{"type": "FeatureCollection", "features": [{"id": "10.1002/advs.201901408", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:14:08Z", "type": "Journal Article", "created": "2019-09-19", "title": "Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms", "description": "Abstract

Biofouling proceeds in successive steps where the primary colonizers affect the phylogenetic and functional structure of a future microbial consortium. Using microbiologically influenced corrosion (MIC) as a study case, a novel approach for material surface protection is described, which does not prevent biofouling, but rather shapes the process of natural biofilm development to exclude MIC\uffe2\uff80\uff90related microorganisms. This approach interferes with the early steps of natural biofilm formation affecting how the community is finally developed. It is based on a multilayer artificial biofilm, composed of electrostatically modified bacterial cells, producing antimicrobial compounds, extracellular antimicrobial polyelectrolyte matrix, and a water\uffe2\uff80\uff90proof rubber elastomer barrier. The artificial biofilm is constructed layer\uffe2\uff80\uff90by\uffe2\uff80\uff90layer (LBL) by manipulating the electrostatic interactions between microbial cells and material surfaces. Field testing on standard steel coupons exposed in the sea for more than 30 days followed by laboratory analyses using molecular\uffe2\uff80\uff90biology tools demonstrate that the preapplied artificial biofilm affects the phylogenetic structure of the developing natural biofilm, reducing phylogenetic diversity and excluding MIC\uffe2\uff80\uff90related bacteria. This sustainable solution for material protection showcases the usefulness of artificially guiding microbial evolutionary processes via the electrostatic modification and controlled delivery of bacterial cells and extracellular matrix to the exposed material surfaces.Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from raw milk to the end product. Routine implementation of high-throughput sequencing would elucidate the factors that influence population dynamics. This will enable a manufacturer to adopt control measures specific to each stage of processing and respond in an effective manner, which would ultimately lead to increased food safety and quality.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "metagenomics", "0303 health sciences", "whole-milk silo", "collection tanker", "bulk tank milk", "Microbiology", "QR1-502", "3. Good health", "03 medical and health sciences", "skimmed milk silo", "skimmed milk powder", "microbiota", "dairy", "processing", "16S rRNA gene amplicon sequencing", "Research Article"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSystems.00226-20"}, {"href": "https://doi.org/10.1128/msystems.00226-20"}, {"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": "10.1128/msystems.00226-20", "name": "item", "description": "10.1128/msystems.00226-20", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00226-20"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-28T00:00:00Z"}}, {"id": "10.3389/fsoil.2022.1020869", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:58Z", "type": "Journal Article", "created": "2022-11-16", "title": "Deciphering the microbial composition of biodynamic preparations and their effects on the apple rhizosphere microbiome", "description": "

Soil microbial communities are crucial for plant growth and are already depleted by anthropogenic activities. The application of microbial transplants provides a strategy to restore beneficial soil traits, but less is known about the microbiota of traditional inoculants used in biodynamic agriculture. In this study, we used amplicon sequencing and quantitative PCR to decipher microbial communities of composts, biodynamic manures, and plant preparations from Austria and France. In addition, we investigated the effect of extracts derived from biodynamic manure and compost on the rhizosphere microbiome of apple trees. Microbiota abundance, composition, and diversity of biodynamic manures, plant preparations, and composts were distinct. Microbial abundances ranged between 1010-1011(bacterial 16S rRNA genes) and 109-1011(fungal ITS genes). The bacterial diversity was significantly higher in biodynamic manures compared to compost without discernible differences in abundance. Fungal diversity was not significantly different while abundance was increased in biodynamic manures. The microbial communities of biodynamic manures and plant preparations were specific for each production site, but all contain potentially plant-beneficial bacterial genera. When applied in apple orchards, biodynamic preparations (extracts) had the non-significant effect of reducing bacterial and fungal abundance in apple rhizosphere (4 months post-application), while increasing fungal and lowering bacterial Shannon diversity. One to four months after inoculation, individual taxa indicated differential abundance. We observed the reduction of the pathogenic fungusAlternaria, and the enrichment of potentially beneficial bacterial genera such asPseudomonas.Our study paves way for the science-based adaptation of empirically developed biodynamic formulations under different farming practices to restore the vitality of agricultural soils.

The targeted application of plant growth promoting rhizobacteria (PGPR) provides the key for a future sustainable agriculture with reduced pesticide application. PGPR interaction with the indigenous microbiota is poorly understood but essential to develop reliable applications. Therefore, Stenotrophomonas rhizophila SPA-P69 was applied as seed coating and in combination with a fungicide based on the active ingredients fludioxonil, metalaxyl-M, captan and ziram. Plant performance and rhizosphere composition of treated and non-treated maize plants of two field trials were analyzed. Plant health was significantly increased by treatment; however overall corn yield was not changed. By applying high-throughput amplicon sequencing of the 16S rRNA and the ITS genes, the bacterial and fungal changes in the rhizosphere due to different treatments were determined. Despite treatments had a significant impact on the rhizosphere microbiota (9- 12%), the field site was identified as main driver (27- 37%). Soil microbiota composition from each site was significantly different, which explains the site-specific effects. In this study we were able to show first indications how PGPR treatments increase plant health via microbiome shifts in a site-specific manner. This way first steps towards a detailed understanding of PGPRs and developments of consistently efficient applications in diverse environments are set.

", "keywords": ["Zea mays", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "plant growth promoting rhizobacteria", "QH301-705.5", "15. Life on land", "maize", "Zea mays", "Article", "12. Responsible consumption", "corn", "03 medical and health sciences", "agricultural_sciences_agronomy", "fungicide", "16S rRNA gene", "ITS", "Biology (General)", "rhizosphere"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://doi.org/10.20944/preprints202008.0471.v1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.20944/preprints202008.0471.v1", "name": "item", "description": "10.20944/preprints202008.0471.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.20944/preprints202008.0471.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-21T00:00:00Z"}}, {"id": "10.3390/microorganisms8101506", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:12Z", "type": "Journal Article", "created": "2020-08-24", "title": "Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant Health", "description": "

The targeted application of plant growth promoting rhizobacteria (PGPR) provides the key for a future sustainable agriculture with reduced pesticide application. PGPR interaction with the indigenous microbiota is poorly understood but essential to develop reliable applications. Therefore, Stenotrophomonas rhizophila SPA-P69 was applied as seed coating and in combination with a fungicide based on the active ingredients fludioxonil, metalaxyl-M, captan and ziram. Plant performance and rhizosphere composition of treated and non-treated maize plants of two field trials were analyzed. Plant health was significantly increased by treatment; however overall corn yield was not changed. By applying high-throughput amplicon sequencing of the 16S rRNA and the ITS genes, the bacterial and fungal changes in the rhizosphere due to different treatments were determined. Despite treatments had a significant impact on the rhizosphere microbiota (9- 12%), the field site was identified as main driver (27- 37%). Soil microbiota composition from each site was significantly different, which explains the site-specific effects. In this study we were able to show first indications how PGPR treatments increase plant health via microbiome shifts in a site-specific manner. This way first steps towards a detailed understanding of PGPRs and developments of consistently efficient applications in diverse environments are set.

", "keywords": ["Zea mays", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "plant growth promoting rhizobacteria", "QH301-705.5", "15. Life on land", "maize", "Zea mays", "Article", "12. Responsible consumption", "corn", "03 medical and health sciences", "agricultural_sciences_agronomy", "fungicide", "16S rRNA gene", "ITS", "Biology (General)", "rhizosphere"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://doi.org/10.3390/microorganisms8101506"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms8101506", "name": "item", "description": "10.3390/microorganisms8101506", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms8101506"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-21T00:00:00Z"}}, {"id": "10.3389/fmicb.2018.00149", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:54Z", "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": "10.3389/fmicb.2022.1004593", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:55Z", "type": "Journal Article", "created": "2022-11-07", "title": "Melon/cowpea intercropping pattern influenced the N and C soil cycling and the abundance of soil rare bacterial taxa", "description": "

The high use of pesticides, herbicides, and unsustainable farming practices resulted in losses of soil quality. Sustainable farming practices such as intercropping could be a good alternative to traditional monocrop, especially using legumes such as cowpea (Vigna unguiculata L. Walp). In this study, different melon and cowpea intercropping patterns (melon mixed with cowpea in the same row (MC1); alternating one melon row and one cowpea row (MC2); alternating two melon rows and one cowpea row (MC3)) were assayed to study the intercropping effect on soil bacterial community through 16S rRNA region in a 3-year experiment. The results indicated that intercropping showed high content of total organic carbon, total nitrogen and ammonium, melon yield, and bacterial diversity as well as higher levels of beneficial soil microorganisms such a Pseudomonas, Aeromicrobium, Niastella, or Sphingomonas which can promote plant growth and plant defense against pathogens. Furthermore, intercropping showed a higher rare taxa diversity in two (MC1 and MC2) out of the three intercropping systems. In addition, N-cycling genes such as nirB, nosZ, and amoA were more abundant in MC1 and MC2 whereas the narG predicted gene was far more abundant in the intercropping systems than in the monocrop at the end of the 3-year experiment. This research fills a gap in knowledge about the importance of soil bacteria in an intercropping melon/cowpea pattern, showing the benefits to yield and soil quality with a decrease in N fertilization.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "15. Life on land", "Microbiology", "QR1-502", "6. Clean water", "cowpea", "03 medical and health sciences", "melon", "nitrogen cycle", "16S rRNA", "PICRUSt2", "intercropping"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2022.1004593"}, {"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.2022.1004593", "name": "item", "description": "10.3389/fmicb.2022.1004593", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2022.1004593"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-07T00:00:00Z"}}, {"id": "10.3389/fpls.2021.642027", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:57Z", "type": "Journal Article", "created": "2021-04-09", "title": "Microbiome-Assisted Breeding to Understand Cultivar-Dependent Assembly in Cucurbita pepo", "description": "

Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepoL. subsp.pepovar.styriacaGreb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction ofEnterobacteriaceae(40\uffe2\uff80\uff9383%). Additionally, potential plant-beneficial bacterial taxa, includingBacillaceae,Burkholderiaceae, andPseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.

There are almost 9500 biogas plants in Germany, which are predominantly operated with energy crops and residues from livestock husbandry over the last two decades. In the future, biogas plants must be enabled to use a much broader range of input materials in a flexible and demand-oriented manner. Hence, the microbial communities will be exposed to frequently varying process conditions, while an overall stable process must be ensured. To accompany this transition, there is the need to better understand how biogas microbiomes respond to management measures and how these responses affect the process efficiency. Therefore, 67 microbiomes originating from 49 agricultural, full-scale biogas plants were taxonomically investigated by 16S rRNA gene amplicon sequencing. These microbiomes were separated into three distinct clusters and one group of outliers, which are characterized by a specific distribution of 253 indicative taxa and their relative abundances. These indicative taxa seem to be adapted to specific process conditions which result from a different biogas plant operation. Based on these results, it seems to be possible to deduce/assess the general process condition of a biogas digester based solely on the microbiome structure, in particular on the distribution of specific indicative taxa, and without knowing the corresponding operational and chemical process parameters. Perspectively, this could allow the development of detection systems and advanced process models considering the microbial diversity.

", "keywords": ["580", "anaerobic digestion", "0301 basic medicine", "2. Zero hunger", "NMDS", "0303 health sciences", "QH301-705.5", "biogas microbiome", "anaerobic digestion; biogas microbiome; taxonomic profiling; 16S rRNA gene amplicon sequencing; NMDS; indicative taxa; Pearson correlations", "Pearson correlations", "7. Clean energy", "Article", "6. Clean water", "660.6", "03 medical and health sciences", "13. Climate action", "indicative taxa", "taxonomic profiling", "Biology (General)", "16S rRNA gene amplicon sequencing"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/9/7/1457/pdf"}, {"href": "https://www.mdpi.com/2076-2607/9/7/1457/pdf"}, {"href": "https://doi.org/10.3390/microorganisms9071457"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms9071457", "name": "item", "description": "10.3390/microorganisms9071457", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms9071457"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-07-07T00:00:00Z"}}, {"id": "10.5281/zenodo.10814159", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-29T16:22:14Z", "type": "Dataset", "title": "Chemical composition, soil water content and 16S rRNA and ITS gene copy numbers of soil aggregates and bulk soil samples", "description": "This repository contains all data to reproduce the analyses presented in 'Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates', Simon et al 2024, The ISME Journal\u00a0(DOI: 10.1093/ismejo/wrae156).", "keywords": ["archaea", "bulk soil sample", "delta 15N", "soil water content", "fungi", "soil aggregate", "ITS gene copy numbers", "carbon content", "delta 13C", "nitrogen content", "16S rRNA gene copy numbers"], "contacts": [{"organization": "Simon, Eva, Kaiser, Christina,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.10814159"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.10814159", "name": "item", "description": "10.5281/zenodo.10814159", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.10814159"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-05T00:00:00Z"}}, {"id": "3124594360", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:26:31Z", "type": "Journal Article", "created": "2020-08-24", "title": "Microbiome Management by Biological and Chemical Treatments in Maize is Linked to Plant Health", "description": "

The targeted application of plant growth promoting rhizobacteria (PGPR) provides the key for a future sustainable agriculture with reduced pesticide application. PGPR interaction with the indigenous microbiota is poorly understood but essential to develop reliable applications. Therefore, Stenotrophomonas rhizophila SPA-P69 was applied as seed coating and in combination with a fungicide based on the active ingredients fludioxonil, metalaxyl-M, captan and ziram. Plant performance and rhizosphere composition of treated and non-treated maize plants of two field trials were analyzed. Plant health was significantly increased by treatment; however overall corn yield was not changed. By applying high-throughput amplicon sequencing of the 16S rRNA and the ITS genes, the bacterial and fungal changes in the rhizosphere due to different treatments were determined. Despite treatments had a significant impact on the rhizosphere microbiota (9- 12%), the field site was identified as main driver (27- 37%). Soil microbiota composition from each site was significantly different, which explains the site-specific effects. In this study we were able to show first indications how PGPR treatments increase plant health via microbiome shifts in a site-specific manner. This way first steps towards a detailed understanding of PGPRs and developments of consistently efficient applications in diverse environments are set.

", "keywords": ["Zea mays", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "plant growth promoting rhizobacteria", "QH301-705.5", "15. Life on land", "maize", "Zea mays", "Article", "12. Responsible consumption", "corn", "03 medical and health sciences", "agricultural_sciences_agronomy", "fungicide", "16S rRNA gene", "ITS", "Biology (General)", "rhizosphere"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://doi.org/3124594360"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3124594360", "name": "item", "description": "3124594360", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3124594360"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-21T00:00:00Z"}}, {"id": "10.7717/peerj.6169", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:24:37Z", "type": "Journal Article", "created": "2019-01-03", "title": "Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe", "description": "

Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune,Nostoc calcicola,Tolypothrix distortaandScytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii,Trichocoleus desertorum, andSchizothrixcf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigidaandOculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "QH301-705.5", "R", "Biological soil crust", "Soil cyanobacteria", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "03 medical and health sciences", "13. Climate action", "Medicine", "16S rRNA gene", "Biology (General)", "Phylogenetic relationships", "Biocrusts"]}, "links": [{"href": "https://peerj.com/articles/6169.pdf"}, {"href": "https://doi.org/10.7717/peerj.6169"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PeerJ", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.7717/peerj.6169", "name": "item", "description": "10.7717/peerj.6169", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.7717/peerj.6169"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-03T00:00:00Z"}}, {"id": "10486/690821", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:01Z", "type": "Journal Article", "created": "2019-01-03", "title": "Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe", "description": "

Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune,Nostoc calcicola,Tolypothrix distortaandScytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii,Trichocoleus desertorum, andSchizothrixcf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigidaandOculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.Biofouling proceeds in successive steps where the primary colonizers affect the phylogenetic and functional structure of a future microbial consortium. Using microbiologically influenced corrosion (MIC) as a study case, a novel approach for material surface protection is described, which does not prevent biofouling, but rather shapes the process of natural biofilm development to exclude MIC\uffe2\uff80\uff90related microorganisms. This approach interferes with the early steps of natural biofilm formation affecting how the community is finally developed. It is based on a multilayer artificial biofilm, composed of electrostatically modified bacterial cells, producing antimicrobial compounds, extracellular antimicrobial polyelectrolyte matrix, and a water\uffe2\uff80\uff90proof rubber elastomer barrier. The artificial biofilm is constructed layer\uffe2\uff80\uff90by\uffe2\uff80\uff90layer (LBL) by manipulating the electrostatic interactions between microbial cells and material surfaces. Field testing on standard steel coupons exposed in the sea for more than 30 days followed by laboratory analyses using molecular\uffe2\uff80\uff90biology tools demonstrate that the preapplied artificial biofilm affects the phylogenetic structure of the developing natural biofilm, reducing phylogenetic diversity and excluding MIC\uffe2\uff80\uff90related bacteria. This sustainable solution for material protection showcases the usefulness of artificially guiding microbial evolutionary processes via the electrostatic modification and controlled delivery of bacterial cells and extracellular matrix to the exposed material surfaces.

There are almost 9500 biogas plants in Germany, which are predominantly operated with energy crops and residues from livestock husbandry over the last two decades. In the future, biogas plants must be enabled to use a much broader range of input materials in a flexible and demand-oriented manner. Hence, the microbial communities will be exposed to frequently varying process conditions, while an overall stable process must be ensured. To accompany this transition, there is the need to better understand how biogas microbiomes respond to management measures and how these responses affect the process efficiency. Therefore, 67 microbiomes originating from 49 agricultural, full-scale biogas plants were taxonomically investigated by 16S rRNA gene amplicon sequencing. These microbiomes were separated into three distinct clusters and one group of outliers, which are characterized by a specific distribution of 253 indicative taxa and their relative abundances. These indicative taxa seem to be adapted to specific process conditions which result from a different biogas plant operation. Based on these results, it seems to be possible to deduce/assess the general process condition of a biogas digester based solely on the microbiome structure, in particular on the distribution of specific indicative taxa, and without knowing the corresponding operational and chemical process parameters. Perspectively, this could allow the development of detection systems and advanced process models considering the microbial diversity.

", "keywords": ["580", "anaerobic digestion", "2. Zero hunger", "0301 basic medicine", "NMDS", "0303 health sciences", "QH301-705.5", "biogas microbiome", "Pearson correlations", "7. Clean energy", "Article", "6. Clean water", "660.6", "03 medical and health sciences", "13. Climate action", "indicative taxa", "taxonomic profiling", "Biology (General)", "16S rRNA gene amplicon sequencing"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/9/7/1457/pdf"}, {"href": "https://www.mdpi.com/2076-2607/9/7/1457/pdf"}, {"href": "https://doi.org/21.11116/0000-0008-DFA2-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "21.11116/0000-0008-DFA2-6", "name": "item", "description": "21.11116/0000-0008-DFA2-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/21.11116/0000-0008-DFA2-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-07-07T00:00:00Z"}}, {"id": "2791089561", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:26:08Z", "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": "2907281909", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:26:12Z", "type": "Journal Article", "created": "2019-01-03", "title": "Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe", "description": "

Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune,Nostoc calcicola,Tolypothrix distortaandScytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii,Trichocoleus desertorum, andSchizothrixcf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigidaandOculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.Biofouling proceeds in successive steps where the primary colonizers affect the phylogenetic and functional structure of a future microbial consortium. Using microbiologically influenced corrosion (MIC) as a study case, a novel approach for material surface protection is described, which does not prevent biofouling, but rather shapes the process of natural biofilm development to exclude MIC\uffe2\uff80\uff90related microorganisms. This approach interferes with the early steps of natural biofilm formation affecting how the community is finally developed. It is based on a multilayer artificial biofilm, composed of electrostatically modified bacterial cells, producing antimicrobial compounds, extracellular antimicrobial polyelectrolyte matrix, and a water\uffe2\uff80\uff90proof rubber elastomer barrier. The artificial biofilm is constructed layer\uffe2\uff80\uff90by\uffe2\uff80\uff90layer (LBL) by manipulating the electrostatic interactions between microbial cells and material surfaces. Field testing on standard steel coupons exposed in the sea for more than 30 days followed by laboratory analyses using molecular\uffe2\uff80\uff90biology tools demonstrate that the preapplied artificial biofilm affects the phylogenetic structure of the developing natural biofilm, reducing phylogenetic diversity and excluding MIC\uffe2\uff80\uff90related bacteria. This sustainable solution for material protection showcases the usefulness of artificially guiding microbial evolutionary processes via the electrostatic modification and controlled delivery of bacterial cells and extracellular matrix to the exposed material surfaces.Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepoL. subsp.pepovar.styriacaGreb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction ofEnterobacteriaceae(40\uffe2\uff80\uff9383%). Additionally, potential plant-beneficial bacterial taxa, includingBacillaceae,Burkholderiaceae, andPseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.

The targeted application of plant growth promoting rhizobacteria (PGPR) provides the key for a future sustainable agriculture with reduced pesticide application. PGPR interaction with the indigenous microbiota is poorly understood but essential to develop reliable applications. Therefore, Stenotrophomonas rhizophila SPA-P69 was applied as seed coating and in combination with a fungicide based on the active ingredients fludioxonil, metalaxyl-M, captan and ziram. Plant performance and rhizosphere composition of treated and non-treated maize plants of two field trials were analyzed. Plant health was significantly increased by treatment; however overall corn yield was not changed. By applying high-throughput amplicon sequencing of the 16S rRNA and the ITS genes, the bacterial and fungal changes in the rhizosphere due to different treatments were determined. Despite treatments had a significant impact on the rhizosphere microbiota (9- 12%), the field site was identified as main driver (27- 37%). Soil microbiota composition from each site was significantly different, which explains the site-specific effects. In this study we were able to show first indications how PGPR treatments increase plant health via microbiome shifts in a site-specific manner. This way first steps towards a detailed understanding of PGPRs and developments of consistently efficient applications in diverse environments are set.

", "keywords": ["Zea mays", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "plant growth promoting rhizobacteria", "QH301-705.5", "15. Life on land", "maize", "Article", "12. Responsible consumption", "corn", "03 medical and health sciences", "agricultural_sciences_agronomy", "fungicide", "16S rRNA gene", "ITS", "Biology (General)", "rhizosphere"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://doi.org/PMC7599774"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC7599774", "name": "item", "description": "PMC7599774", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC7599774"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-21T00:00:00Z"}}, {"id": "PMC8063107", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:28:45Z", "type": "Journal Article", "created": "2021-04-09", "title": "Microbiome-Assisted Breeding to Understand Cultivar-Dependent Assembly in Cucurbita pepo", "description": "

Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepoL. subsp.pepovar.styriacaGreb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction ofEnterobacteriaceae(40\uffe2\uff80\uff9383%). Additionally, potential plant-beneficial bacterial taxa, includingBacillaceae,Burkholderiaceae, andPseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.