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.Soil microbes are essential for maintenance of life\uffe2\uff80\uff90supporting ecosystem services, but projections of how these microbes will be affected by global change scenarios are lacking. Therefore, our aim was to provide projections of future soil microbial distribution using several scenarios of global change.
LocationGlobal.
Time period1950\uffe2\uff80\uff932090.
Major taxa studiedBacteria and fungi.
MethodsWe used a global database of soil microbial communities across six continents to estimate past and future trends of the soil microbiome. To do so, we used structural equation models to include the direct and indirect effects of changes in climate and land use in our predictions, using current climate (temperature and precipitation) and land\uffe2\uff80\uff90use projections between 1950 and 2090.
ResultsLocal bacterial richness will increase in all scenarios of change in climate and land use considered, although this increase will be followed by a generalized community homogenization process affecting >\uffc2\uffa085% of terrestrial ecosystems. Changes in the relative abundance of functional genes associated with the increases in bacterial richness are also expected. Based on an ecological cluster analysis, our results suggest that phylotypes such asGeodermatophilusspp. (typical desert bacteria),Mycobacteriumsp. (which are known to include important human pathogens),Streptomyces mirabilis(major producers of antibiotic resistance genes) or potential fungal soil\uffe2\uff80\uff90borne plant pathogens belonging to Ascomycota fungi (Venturiaspp.,Devriesiaspp.) will become more abundant in their communities.
Main conclusionsOur results provide evidence that climate change has a stronger influence on soil microbial communities than change in land use (often including deforestation and agricultural expansion), although most of the effects of climate are indirect, through other environmental variables (e.g., changes in soil pH). The same was found for microbial functions such as the prevalence of phosphate transport genes. We provide reliable predictions about the changes in the global distribution of microbial communities, showing an increase in alpha diversity and a homogenization of soil microbial communities in the Anthropocene.Low\uffe2\uff80\uff90alpine heathlands are thought to be particularly sensitive to nitrogen (N) deposition, climate and land management change, yet little is known about how these factors regulate key belowground processes, like litter turnover, under field conditions. Here we use an in situ factorial field experiment to test the effects of increased atmospheric N deposition, climate manipulation and past vegetation burning, and their interactions, on litter decomposition and the activity and diversity of associated microorganisms. The use of litter from within (native) and outwith (standard) the experimental plots also enabled us to test whether decomposition and microbial functional diversity is driven primarily by soil conditions or litter chemistry. In general, extracellular enzyme activities of litter were driven by additions of simulated N deposition with phosphatase being the most responsive. We found that standard litter incubated in plots that had been burnt 8 years previously decomposed slower and lost less N and phosphorus than in unburnt plots. This material also had associated with it the greatest activity of glucosidase and the least diverse microbial community, as assessed by culture\uffe2\uff80\uff90independent methods. Although all treatments significantly affected microbial diversity, burning explained most of the variability, indicating a close coupling between plant and microbial communities in these treatments. A striking feature of all the data relating to both standard and native litter was an almost complete lack of interactive effects between the treatments. The lack of interactions between the treatments indicates that each perturbation might affect different mechanisms in the decomposition process (including the composition of associated microbial communities) and nutrient cycling.
", "keywords": ["climate change", "enzyme activities", "soil microorganisms", "soil bacteria", "13. Climate action", "microbial diversity", "soil fungi", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "carbon turnover", "15. Life on land"]}, "links": [{"href": "https://doi.org/10.1111/j.1365-2486.2010.02196.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1365-2486.2010.02196.x", "name": "item", "description": "10.1111/j.1365-2486.2010.02196.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-2486.2010.02196.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-02-05T00:00:00Z"}}, {"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": "10.3389/fmicb.2018.00149", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:36Z", "type": "Journal Article", "created": "2018-02-23", "title": "Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses", "description": "Genetic fingerprinting demonstrated in previous studies that differently sized soil particle fractions (PSFs; clay, silt, and sand with particulate organic matter (POM)) harbor microbial communities that differ in structure, functional potentials and sensitivity to environmental conditions. To elucidate whether specific bacterial or archaeal taxa exhibit preference for specific PSFs, we examined the diversity of PCR-amplified 16S rRNA genes by high-throughput sequencing using total DNA extracted from three long-term fertilization variants (unfertilized, fertilized with minerals, and fertilized with animal manure) of an agricultural loamy sand soil and their PSFs. The PSFs were obtained by gentle ultrasonic dispersion, wet sieving, and centrifugation. The abundance of bacterial taxa assigned to operational taxonomic units (OTUs) differed less than 2.7% between unfractionated soil and soil based on combined PSFs. Across the three soil variants, no archaeal OTUs, but many bacterial OTUs, the latter representing 34-56% of all amplicon sequences, showed significant preferences for specific PSFs. The sand-sized fraction with POM was the preferred site for members of Bacteroidetes and Alphaproteobacteria, while Gemmatimonadales preferred coarse silt, Actinobacteria and Nitrosospira fine silt, and Planctomycetales clay. Firmicutes were depleted in the sand-sized fraction. In contrast, archaea, which represented 0.8% of all 16S rRNA gene sequences, showed only little preference for specific PSFs. We conclude that differently sized soil particles represent distinct microenvironments that support specific bacterial taxa and that these preferences could strongly contribute to the spatial heterogeneity and bacterial diversity found in soils.", "keywords": ["2. Zero hunger", "soil bacteria", "Soil bacteria", "soil DNA", "bacterial diversity", "04 agricultural and veterinary sciences", "Soil DNA", "15. Life on land", "Microbiology", "Soil archaea", "QR1-502", "Archaeal diversity", "Bacterial diversity", "archaeal diversity", "Soil particle size fractions", "0401 agriculture", " forestry", " and fisheries", "soil particle size fractions", "soil archaea", "16S rRNA gene amplicon sequencing"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2018.00149"}, {"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.2018.00149", "name": "item", "description": "10.3389/fmicb.2018.00149", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2018.00149"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-23T00:00:00Z"}}, {"id": "10.3390/agronomy12020316", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:21:44Z", "type": "Journal Article", "created": "2022-01-26", "title": "Long-Term Compost Amendment Changes Interactions and Specialization in the Soil Bacterial Community, Increasing the Presence of Beneficial N-Cycling Genes in the Soil", "description": "Significant differences in the microbial community and diversity in soil have been observed due to organic farming, but little research has been performed for exploring microbial functionality and the co-occurrence of patterns among microbial taxa. In this work, we study soil 16S rDNA amplicons from two long-term organic farming systems (Org_C and Org_M) and a conventional system (Conv) to decipher the differences in microbial interaction and network organization and to predict functional genes (principally related to the N cycle). In general, the network organizations were different in all cropping systems due to agricultural management. Org_C showed the highest negative interactions and modularity and the most altered bacterial niches and interactions, which led to an increase in generalist species that stabilize the bacterial community and improve the response of the soil to adverse conditions. These changes altered the predicted functionality of the bacterial community; Org_C showed higher referred numbers of nitrogen fixation genes, a decrease in the N2O emission genes and could favor the uptake of environmental CO2. Thus, long-term compost amendment application has significant benefits for the farmer and the environment, since prolonged application can reduce the use of fertilizers and pesticides and could create a more stable soil, which could resist the effects of climate change.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "soil bacteria", "S", "PICRUSt", "Agriculture", "15. Life on land", "6. Clean water", "conventional farming", "co-occurrence; conventional farming; manure; organic farming; PICRUSt; soil bacteria", "03 medical and health sciences", "organic farming", "13. Climate action", "manure", "co-occurrence"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/12/2/316/pdf"}, {"href": "https://www.mdpi.com/2073-4395/12/2/316/pdf"}, {"href": "https://doi.org/10.3390/agronomy12020316"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agronomy12020316", "name": "item", "description": "10.3390/agronomy12020316", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agronomy12020316"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-26T00:00:00Z"}}, {"id": "10.4067/s0718-95162014005000045", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:22:14Z", "type": "Journal Article", "created": "2014-08-22", "description": "Nitrogen (N) deposition greatly affects the above ground biological composition of grasslands and soil properties. However, its influence on the relationship among soil, plant and bacterial communities remain controversy. We calculated Shannon-wiener index to measure the soil bacterial diversity based on denaturing gradient gel electrophoresis, and investigate the roles of vegetation and soil properties on the soil bacterial community under N addition. A three-year simulated N deposition experiment was conducted in a forbs community dominated by Leymus chinensis (Trin.) Tzvel. and Artemisia scoparia Wald. Et. Kit. N was added at five levels (0, 23, 46, 69, 92 kg ha -1 yr -1 ). Our results showed that N addition increased the soil microbial biomass carbon (SMBC) and soil bacterial diversity. Moderate N (23, 46, 69 kg ha -1 yr -1 ) addition increased the soil bacterial diversity, whereas excess N (92 kg ha -1 yr -1 ) addition inhibited it. The SMBC and soil bacterial diversity were related to richness of plant functional groups. In particular, SMBC had positive correlation with biomass of annuals and biennials, suggesting that the effects of the plant community on the soil bacteria could be explained by a relationship between the soil bacterial community and a subset of plant species rather than all species.", "keywords": ["Songnen grassland", "13. Climate action", "soil bacterial community", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "species richness", "15. Life on land", "Nitrogen deposition", "resource availability"], "contacts": [{"organization": "Sun, S, Xing, F, Zhao, H, Gao, Y, Bai, Z, Dong, Y,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.4067/s0718-95162014005000045"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20soil%20science%20and%20plant%20nutrition", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.4067/s0718-95162014005000045", "name": "item", "description": "10.4067/s0718-95162014005000045", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.4067/s0718-95162014005000045"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-01-01T00:00:00Z"}}, {"id": "10.5281/zenodo.14626839", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:23:39Z", "type": "Dataset", "title": "Data set of soil microbial components in response to extreme spring events at variable temperatures", "description": "The soil microbial response to prolonged soil drought (20% field capacity FC), wetness (above FC) and moderate drought (common at 50% FC) was simulated in pots at two spring temperatures - 2\u00b0C and +2.5\u00b0C colder and warmer, respectively, compared to the average in the central-eastern Po Valley, Italy (decade 2014-2024).\u00a0 Two soils (a ploughed soil and an adjacent renatured soil) were subjected to two 60-day cycles (cold and warm spring) at three levels of soil water content. The climate simulation started after the wheat seedlings had reached the two-leaf stage in all pots. Soil samples were taken from the wheat rhizome at the end of each experiment. The response of microbial biomass was evaluated in terms of double-stranded DNA (dsDNA), total bacteria quantified as 16S gene copy number using Real Time PCR and total fungi quantified as 18S gene copy number using Digital PCR. Three major bacterial groups, Pseudomonas, Actinomycetes and Bacillus, were quantified by real-time PCR using specific primers of the 16S region (F968/Ps-r; F243/518r; BacF/518). Twenty-two enzyme activities were also quantified in soil samples. The data set contains a total of twenty-eight variables.", "keywords": ["climate change", "microbial biomass", "soil bacteria", "Pseudomonas", "actinomycetes", "estreme events", "soil fungi", "microrganisms", "Bacillus", "metabolic activity", "soil"], "contacts": [{"organization": "Manici, Luisa M.", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.14626839"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.14626839", "name": "item", "description": "10.5281/zenodo.14626839", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.14626839"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2026-01-10T00:00:00Z"}}, {"id": "2791089561", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:27:12Z", "type": "Journal Article", "created": "2018-02-23", "title": "Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses", "description": "Genetic fingerprinting demonstrated in previous studies that differently sized soil particle fractions (PSFs; clay, silt, and sand with particulate organic matter (POM)) harbor microbial communities that differ in structure, functional potentials and sensitivity to environmental conditions. To elucidate whether specific bacterial or archaeal taxa exhibit preference for specific PSFs, we examined the diversity of PCR-amplified 16S rRNA genes by high-throughput sequencing using total DNA extracted from three long-term fertilization variants (unfertilized, fertilized with minerals, and fertilized with animal manure) of an agricultural loamy sand soil and their PSFs. The PSFs were obtained by gentle ultrasonic dispersion, wet sieving, and centrifugation. The abundance of bacterial taxa assigned to operational taxonomic units (OTUs) differed less than 2.7% between unfractionated soil and soil based on combined PSFs. Across the three soil variants, no archaeal OTUs, but many bacterial OTUs, the latter representing 34-56% of all amplicon sequences, showed significant preferences for specific PSFs. The sand-sized fraction with POM was the preferred site for members of Bacteroidetes and Alphaproteobacteria, while Gemmatimonadales preferred coarse silt, Actinobacteria and Nitrosospira fine silt, and Planctomycetales clay. Firmicutes were depleted in the sand-sized fraction. In contrast, archaea, which represented 0.8% of all 16S rRNA gene sequences, showed only little preference for specific PSFs. We conclude that differently sized soil particles represent distinct microenvironments that support specific bacterial taxa and that these preferences could strongly contribute to the spatial heterogeneity and bacterial diversity found in soils.", "keywords": ["2. Zero hunger", "soil bacteria", "Soil bacteria", "soil DNA", "bacterial diversity", "04 agricultural and veterinary sciences", "Soil DNA", "15. Life on land", "Microbiology", "Soil archaea", "QR1-502", "Archaeal diversity", "Bacterial diversity", "archaeal diversity", "Soil particle size fractions", "0401 agriculture", " forestry", " and fisheries", "soil particle size fractions", "soil archaea", "16S rRNA gene amplicon sequencing"]}, "links": [{"href": "https://doi.org/2791089561"}, {"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": "2791089561", "name": "item", "description": "2791089561", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2791089561"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-23T00:00:00Z"}}, {"id": "1959.7/uws:64812", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:26:34Z", "type": "Journal Article", "created": "2021-02-21", "title": "Global projections of the soil microbiome in the Anthropocene", "description": "AbstractAimSoil microbes are essential for maintenance of life\uffe2\uff80\uff90supporting ecosystem services, but projections of how these microbes will be affected by global change scenarios are lacking. Therefore, our aim was to provide projections of future soil microbial distribution using several scenarios of global change.
LocationGlobal.
Time period1950\uffe2\uff80\uff932090.
Major taxa studiedBacteria and fungi.
MethodsWe used a global database of soil microbial communities across six continents to estimate past and future trends of the soil microbiome. To do so, we used structural equation models to include the direct and indirect effects of changes in climate and land use in our predictions, using current climate (temperature and precipitation) and land\uffe2\uff80\uff90use projections between 1950 and 2090.
ResultsLocal bacterial richness will increase in all scenarios of change in climate and land use considered, although this increase will be followed by a generalized community homogenization process affecting >\uffc2\uffa085% of terrestrial ecosystems. Changes in the relative abundance of functional genes associated with the increases in bacterial richness are also expected. Based on an ecological cluster analysis, our results suggest that phylotypes such asGeodermatophilusspp. (typical desert bacteria),Mycobacteriumsp. (which are known to include important human pathogens),Streptomyces mirabilis(major producers of antibiotic resistance genes) or potential fungal soil\uffe2\uff80\uff90borne plant pathogens belonging to Ascomycota fungi (Venturiaspp.,Devriesiaspp.) will become more abundant in their communities.
Main conclusionsOur results provide evidence that climate change has a stronger influence on soil microbial communities than change in land use (often including deforestation and agricultural expansion), although most of the effects of climate are indirect, through other environmental variables (e.g., changes in soil pH). The same was found for microbial functions such as the prevalence of phosphate transport genes. We provide reliable predictions about the changes in the global distribution of microbial communities, showing an increase in alpha diversity and a homogenization of soil microbial communities in the Anthropocene.