphere.00130-21", "name": "item", "description": "10.1128/msphere.00130-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msphere.00130-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-25T00:00:00Z"}}, {"id": "10.1186/s12916-021-01913-w", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:18:09Z", "type": "Journal Article", "created": "2021-02-11", "title": "High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome", "description": "Abstract Background

Chronic inflammation, which can be modulated by diet, is linked to high white blood cell counts and correlates with higher cardiometabolic risk and risk of more severe infections, as in the case of COVID-19.

Methods

Here, we assessed the association between white blood cell profile (lymphocytes, basophils, eosinophils, neutrophils, monocytes and total white blood cells) as markers of chronic inflammation, habitual diet and gut microbiome composition (determined by sequencing of the 16S RNA) in 986 healthy individuals from the PREDICT-1 nutritional intervention study. We then investigated whether the gut microbiome mediates part of the benefits of vegetable intake on lymphocyte counts.

Results

Higher levels of white blood cells, lymphocytes and basophils were all significantly correlated with lower habitual intake of vegetables, with vegetable intake explaining between 3.59 and 6.58% of variation in white blood cells after adjusting for covariates and multiple testing using false discovery rate (q\uffe2\uff80\uff89<\uffe2\uff80\uff890.1). No such association was seen with fruit intake. A mediation analysis found that 20.00% of the effect of vegetable intake on lymphocyte counts was mediated by one bacterial genus, Collinsella, known to increase with the intake of processed foods and previously associated with fatty liver disease. We further correlated white blood cells to other inflammatory markers including IL6 and GlycA, fasting and post-prandial glucose levels and found a significant relationship between inflammation and diet.

Conclusion

A habitual diet high in vegetables, but not fruits, is linked to a lower inflammatory profile for white blood cells, and a fifth of the effect is mediated by the genus Collinsella.

Trial registration

The ClinicalTrials.gov registration identifier is NCT03479866.

", "keywords": ["Adult", "Male", "0301 basic medicine", "610", "Leukocyte Count", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Leukocytes", "Humans", "Lymphocyte Count", "White blood cell", " Gut microbiome", " Diet", " Vegetable intake", " Chronic inflammation", "White blood cell", "Clostridium", "2. Zero hunger", "Gut microbiome", "Clostridiales", "0303 health sciences", "Mediation Analysis", "Interleukin-6", "R", "COVID-19", "Chronic inflammation; Diet; Gut microbiome; Vegetable intake; White blood cell", "Chronic inflammation", "General Medicine", "Fasting", "Middle Aged", "Diet", "Gastrointestinal Microbiome", "3. Good health", "Actinobacteria", "Vegetable intake", "Fruit", "Medicine", "Female", "Biomarkers", "Research Article"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/1101012/2/s12916-021-01913-w.pdf"}, {"href": "https://iris.unitn.it/bitstream/11572/329112/1/s12916-021-01913-w.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1186/s12916-021-01913-w.pdf"}, {"href": "https://doi.org/10.1186/s12916-021-01913-w"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BMC%20Medicine", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s12916-021-01913-w", "name": "item", "description": "10.1186/s12916-021-01913-w", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s12916-021-01913-w"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-11T00:00:00Z"}}, {"id": "10.1155/2018/9264259", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:18:06Z", "type": "Journal Article", "created": "2018-09-06", "title": "Effects of Aged Oil Sludge on Soil Physicochemical Properties and Fungal Diversity Revealed by High-Throughput Sequencing Analysis", "description": "

The oilfield soil was contaminated for years by large quantities of aged oil sludge generated in the petroleum industry. In this study, physicochemical properties, contents of main pollutants, and fungal diversity of the aged oil sludge-contaminated soil were analyzed. Results revealed that aged oil sludge significantly changed physical and chemical properties of the receiving soil and increased the contents of main pollutants (petroleum hydrocarbons and heavy metals) in soil. Meanwhile, the internal transcribed spacer (ITS) sequencing by Illumina Miseq platform at each taxonomic level demonstrated that the toxicological effect of oil pollutants obviously influenced the fungal diversity and community structure in soil. Moreover, it was found that the presence of three genera (Cephalotheca, Lecanicillium, and Septoriella) appeared in aged oil sludge-contaminated soil. And oil pollutants promoted the growth of certain genera in Ascomycota (70.83%) and Basidiomycota (10.78%), such as Venturia, Alternaria, and Piloderma. Nevertheless, the growth of Mortierella (9.16%), Emericella (6.02%), and Bjerkandera (0.00%) was intensively limited. This study would aid thorough understanding of microbial diversity in oil-contaminated soil and thus provide new point of view to soil bioremediation.Soil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition.

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

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

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

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

", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Science", "Microbial Consortia", "DIVERSITY", "SOFTWARE", "Real-Time Polymerase Chain Reaction", "BACILLUS-SUBTILIS", "BIOMASS", "03 medical and health sciences", "BIOAUGMENTATION", "DNA", " Bacterial/chemistry", "MICROBIAL COMMUNITIES", "Soil Microbiology", "2. Zero hunger", "0303 health sciences", "16S RIBOSOMAL-RNA", "Q", "R", "PROFILES", "ACIDS", "TRANSFORMATION", "6. Clean water", "Microbial Consortia/genetics", "Enhancer Elements", " Genetic", "13. Climate action", "Medicine", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/365395v1.full.pdf"}, {"href": "https://doi.org/10.1371/journal.pone.0200979"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0200979", "name": "item", "description": "10.1371/journal.pone.0200979", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0200979"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-09T00:00:00Z"}}, {"id": "10.1371/journal.pone.0038858", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:18:14Z", "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": "2026-08-25T16:18:16Z", "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": "10.1890/10-0426.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:18:34Z", "type": "Journal Article", "created": "2010-12-17", "title": "Consistent Effects Of Nitrogen Fertilization On Soil Bacterial Communities In Contrasting Systems", "description": "

Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) through anthropogenic activities. Although the effects of increased N inputs on plant communities have been reasonably well studied, few comparable studies have examined impacts on whole soil bacterial communities, though they play critical roles in ecosystem functioning. We sampled soils from two long\uffe2\uff80\uff90term ecological research (LTER) experimental N gradients, both of which have been amended with NH4NO3; a grassland at Cedar Creek (27 years of N additions) and an agricultural field at Kellogg Biological Station (8 years of N additions). By examining shifts in bacterial communities across these contrasting ecosystem types, we could test competing hypotheses about the direct and indirect factors that might drive bacterial responses to elevated N inputs. Bacterial community structure was highly responsive to N additions. We observed predictable and consistent changes in the structure of the bacterial communities across both ecosystem types. Our results suggest that bacterial communities across these gradients are more structured by N and/or soil carbon availability than by shifts in the plant community or soil pH associated with the elevated nitrogen inputs. In contrast to the pronounced shifts in bacterial community composition and in direct contrast to the patterns often observed in plant communities, increases in N availability did not have consistent effects on the richness and diversity of soil bacterial communities.

", "keywords": ["2. Zero hunger", "Michigan", "Bacteria", "Nitrogen", "Minnesota", "04 agricultural and veterinary sciences", "15. Life on land", "RNA", " Bacterial", "13. Climate action", "RNA", " Ribosomal", " 16S", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Ecosystem", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1890/10-0426.1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1890/10-0426.1", "name": "item", "description": "10.1890/10-0426.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1890/10-0426.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-12-01T00:00:00Z"}}, {"id": "10.2527/jas.2009-1786", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:19:01Z", "type": "Journal Article", "created": "2009-06-20", "title": "Effect Of Sward Dry Matter Digestibility On Methane Production, Ruminal Fermentation, And Microbial Populations Of Zero-Grazed Beef Cattle", "description": "Increasing the digestibility of pasture for grazing ruminants has been proposed as a low-cost practical means of reducing ruminant CH(4) emissions. At high feed intake levels, the proportion of energy lost as CH(4) decreases as the digestibility of the diet increases. Therefore, improving forage digestibility may improve productivity as DM and energy intake are increased. A zero-grazing experiment was conducted to determine the effect of sward DM digestibility (DMD) on DMI, CH(4) emissions, and indices of rumen fermentation of beef animals. Twelve Charolais-cross heifers were assigned to 1 of 2 treatments, with 6 heifers per dietary treatment. Additionally, 4 cannulated Aberdeen Angus-cross steers were randomly allocated to each of these 2 treatments in a crossover design. Dietary treatments consisted of swards managed to produce (i) high digestibility pasture (high DMD) or (ii) pasture with less digestibility (low DMD), both offered for ad libitum intake. All animals were zero-grazed and offered freshly cut herbage twice daily. In vitro DMD values for the high and low DMD swards were 816 and 706 g/kg of DM. Heifers offered the high DMD grass had greater (P < 0.001) daily DMI of 7.66 kg compared with 5.38 kg for those offered the low DMD grass. Heifers offered the high DMD grass had greater (P = 0.003) daily CH(4) production (193 g of CH(4)/d) than those offered the low DMD grass (138 g of CH(4)/d). However, when corrected for DMI, digestible DMI, or ingested gross energy, there was no difference (P > 0.05) in CH(4) production between dietary treatments. For cannulated steers, intake tended (P = 0.06) to be greater for the high DMD grass (5.56 vs. 4.27 kg of DM/d), but rumen protozoa (4.95 x 10(4)/mL; P = 0.62); rumen ammonia (34 mg of N/L; P = 0.24); rumen total VFA (103 mM; P = 0.58), and rumen pH (6.8; P = 0.43) did not differ between treatments. There was no difference in total bacteria numbers, relative expression of the mcrA gene, and numbers of cycles to threshold for fungi when determined using quantitative PCR between dietary treatments with mean values of 73.0 ng/microL, 0.958, and 21.75 C(T), respectively. Results of this study demonstrate that there was no difference in CH(4) production when corrected for intake or rumen fermentation variables of beef cattle offered a high or low digestibility sward.", "keywords": ["DNA", " Bacterial", "Male", "2. Zero hunger", "Rumen", "0402 animal and dairy science", "04 agricultural and veterinary sciences", "Fatty Acids", " Volatile", "Polymerase Chain Reaction", "Random Allocation", "Ammonia", "RNA", " Ribosomal", " 16S", "Lolium", "Animals", "Cattle", "Digestion", "Female", "Least-Squares Analysis", "Methane"]}, "links": [{"href": "https://doi.org/10.2527/jas.2009-1786"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Animal%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2527/jas.2009-1786", "name": "item", "description": "10.2527/jas.2009-1786", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2527/jas.2009-1786"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-06-19T00:00:00Z"}}, {"id": "10.3390/genes10060456", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:19:15Z", "type": "Journal Article", "created": "2019-06-14", "title": "Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil", "description": "

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/10.3390/genes10060456"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10060456", "name": "item", "description": "10.3390/genes10060456", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10060456"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "10754/680032", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:22:10Z", "type": "Journal Article", "created": "2022-07-26", "title": "Pollution and edaphic factors shape bacterial community structure and functionality in historically contaminated soils", "description": "Studies about biodegradation potential in soils often refer to artificially contaminated and simplified systems, overlooking the complexity associated with contaminated sites in a real context. This work aims to provide a holistic view on microbiome assembly and functional diversity in the model site SIN Brescia-Caffaro (Italy), characterized by historical and uneven contamination by organic and inorganic compounds. Here, physical and chemical analyses and microbiota characterization were applied on one-hundred-twenty-seven soil samples to unravel the environmental factors driving bacterial community assembly and biodegradation potential in three former agricultural fields. Chemical analyses showed a patchy distribution of metals, metalloids and polychlorinated biphenyls (PCB) and allowed soil categorization according to depth and area of collections. Likewise, the bacterial community structure, described by molecular fingerprinting and 16S rRNA gene analyses, was significantly different according to collection site and depth. Pollutant concentrations (i.e., hexachloro-biphenyls, arsenic and mercury), nitrogen content and parameters related to soil texture were identified as main drivers of microbiota assembly, being significantly correlated to bacterial community composition. Moreover, bacteria putatively involved in the aerobic degradation of PCBs were enriched over the total bacterial community in topsoils, where the highest activity was recorded using fluorescein hydrolysis as proxy. Metataxonomic analyses revealed the presence of bacteria having metabolic pathways related to PCB degradation and tolerance to heavy metals and metalloids in the topsoil samples collected in all areas. Overall, the provided dissection of soil microbiota structure and its degradation potential in the SIN Brescia-Caffaro can contribute to target specific areas for rhizoremediation implementation. Metagenomics studies could be implemented in the future to understand if specific degradative pathways are present in historically polluted sites characterized by the co-occurrence of multiple classes of contaminants.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "15. Life on land", "Polychlorinated Biphenyls", "6. Clean water", "Soil", "03 medical and health sciences", "Biodegradation", " Environmental", "13. Climate action", "RNA", " Ribosomal", " 16S", "Environmental selection; Heavy metals; PCB; Soil microbiota; bphA", "Soil Pollutants", "Soil Microbiology", "Metalloids"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/935372/3/Mapelli%2bet%2bal_MS_04032022.pdf"}, {"href": "https://air.unimi.it/bitstream/2434/935372/4/1-s2.0-S0944501322001847-main.pdf"}, {"href": "https://doi.org/10754/680032"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiological%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10754/680032", "name": "item", "description": "10754/680032", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10754/680032"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-10-01T00:00:00Z"}}, {"id": "10.4238/2015.december.15.5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:19:34Z", "type": "Journal Article", "created": "2015-12-15", "title": "Diversity And Structure Of A Bacterial Community In Grassland Soils Disturbed By Sheep Grazing, In The Loess Plateau Of Northwestern China", "description": "The relationship between disturbance, biodiversity, and ecosystem function has been a hot topic recently in international ecological research, and a universally applicable model remains elusive. In this study, we assessed the diversity and structure of a bacterial community in grassland soils along a disturbance gradient due to sheep grazing. Bacteria were identified based on 16S rDNA gene libraries prepared from a 12-year field experiment that included four grazing, intensity treatments: no grazing, light grazing, moderate grazing and heavy grazing in the Loess Plateau of northwestern China. We found that diversity indices of bacterial 16S rDNA increased with grazing intensity, suggesting that disturbance led to higher bacterial diversity. The bacterial community structure, measured as species composition, was also affected by grazing. In addition, the change in soil bacterial community composition was maximum under heavy grazing, based on the Sorensen similarity index. Overall, the relationship between disturbance and bacterial diversity is complex, therefore, more studies are required to determine the possibility of using microbial diversity as an indicator of ecosystem stability.", "keywords": ["2. Zero hunger", "China", "Sheep", "Bacteria", "Biodiversity", "04 agricultural and veterinary sciences", "15. Life on land", "13. Climate action", "RNA", " Ribosomal", " 16S", "Animals", "0401 agriculture", " forestry", " and fisheries", "Herbivory", "Ecosystem", "Phylogeny", "Soil Microbiology", "Gene Library"]}, "links": [{"href": "https://doi.org/10.4238/2015.december.15.5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genetics%20and%20Molecular%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.4238/2015.december.15.5", "name": "item", "description": "10.4238/2015.december.15.5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.4238/2015.december.15.5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-01-01T00:00:00Z"}}, {"id": "10754/685569", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:22:10Z", "type": "Journal Article", "created": "2022-11-03", "title": "Environmental micro\u2010niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas' glacier forefield", "description": "Abstract

The pedogenesis from the mineral substrate released upon glacier melting has been explained with the succession of consortia of pioneer microorganisms, whose structure and functionality are determined by the environmental conditions developing in the moraine. However, the microbiome variability that can be expected in the environmentally heterogeneous niches occurring in a moraine at a given successional stage is poorly investigated. In a 50\uffe2\uff80\uff89m2 area in the forefield of the Lobuche glacier (Himalayas, 5050\uffe2\uff80\uff89m above sea level), we studied six sites of primary colonization presenting different topographical features (orientation, elevation and slope) and harbouring greyish/dark biological soil crusts (BSCs). The spatial vicinity of the sites opposed to their topographical differences, allowed us to examine the effect of environmental conditions independently from the time of deglaciation. The bacterial microbiome diversity and their co\uffe2\uff80\uff90occurrence network, the bacterial metabolisms predicted from 16S rRNA gene high\uffe2\uff80\uff90throughput sequencing, and the microbiome intact polar lipids were investigated in the BSCs and the underlying sediment deep layers (DLs). Different bacterial microbiomes inhabited the BSCs and the DLs, and their composition varied among sites, indicating a niche\uffe2\uff80\uff90specific role of the micro\uffe2\uff80\uff90environmental conditions in the bacterial communities' assembly. In the heterogeneous sediments of glacier moraines, physico\uffe2\uff80\uff90chemical and micro\uffe2\uff80\uff90climatic variations at the site\uffe2\uff80\uff90spatial scale are crucial in shaping the microbiome microvariability and structuring the pioneer bacterial communities during pedogenesis.

We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community\u2019s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 \u00b0C + 50% water holding capacity (WHC)); increased air temperature (15\u201325 \u00b0C or 20\u201330 \u00b0C + 50% WHC); flood (20 \u00b0C + 75% WHC); drought (20 \u00b0C + 25% WHC); and ultraviolet radiation (UV) (20 \u00b0C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community\u2019s physiological profile and the bacterial community\u2019s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20\u201330 \u00b0C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome\u2013invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.

", "keywords": ["0301 basic medicine", "Soil invertebrates", "Ultraviolet Rays", "drought", "microbial activity", "DNA", " Ribosomal", "Flood", "Article", "Quantitative PCR", "Soil", "03 medical and health sciences", "soil microbiome", "2. Zero hunger", "metagenomics", "increased temperature; drought; flood; UV exposure; microbial activity; bacterial diversity; metagenomics; quantitative PCR; soil microbiome; soil invertebrates", "Soil microbiome", "0303 health sciences", "Drought", "Bacteria", "Microbiota", "bacterial diversity", "Temperature", "Water", "flood", "15. Life on land", "soil invertebrates", "6. Clean water", "UV exposure", "Microbial activity", "Bacterial diversity", "13. Climate action", "quantitative PCR", "Metagenomics", "Increased temperature", "increased temperature"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/13/5/850/pdf"}, {"href": "https://doi.org/10400.14/37827"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10400.14/37827", "name": "item", "description": "10400.14/37827", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10400.14/37827"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-10T00:00:00Z"}}, {"id": "10486/713957", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:22:08Z", "type": "Journal Article", "created": "2019-06-14", "title": "Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil", "description": "

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/10486/713957"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10486/713957", "name": "item", "description": "10486/713957", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10486/713957"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "11104/0309544", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:22:12Z", "type": "Journal Article", "created": "2020-04-02", "title": "Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence", "description": "

The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA\uffe2\uff80\uff93DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.Polychlorinated biphenyl (PCB)-contaminated soils represent a major treat for ecosystems health. Plant biostimulation of autochthonous microbial PCB degraders is a way to restore polluted sites where traditional remediation techniques are not sustainable, though its success requires the understanding of site-specific plant\uffe2\uff80\uff93microbe interactions. In an historical PCB contaminated soil, we applied DNA stable isotope probing (SIP) using 13C-labeled 4-chlorobiphenyl (4-CB) and 16S rRNA MiSeq amplicon sequencing to determine how the structure of total and PCB-degrading bacterial populations were affected by different treatments: biostimulation with Phalaris arundinacea subjected (PhalRed) or not (Phal) to a redox cycle and the non-planted controls (Bulk and BulkRed). Phal soils hosted the most diverse community and plant biostimulation induced an enrichment of Actinobacteria. Mineralization of 4-CB in SIP microcosms varied between 10% in Bulk and 39% in PhalRed soil. The most abundant taxa deriving carbon from PCB were Betaproteobacteria and Actinobacteria. Comamonadaceae was the family most represented in Phal soils, Rhodocyclaceae and Nocardiaceae in non-planted soils. Planted soils subjected to redox cycle enriched PCB degraders affiliated to Pseudonocardiaceae, Micromonosporaceae and Nocardioidaceae. Overall, we demonstrated different responses of soil bacterial taxa to specific rhizoremediation treatments and we provided new insights into the populations active in PCB biodegradation.The oilfield soil was contaminated for years by large quantities of aged oil sludge generated in the petroleum industry. In this study, physicochemical properties, contents of main pollutants, and fungal diversity of the aged oil sludge-contaminated soil were analyzed. Results revealed that aged oil sludge significantly changed physical and chemical properties of the receiving soil and increased the contents of main pollutants (petroleum hydrocarbons and heavy metals) in soil. Meanwhile, the internal transcribed spacer (ITS) sequencing by Illumina Miseq platform at each taxonomic level demonstrated that the toxicological effect of oil pollutants obviously influenced the fungal diversity and community structure in soil. Moreover, it was found that the presence of three genera (Cephalotheca, Lecanicillium, and Septoriella) appeared in aged oil sludge-contaminated soil. And oil pollutants promoted the growth of certain genera in Ascomycota (70.83%) and Basidiomycota (10.78%), such as Venturia, Alternaria, and Piloderma. Nevertheless, the growth of Mortierella (9.16%), Emericella (6.02%), and Bjerkandera (0.00%) was intensively limited. This study would aid thorough understanding of microbial diversity in oil-contaminated soil and thus provide new point of view to soil bioremediation.

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/2950940967"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2950940967", "name": "item", "description": "2950940967", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2950940967"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "PMC10938371", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-08-25T16:24:36Z", "type": "Journal Article", "created": "2024-01-29", "title": "Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth", "description": "Abstract

Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth. Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s V = 0.857, and Theil\uffe2\uff80\uff99s U = 0.316). For species-level community profiling, we found strong correlations ( r s > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average r s = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.

IMPORTANCE

A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.

", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/PMC11494973"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11494973", "name": "item", "description": "PMC11494973", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11494973"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "PMC6146557", "type": "Feature", "geometry": null, "properties": {"updated": "2026-08-25T16:24:39Z", "type": "Journal Article", "created": "2018-09-06", "title": "Effects of Aged Oil Sludge on Soil Physicochemical Properties and Fungal Diversity Revealed by High-Throughput Sequencing Analysis", "description": "

The oilfield soil was contaminated for years by large quantities of aged oil sludge generated in the petroleum industry. In this study, physicochemical properties, contents of main pollutants, and fungal diversity of the aged oil sludge-contaminated soil were analyzed. Results revealed that aged oil sludge significantly changed physical and chemical properties of the receiving soil and increased the contents of main pollutants (petroleum hydrocarbons and heavy metals) in soil. Meanwhile, the internal transcribed spacer (ITS) sequencing by Illumina Miseq platform at each taxonomic level demonstrated that the toxicological effect of oil pollutants obviously influenced the fungal diversity and community structure in soil. Moreover, it was found that the presence of three genera (Cephalotheca, Lecanicillium, and Septoriella) appeared in aged oil sludge-contaminated soil. And oil pollutants promoted the growth of certain genera in Ascomycota (70.83%) and Basidiomycota (10.78%), such as Venturia, Alternaria, and Piloderma. Nevertheless, the growth of Mortierella (9.16%), Emericella (6.02%), and Bjerkandera (0.00%) was intensively limited. This study would aid thorough understanding of microbial diversity in oil-contaminated soil and thus provide new point of view to soil bioremediation. Soil-transmitted helminth infections represent a large burden with over a quarter of the world\uffe2\uff80\uff99s population at risk. Low cure rates are observed with standard of care (albendazole); therefore, a more effective combination therapy (albendazole and ivermectin) is being investigated but showed variable treatment efficacies without evidence of intrinsic parasite resistance. Here, we analyzed the microbiome of Trichuris trichiura and hookworm-infected patients and found an association of different enterotypes with treatment efficacy. 80\uffe2\uff80\uff89 T. trichiura -infected patients with hookworm co-infections\uffc2\uffa0from Pak-Khan, Laos, received either albendazole ( n \uffe2\uff80\uff89=\uffe2\uff80\uff8941) or albendazole and ivermectin combination therapy ( n \uffe2\uff80\uff89=\uffe2\uff80\uff8939). Pre-/post-treatment stool samples were collected to monitor treatment efficacy and microbial communities were profiled using 16S rRNA gene sequencing, qPCR, and shotgun sequencing. We identified three bacterial enterotypes and show that pre-treatment enterotype is associated with efficacy of the combination treatment for both T. trichiura (CR ET1 \uffe2\uff80\uff89=\uffe2\uff80\uff895.8%; CR ET2 \uffe2\uff80\uff89=\uffe2\uff80\uff8916.6%; CR ET3 \uffe2\uff80\uff89=\uffe2\uff80\uff8968.8%) and hookworm (CR ET1 \uffe2\uff80\uff89=\uffe2\uff80\uff8931.3%; CR ET2 \uffe2\uff80\uff89=\uffe2\uff80\uff8916.6%; CR ET3 \uffe2\uff80\uff89=\uffe2\uff80\uff8978.6%). This study shows that pre-treatment enterotype enables predicting treatment outcome of combination therapy for T. trichiura and hookworm infections.

Trial registration: ClinicalTrials.gov, NCT03527732. Registered 17 May 2018, https://clinicaltrials.gov/ct2/show/NCT03527732 .