{"type": "FeatureCollection", "features": [{"id": "10.1111/nph.18309", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:19Z", "type": "Journal Article", "created": "2022-06-15", "title": "Recent and ancient evolutionary events shaped plant elemental composition of edaphic endemics: a phylogeny\u2010wide analysis of Iberian gypsum plants", "description": "Summary

The analysis of plant elemental composition and the underlying factors affecting its variation are a current hot topic in ecology. Ecological adaptation to atypical soils may shift plant elemental composition. However, no previous studies have evaluated its relevance against other factors such as phylogeny, climate or individual soil conditions.

We evaluated the effect of the phylogeny, environment (climate, soil), and affinity to gypsum soils on the elemental composition of 83 taxa typical of Iberian gypsum ecosystems. We used a new statistical procedure (multiple phylogenetic variance decomposition, MPVD) to decompose total explained variance by different factors across all nodes in the phylogenetic tree of target species (covering 120\uffe2\uff80\uff89million\uffe2\uff80\uff89years of Angiosperm evolution).

Our results highlight the relevance of phylogeny on the elemental composition of plants both at early (with the development of key preadaptive traits) and recent divergence times (diversification of the Iberian gypsum flora concurrent with Iberian gypsum deposit accumulation). Despite the predominant phylogenetic effect, plant adaptation to gypsum soils had a strong impact on the elemental composition of plants, particularly on sulphur concentrations, while climate and soil effects were smaller.

Accordingly, we detected a convergent evolution of gypsum specialists from different lineages on increased sulphur and magnesium foliar concentrations.

The influence of long\uffe2\uff80\uff90term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22\uffe2\uff80\uff90year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array\uffe2\uff80\uff90based analysis revealed that long\uffe2\uff80\uff90term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer\uffe2\uff80\uff90induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P\uffe2\uff80\uff90limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions.

", "keywords": ["2. Zero hunger", "Bacteria", "Nitrogen", "Oryza", "Phosphorus", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Nitrogen Cycle", "15. Life on land", "6. Clean water", "Carbon Cycle", "Soil", "13. Climate action", "RNA", " Ribosomal", " 16S", "Potassium", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Fertilizers", "Ecosystem", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/mec.13010"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecular%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/mec.13010", "name": "item", "description": "10.1111/mec.13010", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/mec.13010"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-12-31T00:00:00Z"}}, {"id": "10.1111/mec.14358", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:18Z", "type": "Journal Article", "created": "2017-09-19", "title": "Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles", "description": "Abstract

Dispersal is a critical factor determining the spatial scale of speciation, which is constrained by the ecological characteristics and distribution of a species\uffe2\uff80\uff99 habitat and the intrinsic traits of species. Endogean taxa are strongly affected by the unique qualities of the below\uffe2\uff80\uff90ground environment and its effect on dispersal, and contrasting reports indicate either high dispersal capabilities favoured by small body size and mediated by passive mechanisms, or low dispersal due to restricted movement and confinement inside the soil. We studied a species\uffe2\uff80\uff90rich endogean ground beetle lineage, Typhlocharina, including three genera and more than 60 species, as a model for the evolutionary biology of dispersal and speciation in the deep soil. A time\uffe2\uff80\uff90calibrated molecular phylogeny generated from >400 individuals was used to delimit candidate species, to study the accumulation of lineages through space and time by species\uffe2\uff80\uff93area\uffe2\uff80\uff93age relationships and to determine the geographical structure of the diversification using the relationship between phylogenetic and geographic distances across the phylogeny. Our results indicated a small spatial scale of speciation in Typhlocharina and low dispersal capacity combined with sporadic long distance, presumably passive dispersal events that fuelled the speciation process. Analysis of lineage growth within Typhlocharina revealed a richness plateau correlated with the range of distribution of lineages, suggesting a long\uffe2\uff80\uff90term species richness equilibrium mediated by density dependence through limits of habitat availability. The interplay of area\uffe2\uff80\uff90 and age\uffe2\uff80\uff90dependent processes ruling the lineage diversification in Typhlocharina may serve as a general model for the evolution of high species diversity in endogean mesofauna.

There is strong evidence for a phylogenetic signal in the degree to which species share co\uffe2\uff80\uff90evolved biotic partners and in the outcomes of biotic interactions. This implies there should be a phylogenetic signal in the outcome of feedbacks between plants and the soil microbiota they cultivate. However, attempts to identify a phylogenetic signal in plant\uffe2\uff80\uff93soil feedbacks have produced mixed results.

Here we clarify how phylogenetic signals could arise in plant\uffe2\uff80\uff93soil feedbacks and use a recent compilation of data from feedback experiments to identify: whether there is a phylogenetic signal in the outcome of plant\uffe2\uff80\uff93soil feedbacks; and whether any signal arises through directional or divergent changes in feedback outcomes with evolutionary time.

We find strong evidence for a divergent phylogenetic signal in feedback outcomes. Distantly related plant species show more divergent responses to each other\uffe2\uff80\uff99s soil microbiota compared with closely related plant species. The pattern of divergence implies occasional co\uffe2\uff80\uff90evolutionary shifts in how plants interact with soil microbiota, with strongly contrasting feedback responses among some plant lineages.

Our results highlight that it is difficult to predict feedback outcomes from phylogeny alone, other than to say that more closely related species tend to have more similar responses.

Feedback between plants and soil microbial communities can be a powerful driver of vegetation dynamics. Plants elicit changes in the soil microbiome that either promote or suppress conspecifics at the same location, thereby regulating population density\uffe2\uff80\uff90dependence and species co\uffe2\uff80\uff90existence. Such effects are often attributed to the accumulation of host\uffe2\uff80\uff90specific antagonistic or beneficial microbiota in the rhizosphere. However, the identity and host\uffe2\uff80\uff90specificity of the microbial taxa involved are rarely empirically assessed. Here we review the evidence for host\uffe2\uff80\uff90specificity in plant\uffe2\uff80\uff90associated microbes and propose that specific plant\uffe2\uff80\uff93soil feedbacks can also be driven by generalists. We outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plant\uffe2\uff80\uff93soil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities. Identifying factors that promote specialization or generalism in plant\uffe2\uff80\uff93microbial interactions and thereby modulate the impact of microbiota on plant performance will advance our understanding of the mechanisms underlying plant\uffe2\uff80\uff93soil feedback and the ways it contributes to plant co\uffe2\uff80\uff90existence.

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

", "keywords": ["Supplementary Data", "biodiversity", " fungi", " ecology", "QH301 Biology", "Diversity (politics)", "Plant Science", "Biodiversity conservation", "Fungal Diversity", "Agricultural and Biological Sciences", "Soil", "Life", "Sociology", "WATER", "Global biodiversity distribution", "Fungal diversity", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Multidisciplinary", "Earth", " Environmental", " Ecological", " and Space Sciences", "Geography", "Ecology", "soil fungal diversity", "4. Education", "SPECIES RICHNESS", "Life Sciences", "https://www.science.org/doi/suppl/10.1126/sciadv.adj8016/suppl_file/sciadv.adj8016_sm.pdf", "Biodiversity", "FOS: Sociology", "global biodiversity distribution", "sienet", "https://www.science.org/doi/suppl/10.1126/sciadv.adj8016/suppl_file/sciadv.adj8016_tables_s1_to_s13.zip", "Diversity and Evolution of Fungal Pathogens", "570", "Supplementary Information", "DNA markers", "QH301", "Sequencing high-resolution DNA", "Biochemistry", " Genetics and Molecular Biology", "monimuotoisuus", "Mycorrhizal Fungi and Plant Interactions", "Life Science", "Humans", "14. Life underwater", "General", "Global ecological processes", "Biology", "Ecosystem", "Ecology", " Evolution", " Behavior and Systematics", "global ecological processes", "Soil fungal diversity", "microbiology", "Fungi", "Water", "Cell Biology", "15. Life on land", "luonnon monimuotoisuus", "Agronomy", "biodiversiteetti", "LIFE", "ekosysteemit (ekologia)", "Evolution and Ecology of Endophyte-Grass Symbiosis", "13. Climate action", "Ecology", " evolutionary biology", "Earth and Environmental Sciences", "FOS: Biological sciences", "Anthropology", "ta1181", "biodiversity conservation", "Species richness"]}, "links": [{"href": "https://www.science.org/doi/epdf/10.1126/sciadv.adj8016"}, {"href": "https://www.science.org/doi/pdf/10.1126/sciadv.adj8016"}, {"href": "https://doi.org/10.1126/sciadv.adj8016"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20Advances", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1126/sciadv.adj8016", "name": "item", "description": "10.1126/sciadv.adj8016", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1126/sciadv.adj8016"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "10.1126/science.aap9516", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:22Z", "type": "Journal Article", "created": "2018-01-18", "title": "A global atlas of the dominant bacteria found in soil", "description": "A global map of soil bacteria

Soil bacteria play key roles in regulating terrestrial carbon dynamics, nutrient cycles, and plant productivity. However, the natural histories and distributions of these organisms remain largely undocumented. Delgado-Baquerizo et al. provide a survey of the dominant bacterial taxa found around the world. In soil collections from six continents, they found that only 2% of bacterial taxa account for nearly half of the soil bacterial communities across the globe. These dominant taxa could be clustered into ecological groups of co-occurring bacteria that share habitat preferences. The findings will allow for a more predictive understanding of soil bacterial diversity and distribution.

Science , this issue p. 320 Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even on Earth, the limitations imposed on microbial processes by saturation-level salinity have rarely been studied in situ . The effects of mineral fertilizer (NPK) and organic manure on the community structure of soil ammonia-oxidizing bacteria (AOB) was investigated in a long-term (16-year) fertilizer experiment. The experiment included seven treatments: organic manure, half organic manure N plus half fertilizer N, fertilizer NPK, fertilizer NP, fertilizer NK, fertilizer PK, and the control (without fertilization). N fertilization greatly increased soil nitrification potential, and mineral N fertilizer had a greater impact than organic manure, while N deficiency treatment (PK) had no significant effect. AOB community structure was analyzed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of the amoA gene, which encodes the \uffce\uffb1 subunit of ammonia monooxygenase. DGGE profiles showed that the AOB community was more diverse in N-fertilized treatments than in the PK-fertilized treatment or the control, while one dominant band observed in the control could not be detected in any of the fertilized treatments. Phylogenetic analysis showed that the DGGE bands derived from N-fertilized treatments belonged to Nitrosospira cluster 3, indicating that N fertilization resulted in the dominance of Nitrosospira cluster 3 in soil. These results demonstrate that long-term application of N fertilizers could result in increased soil nitrification potential and the AOB community shifts in soil. Our results also showed the different effects of mineral fertilizer N versus organic manure N; the effects of P and K on the soil AOB community; and the importance of balanced fertilization with N, P, and K in promoting nitrification functions in arable soils.

", "keywords": ["2. Zero hunger", "Minerals", "Bacteria", "Nitrogen", "Molecular Sequence Data", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "6. Clean water", "Manure", "Ammonia", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidoreductases", "Ecosystem", "Gammaproteobacteria", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1128/aem.01536-06"}, {"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.01536-06", "name": "item", "description": "10.1128/aem.01536-06", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01536-06"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-01-15T00:00:00Z"}}, {"id": "10.1128/aem.02209-19", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:23Z", "type": "Journal Article", "created": "2019-12-04", "title": "Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous \u201cMost-Wanted\u201d Core Bacterial Taxon from Municipal Wastewater Treatment Plants", "description": "

The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.

", "keywords": ["0301 basic medicine", "activated sludge microbiome", "DATABASE", "DIVERSITY", "nitrogen and phosphorus removal", "GENOME ANNOTATION", "POLYPHOSPHATE-ACCUMULATING ORGANISMS", "12. Responsible consumption", "ACTIVATED-SLUDGE", "03 medical and health sciences", "SEARCH", "RNA", " Ribosomal", " 16S", "11. Sustainability", "microbial network", "Phylogeny", "WWTP", "0303 health sciences", "IDENTIFICATION", "Sewage", "Microbiota", "Betaproteobacteria", "core taxa", "15. Life on land", "6. Clean water", "COMMUNITY", "RNA", " Bacterial", "Casimicrobium huifangae", "13. Climate action", "Earth and Environmental Sciences", "BIOLOGICAL PHOSPHORUS REMOVAL", "municipal wastewater treatment plant", "CARBON SOURCE"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.02209-19"}, {"href": "https://doi.org/10.1128/aem.02209-19"}, {"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.02209-19", "name": "item", "description": "10.1128/aem.02209-19", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02209-19"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-03T00:00:00Z"}}, {"id": "10.1128/aem.02218-17", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:23Z", "type": "Journal Article", "created": "2017-11-27", "title": "Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog", "description": "ABSTRACT

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA -based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities.

IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects.

", "keywords": ["0301 basic medicine", "570", "oxidation", "hiili", "ta1172", "Euryarchaeota", "630", "Mining", "Soil", "03 medical and health sciences", "Sphagnum", "Bacterial Proteins", "Nitrogen Fixation", "Sphagnopsida", "14. Life underwater", "ennallistaminen", "turvemaat", "Ecosystem", "Phylogeny", "Soil Microbiology", "0303 health sciences", "nifH", "methane", "Microbiota", "ta1182", "land use", "methanogenesis", "15. Life on land", "Carbon", "kasvihuonekaasup\u00e4\u00e4st\u00f6t", "nitrogen fixation", "13. Climate action", "international", "Wetlands", "Oxygenases", "ta1181", "Methane", "Oxidation-Reduction"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.02218-17"}, {"href": "https://doi.org/10.1128/aem.02218-17"}, {"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.02218-17", "name": "item", "description": "10.1128/aem.02218-17", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02218-17"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-01T00:00:00Z"}}, {"id": "10.1128/mBio.00799-17", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:23Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics", "description": "Abstract

Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.

", "keywords": ["Q Science", "0301 basic medicine", "330", "Supplementary Data", "ecophysiology", "Ecophysiology", "NE/E006353/1", "Bacterial Physiological Phenomena", "Microbiology", "Soil", "03 medical and health sciences", "Virology", "European Commission", "Ecosystem", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "655240", "metagenomics", "0303 health sciences", "Bacteria", "Natural Environment Research Council (NERC)", "Q", "NE/M017125/1", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Adaptation", " Physiological", "soil microbiology", "QR1-502", "United Kingdom", "3. Good health", "Soil microbiology", "Metagenomics", "Genome", " Bacterial", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/117887v1.full.pdf"}, {"href": "https://journals.asm.org/doi/pdf/10.1128/mBio.00799-17"}, {"href": "https://doi.org/10.1128/mBio.00799-17"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mBio", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/mBio.00799-17", "name": "item", "description": "10.1128/mBio.00799-17", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/mBio.00799-17"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-18T00:00:00Z"}}, {"id": "10.1186/s12864-019-5692-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:30Z", "type": "Journal Article", "created": "2019-05-02", "title": "Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains", "description": "Oenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethanol-rich environments of wine and cider fermentation, where it performs the crucial role of malolactic fermentation. It has a small genome and has lost the mutS-mutL DNA mismatch repair genes, making it a hypermutable and highly specialized species. Two main lineages of strains, named groups A and B, have been described to date, as well as other subgroups correlated to different types of wines or regions. A third group 'C' has also been hypothesized based on sequence analysis, but it remains controversial. In this study we have elucidated the species population structure by sequencing 14 genomes of new strains isolated from cider and kombucha and performing comparative genomics analyses.Sequence-based phylogenetic trees confirmed a population structure of 4 clades: The previously identified A and B, a third group 'C' consisting of the new cider strains and a small subgroup of wine strains previously attributed to group B, and a fourth group 'D' exclusively represented by kombucha strains. A pair of complete genomes from group C and D were compared to the circularized O. oeni PSU-1 strain reference genome and no genomic rearrangements were found. Phylogenetic trees, K-means clustering and pangenome gene clusters evidenced the existence of smaller, specialized subgroups of strains. Using the pangenome, genomic differences in stress resistance and biosynthetic pathways were found to uniquely distinguish the C and D clades.The obtained results, including the additional cider and kombucha strains, firmly established the O. oeni population structure. Group C does not appear as fully domesticated as group A to wine, but showed several unique patterns which may be due to ongoing specialization to the cider environment. Group D was shown to be the most divergent member of O. oeni to date, appearing as the closest to a pre-domestication state of the species.", "keywords": ["0301 basic medicine", "570", "Wine", "QH426-470", "Pan-genome", "Industrial microbiology", "630", "03 medical and health sciences", "Lactic acid bacteria", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Oenococcus", "Phylogeny", "2. Zero hunger", "0303 health sciences", "Genome", "Whole Genome Sequencing", "Comparative genomics", "Bacterial", "Phylogenomics", "Kombucha Tea", "Biodiversity", "15. Life on land", "Malus", "Oenococcus oeni", "TP248.13-248.65", "Genome", " Bacterial", "Biotechnology", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s12864-019-5692-3.pdf"}, {"href": "https://doi.org/10.1186/s12864-019-5692-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BMC%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s12864-019-5692-3", "name": "item", "description": "10.1186/s12864-019-5692-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s12864-019-5692-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-02T00:00:00Z"}}, {"id": "10.1186/s40168-018-0607-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:30Z", "type": "Journal Article", "created": "2018-12-07", "title": "Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment", "description": "Approximately 500\u00a0Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the \u03b1-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments.The new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria.This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas.", "keywords": ["0301 basic medicine", "570", "Isoprene", "Climate", "Mixed Function Oxygenases", "Microbial ecology", "Comamonadaceae", "03 medical and health sciences", "Hemiterpenes", "Bacterial Proteins", "Butadienes", "Isoprene monooxygenase", "Rhodococcus", "Gene probes", "14. Life underwater", "Phylogeny", "Soil Microbiology", "DNA Primers", "0303 health sciences", "Bacteria", "Research", "isoA", "QR100-130", "QR Microbiology", "Sequence Analysis", " DNA", "15. Life on land", "Sphingomonadaceae", "Biodegradation", " Environmental", "13. Climate action"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/69294/1/Published_manuscript.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1186/s40168-018-0607-0.pdf"}, {"href": "https://repository.essex.ac.uk/23630/1/s40168-018-0607-0.pdf"}, {"href": "https://doi.org/10.1186/s40168-018-0607-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-018-0607-0", "name": "item", "description": "10.1186/s40168-018-0607-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-018-0607-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-01T00:00:00Z"}}, {"id": "10.1186/s40168-019-0757-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:30Z", "type": "Journal Article", "created": "2019-10-31", "title": "Suppressed N fixation and diazotrophs after four decades of fertilization", "description": "Abstract Background

N fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answered is whether such a fundamental process would still be that important in an over-fertilized world, as the long-term effects of fertilization on N fixation and associated diazotrophic communities remain to be tested. Here, we used a 35-year fertilization experiment, and investigated the changes in N fixation rates and the diazotrophic community in response to long-term inorganic and organic fertilization.

Results

It was found that N fixation was drastically reduced (dropped by 50%) after almost four decades of fertilization. Our results further indicated that functionality losses were associated with reductions in the relative abundance of keystone and phylogenetically clustered N fixers such as Geobacter spp.

Conclusions

Our work suggests that long-term fertilization might have selected against N fixation and specific groups of N fixers. Our study provides solid evidence that N fixation and certain groups of diazotrophic taxa will be largely suppressed in a more and more fertilized world, with implications for soil biodiversity and ecosystem functions.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "Diazotrophs", "0303 health sciences", "Nitrogen", "Research", "QR100-130", "Agriculture", "Biodiversity", "15. Life on land", "Microbial ecology", "03 medical and health sciences", "13. Climate action", "Nitrogen Fixation", "XXXXXX - Unknown", "Long-term fertilization", "Ecological clusters", "Fertilizers", "Ecosystem", "Phylogeny", "Soil Microbiology", "Nitrogen fixation rates"]}, "links": [{"href": "https://doi.org/10.1186/s40168-019-0757-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-019-0757-8", "name": "item", "description": "10.1186/s40168-019-0757-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-019-0757-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-31T00:00:00Z"}}, {"id": "10.1266/ggs.88.93", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:31Z", "type": "Journal Article", "created": "2015-03-03", "title": "Soil Bacterial Community Structure In Five Tropical Forests In Malaysia And One Temperate Forest In Japan Revealed By Pyrosequencing Analyses Of 16s Rrna Gene Sequence Variation", "description": "Bacterial community structure was investigated in five tropical rainforests in Sarawak, Malaysia and one temperate forest in Kyoto, Japan. A hierarchical sampling approach was employed, in which soil samples were collected from five sampling-sites within each forest. Pyrosequencing was performed to analyze a total of 493,790 16S rRNA amplicons. Despite differences in aboveground conditions, the composition of bacterial groups was similar across all sampling-sites and forests, with Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes and Bacteroidetes accounting for 90% of all Phyla detected. At higher taxonomic levels, the same taxa were predominant, although there was significant heterogeneity in relative abundance of specific taxa across sampling-sites within one forest or across different forests. In all forests, the level of bacterial diversity, estimated using the Chao1 index, was on the order of 1,000, suggesting that tropical rainforests did not necessarily have a large soil bacterial diversity. The average number of reads per species (OTUs) per sampling-site was 8.0, and more than 40-50% of species were singletons, indicating that most bacterial species occurred infrequently and that few bacterial species achieved high predominance. Approximately 30% of species were specific to one sampling-site within a forest, and 40-60% of species were uniquely detected in one of the six forests studied here. Only 0.2% of species were detected in all forests, while on average 32.1% of species were detected in all sampling-sites within a forest. The results suggested that bacterial communities adapted to specific micro- and macro-environments, but macro-environmental diversity made a larger contribution to total bacterial diversity in forest soil.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "0303 health sciences", "Bacteria", "Malaysia", "Genetic Variation", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "Polymerase Chain Reaction", "Trees", "03 medical and health sciences", "Japan", "RNA", " Ribosomal", " 16S", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1266/ggs.88.93"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes%20%26amp%3B%20Genetic%20Systems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1266/ggs.88.93", "name": "item", "description": "10.1266/ggs.88.93", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1266/ggs.88.93"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-01-01T00:00:00Z"}}, {"id": "10.3390/v11070611", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:19:48Z", "type": "Journal Article", "created": "2019-06-12", "title": "Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum\u2014A Novel Lineage of Lactobacillus Phages Comprising Five New Members", "description": "

Lactobacillus plantarum is a bacterium with promising applications to the food industry and agriculture and probiotic properties. So far, bacteriophages of this bacterium have been moderately addressed. We examined the diversity of five new L. plantarum phages via whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. These analyses revealed a high degree of similarity among the five phages, which extended to the vast majority of predicted virion-associated proteins. Based on these, we selected one of the phages as a representative and performed transmission electron microscopy and structural protein sequencing tests. Overall, the results suggested that the five phages belong to the family Myoviridae, they have a long genome of 137.973-141.344 bp, a G/C content of 36,3-36,6% that is quite distinct from their host’s, and, surprisingly, seven to 15 tRNAs. Only an average 41/174 of their predicted genes were assigned a function. The comparative analyses unraveled considerable genetic diversity for the five L. plantarum phages of this study. Hence, the new genus “Semelevirus” was proposed, which comprises exclusively the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp.. The five new Lactobacillus phages have a potential value for the development of more robust starters through, for example, the selection of mutants insensitive to phage infections. The five phages could also form part of phage cocktails, which producers would apply in different stages of L. plantarum fermentations in order to create a range of organoleptic outputs.

", "keywords": ["0301 basic medicine", "Annotation", "comparative genomics", "Genome", " Viral", "Lactobacillus plantarum", "Microbiology", "Article", "Isolation", "diversity", "03 medical and health sciences", "Microscopy", " Electron", " Transmission", "DNA Packaging", "phage", "Bacteriophages", "Phylogeny", "Viral Structural Proteins", "2. Zero hunger", "Diversity", "Base Composition", "0303 health sciences", "Comparative genomics", "new genus", "Genomics", "Sequence Analysis", " DNA", "QR1-502", "virology", "Phylogenetics", "phylogenetics", "Lactobacillus", "annotation", "Myoviridae", "Phage", "New genus", "isolation", "Lactobacillus plantarum"]}, "links": [{"href": "http://www.mdpi.com/1999-4915/11/7/611/pdf"}, {"href": "https://www.mdpi.com/1999-4915/11/7/611/pdf"}, {"href": "https://doi.org/10.3390/v11070611"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Viruses", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/v11070611", "name": "item", "description": "10.3390/v11070611", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/v11070611"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-11T00:00:00Z"}}, {"id": "10.1371%2fjournal.pone.0044697", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:35Z", "type": "Journal Article", "created": "2012-09-11", "title": "A Novel Stress-Induced Sugarcane Gene Confers Tolerance To Drought, Salt And Oxidative Stress In Transgenic Tobacco Plants", "description": "Drought is a major abiotic stress that affects crop productivity worldwide. Sugarcane can withstand periods of water scarcity during the final stage of culm maturation, during which sucrose accumulation occurs. Meanwhile, prolonged periods of drought can cause severe plant losses.In a previous study, we evaluated the transcriptome of drought-stressed plants to better understand sugarcane responses to drought. Among the up-regulated genes was Scdr1 (sugarcane drought-responsive 1). The aim of the research reported here was to characterize this gene. Scdr1 encodes a putative protein containing 248 amino acids with a large number of proline (19%) and cysteine (13%) residues. Phylogenetic analysis showed that ScDR1is in a clade with homologs from other monocotyledonous plants, separate from those of dicotyledonous plants. The expression of Scdr1 in different varieties of sugarcane plants has not shown a clear association with drought tolerance.The overexpression of Scdr1 in transgenic tobacco plants increased their tolerance to drought, salinity and oxidative stress, as demonstrated by increased photosynthesis, water content, biomass, germination rate, chlorophyll content and reduced accumulation of ROS. Physiological parameters, such as transpiration rate (E), net photosynthesis (A), stomatal conductance (gs) and internal leaf CO(2) concentration, were less affected by abiotic stresses in transgenic Scdr1 plants compared with wild-type plants. Overall, our results indicated that Scdr1 conferred tolerance to multiple abiotic stresses, highlighting the potential of this gene for biotechnological applications.", "keywords": ["Chlorophyll", "Nicotiana", "0301 basic medicine", "Sucrose", "Science", "Molecular Sequence Data", "03 medical and health sciences", "Amino Acid Sequence", "Biomass", "Transgenes", "Photosynthesis", "Phylogeny", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Base Sequence", "Sequence Homology", " Amino Acid", "Q", "R", "Water", "15. Life on land", "Plants", " Genetically Modified", "6. Clean water", "Droughts", "Saccharum", "Oxidative Stress", "Medicine", "Salts", "Reactive Oxygen Species", "Research Article", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1371%2fjournal.pone.0044697"}, {"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%2fjournal.pone.0044697", "name": "item", "description": "10.1371%2fjournal.pone.0044697", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371%2fjournal.pone.0044697"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-09-11T00:00:00Z"}}, {"id": "10.1371/journal.pone.0034887", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:35Z", "type": "Journal Article", "created": "2012-04-19", "title": "Changes In The Diversity Of Soil Arbuscular Mycorrhizal Fungi After Cultivation For Biofuel Production In A Guantanamo (Cuba) Tropical System", "description": "Open AccessLes champignons mycorhiziens arbusculaires (FMA) sont un \u00e9l\u00e9ment cl\u00e9 et int\u00e9gral de la stabilit\u00e9, de la durabilit\u00e9 et du fonctionnement des \u00e9cosyst\u00e8mes. Dans cette \u00e9tude, nous avons caract\u00e9ris\u00e9 la biodiversit\u00e9 de l'AMF dans un sol v\u00e9g\u00e9tal natif et dans un sol cultiv\u00e9 avec Jatropha curcas ou Ricinus communis, dans un syst\u00e8me tropical \u00e0 Guantanamo (Cuba), afin de v\u00e9rifier si un changement d'utilisation des terres pour la production de plantes biocarburants a eu un effet sur les communaut\u00e9s de l'AMF. Nous \u00e9valuons \u00e9galement si certaines propri\u00e9t\u00e9s du sol li\u00e9es \u00e0 la fertilit\u00e9 du sol (N total, C organique, biomasse microbienne C, pourcentage de stabilit\u00e9 globale, pH et conductivit\u00e9 \u00e9lectrique) ont \u00e9t\u00e9 modifi\u00e9es avec la culture des deux esp\u00e8ces de cultures. Les g\u00e8nes d'ARNr de la petite sous-unit\u00e9 fongique AM (SSU) ont \u00e9t\u00e9 soumis \u00e0 une PCR, \u00e0 un clonage, \u00e0 un s\u00e9quen\u00e7age et \u00e0 des analyses phylog\u00e9n\u00e9tiques. Vingt types de s\u00e9quences fongiques AM ont \u00e9t\u00e9 identifi\u00e9s\u00a0: 19 appartiennent aux Glomeraceae et un aux Paraglomeraceae. Deux types de s\u00e9quences d'AMF li\u00e9s \u00e0 des esp\u00e8ces d'AMF cultiv\u00e9es (Glo G3 pour Glomus sinuosum et Glo G6 pour Glomus intraradices-G. fasciculatum-G. irregulare) ne se sont pas produits dans le sol cultiv\u00e9 avec J. curcas et R. communis. Les propri\u00e9t\u00e9s du sol (N total, C organique et biomasse microbienne C) \u00e9taient plus \u00e9lev\u00e9es dans le sol cultiv\u00e9 avec les deux esp\u00e8ces v\u00e9g\u00e9tales. La diversit\u00e9 de la communaut\u00e9 AMF a diminu\u00e9 dans le sol des deux cultures, par rapport au sol v\u00e9g\u00e9tal indig\u00e8ne, et variait consid\u00e9rablement en fonction des esp\u00e8ces cultiv\u00e9es plant\u00e9es. Ainsi, le sol de R. communis pr\u00e9sentait une diversit\u00e9 AMF plus \u00e9lev\u00e9e que le sol de J. curcas. En conclusion, R. communis pourrait \u00eatre plus adapt\u00e9 \u00e0 la conservation \u00e0 long terme et \u00e0 la gestion durable de ces \u00e9cosyst\u00e8mes tropicaux.", "keywords": ["Biomass (ecology)", "Jatropha", "Plant Science", "Plant Roots", "7. Clean energy", "Fungal Diversity", "Agricultural and Biological Sciences", "Soil", "Mycorrhizae", "Jatropha curcas", "Soil water", "Saproxylic Insect Ecology and Forest Management", "Mycological Typing Techniques", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Ecology", "Q", "R", "Cuba", "Life Sciences", "Agriculture", "Biodiversity", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Medicine", "Research Article", "Science", "Soil fertility", "12. Responsible consumption", "Mycorrhizal Fungi and Plant Interactions", "Health Sciences", "Biology", "Ecosystem", "Ribosome Subunits", " Small", " Eukaryotic", "Pharmacology", "Tropical Climate", "Soil organic matter", "Electric Conductivity", "Botany", "Medicinal Mushrooms: Antitumor and Immunomodulating Properties", "Spore", "15. Life on land", "Agronomy", "Glomus", "Molecular Typing", "Biofuels", "Insect Science", "FOS: Biological sciences", "0401 agriculture", " forestry", " and fisheries", "Ricinus communis"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0034887"}, {"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.0034887", "name": "item", "description": "10.1371/journal.pone.0034887", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0034887"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-04-19T00:00:00Z"}}, {"id": "10.1371/journal.pone.0076447", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:36Z", "type": "Journal Article", "created": "2013-09-26", "title": "The Arbuscular Mycorrhizal Fungal Community Response To Warming And Grazing Differs Between Soil And Roots On The Qinghai-Tibetan Plateau", "description": "Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most plant species in terrestrial ecosystems, and are affected by environmental variations. To reveal the impact of disturbance on an AM fungal community under future global warming, we examined the abundance and community composition of AM fungi in both soil and mixed roots in an alpine meadow on the Qinghai-Tibetan Plateau, China. Warming and grazing had no significant effect on AM root colonization, spore density and extraradical hyphal density. A total of 65 operational taxonomic units (OTUs) of AM fungi were identified from soil and roots using molecular techniques. AM fungal OTU richness was higher in soil (54 OTUs) than in roots (34 OTUs), and some AM fungi that differed between soil and roots, showed significantly biased occurrence to warming or grazing. Warming and grazing did not significantly affect AM fungal OTU richness in soil, but warming with grazing significantly increased AM fungal OTU richness in roots compared to the grazing-only treatment. Non-metric multidimensional scaling analysis showed that the AM fungal community composition was significantly different between soil and roots, and was significantly affected by grazing in roots, whereas in soil it was significantly affected by warming and plant species richness. The results suggest that the AM fungal community responds differently to warming and grazing in soil compared with roots. This study provides insights into the role of AM fungi under global environmental change scenarios in alpine meadows of the Qinghai-Tibetan Plateau.", "keywords": ["0106 biological sciences", "Hot Temperature", "Science", "Molecular Sequence Data", "Population Dynamics", "Global Warming", "Plant Roots", "Polymerase Chain Reaction", "01 natural sciences", "Species Specificity", "Mycorrhizae", "Herbivory", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Analysis of Variance", "Base Sequence", "Models", " Genetic", "Altitude", "Q", "R", "Bayes Theorem", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Spores", " Fungal", "15. Life on land", "Biota", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Polymorphism", " Restriction Fragment Length", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0076447"}, {"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.0076447", "name": "item", "description": "10.1371/journal.pone.0076447", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0076447"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-09-26T00:00:00Z"}}, {"id": "10.1371/journal.pone.0307156", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-10-06T16:18:38Z", "type": "Journal Article", "created": "2024-07-31", "title": "Optimal inventorying and monitoring of taxonomic, phylogenetic and functional diversity", "description": "

Comparable data is essential to understand biodiversity patterns. While assemblage or community inventorying requires comprehensive sampling, monitoring focuses on as few components as possible to detect changes. Quantifying species, their evolutionary history, and the way they interact requires studying changes in taxonomic (TD), phylogenetic (PD) and functional diversity (FD). Here we propose a method for the optimization of sampling protocols for inventorying and monitoring assemblages or communities across these three diversity dimensions taking sampling costs into account. We used Iberian spiders and Amazonian bats as two case-studies. The optimal combination of methods for inventorying and monitoring required optimizing the accumulation curve of \u03b1-diversity and minimizing the difference between sampled and estimated \u03b2-diversity (bias), respectively. For Iberian spiders, the optimal combination for TD, PD and FD allowed sampling at least 50% of estimated diversity with 24 person-hours of fieldwork. The optimal combination of six person-hours allowed reaching a bias below 8% for all dimensions. For Amazonian bats, surveying all the 12 sites with mist-nets and 0 or 1 acoustic recorders was the optimal combination for almost all diversity types, resulting in >89% of the diversity and <10% bias with roughly a third of the cost. Only for phylogenetic \u03b1-diversity, the best solution was less clear and involved surveying both with mist nets and acoustic recorders. The widespread use of optimized and standardized sampling protocols and regular repetition in time will radically improve global inventory and monitoring of biodiversity. We strongly advocate for the global adoption of sampling protocols for both inventory and monitoring of taxonomic, phylogenetic and functional diversity.

", "keywords": ["0106 biological sciences", "chiroptera", "Science", "Q", "R", "Spiders", "Biodiversity", "15. Life on land", "phylogeny", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "01 natural sciences", "Environmental sciences", "Ecology", " evolutionary biology", "Chiroptera", "Medicine", "Animals", "Phylogeny", "biodiversity", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/060400v1.full.pdf"}, {"href": "https://doi.org/10.1371/journal.pone.0307156"}, {"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.0307156", "name": "item", "description": "10.1371/journal.pone.0307156", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0307156"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-23T00:00:00Z"}}, {"id": "10.15482/usda.adc/1518485", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:46Z", "type": "Dataset", "title": "Data from: Genome sequence of the chestnut blight fungus Cryphonectria parasitica EP155: A fundamental resource for an archetypical invasive plant pathogen", "description": "The ascomycete fungus Cryphonectria parasitica is the causal agent of chestnut blight disease. This deadly fungal pathogen was introduced into North America from Asia before the turn of the 20th century, quickly spreading throughout the natural range of the American chestnut tree. In the course of a single generation, chestnut blight destroyed billions of American chestnut trees in forests across North America, driving it almost to extinction. The genome assembly for C. parasitica EP155 (v. 2.0, available at https://mycocosm.jgi.doe.gov/Crypa2/Crypa2.info.html) contains 26 main genome scaffolds totaling 43.9 Mb, and was sequenced at the U.S. Department of Energy Joint Genome Institute. The information and documents contained within this Ag Data Commons dataset provide supplementary data about the EP155 genome assembly, including scaffold summaries, genetic maps, mitochondrial DNA, P450s, secondary metabolite clusters, vegetative incompatibility genes, and transposable elements. These data are freely available for research purposes.", "keywords": ["15. Life on land", "chestnut blight", "Cryphonectria parasitica", "vegetative incompatibility", "transposons", "P450", "secondary metabolite", "mitochondria", "fungi", "Forest & Plant Health", "american chestnut", "genome assembly", "transposable elements", "genetic maps", "NP303", "Cryphonectria parasitica", "fungi", "invasive species", "plant pathogens", "Asia", "Castanea dentata", "trees", "forests", "extinction", "genome assembly", "United States", "silver", "data collection", "mitochondrial DNA", "secondary metabolites", "genes", "transposons", "phylogeny", "cytochrome P-450", "enzymes", "nuclear genome", "mitochondria"]}, "links": [{"href": "https://doi.org/10.15482/usda.adc/1518485"}, {"rel": "self", "type": "application/geo+json", "title": "10.15482/usda.adc/1518485", "name": "item", "description": "10.15482/usda.adc/1518485", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.15482/usda.adc/1518485"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "10.1631/jzus.b1200013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:50Z", "type": "Journal Article", "created": "2012-10-03", "title": "Abundance And Composition Of Ammonia-Oxidizing Bacteria And Archaea In Different Types Of Soil In The Yangtze River Estuary", "description": "Tidal flats are soil resources of great significance. Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process. The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR). The different abundances of AOB and AOA were negatively correlated with the salinity. The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene. Among AOB, nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process, i.e., tidal flats, while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process, farm land and wild land. The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate. As for AOA, there was no obvious correlation with the changes in the physicochemical properties of the soil. This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "China", "Conservation of Natural Resources", "Archaeal Proteins", "Molecular Sequence Data", "Genes", " Archaeal", "03 medical and health sciences", "Bacterial Proteins", "Rivers", "Ammonia", "14. Life underwater", "Phylogeny", "0303 health sciences", "Bacteria", "Biodiversity", "Nitrogen Cycle", "15. Life on land", "Archaea", "Nitrification", "6. Clean water", "DNA", " Archaeal", "Genes", " Bacterial", "13. Climate action", "Estuaries", "Oxidoreductases", "Oxidation-Reduction"]}, "links": [{"href": "https://doi.org/10.1631/jzus.b1200013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Zhejiang%20University%20SCIENCE%20B", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1631/jzus.b1200013", "name": "item", "description": "10.1631/jzus.b1200013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1631/jzus.b1200013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-01T00:00:00Z"}}, {"id": "10.1890/10-0426.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:18:56Z", "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": "10.3390/genes10060424", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:19:39Z", "type": "Journal Article", "created": "2019-06-03", "title": "Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes", "description": "

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe\u2013plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant\u2013growth\u2013promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

", "keywords": ["0301 basic medicine", "570", "plant\u2013growth\u2013promotion (PGP)", "metagenomically-assembled-genomes (MAGs)", "Article", "03 medical and health sciences", "carbon dioxide fixation", "Ammonia", "metagenomic binning", "Germany", "soil microbiome", "Proteobacteria", "Humans", "biocontrol", "secondary metabolite synthesis", "suppressive soil", "Phylogeny", "Soil Microbiology", "soil microbiome; suppressive soil; biocontrol; plant\u2013growth\u2013promotion (PGP); metagenomic binning; metagenomically-assembled-genomes (MAGs); secondary metabolite synthesis; carbon dioxide fixation; carbohydrate-active enzymes; differentially abundant features (DAFs)", "2. Zero hunger", "Bacteria", "Bacteroidetes", "Agriculture", "differentially abundant features (DAFs)", "15. Life on land", "Archaea", "Actinobacteria", "13. Climate action", "carbohydrate-active enzymes", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://doi.org/10.3390/genes10060424"}, {"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/genes10060424", "name": "item", "description": "10.3390/genes10060424", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10060424"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-03T00:00:00Z"}}, {"id": "10.3390/genes10060456", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:19:39Z", "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": "10.3897/zse.101.144719", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-10-06T16:19:52Z", "type": "Journal Article", "created": "2025-02-28", "title": "Retrieval of the genus Capitellus Siddiqi, 1983, with description of C. caramborum sp. nov. (Dorylaimida, Belondiridae) associated with Andalusian (Spain) olive groves", "description": "

A new species of belondirid nematode, collected in olive groves of the southern Iberian Peninsula, is described, including SEM observations and molecular (LSU, SSU) study. Capitellus caramborumsp. nov. is characterized by its 0.82\uffe2\uff80\uff931.09 mm long body, lip region offset by constriction and 6.0\uffe2\uff80\uff936.5 \uffc2\uffb5m wide with a distinct perioral refractive disc 4.0\uffe2\uff80\uff934.5 \uffc2\uffb5m wide, odontostyle 6.0\uffe2\uff80\uff936.5 \uffc2\uffb5m long, odontophore bearing basal flanges and 1.8\uffe2\uff80\uff932.0 times the odontostyle long, neck 223\uffe2\uff80\uff93296 \uffc2\uffb5m long, pharyngeal expansion occupying 53\uffe2\uff80\uff9359% of the total neck length, female genital system diovarian, uterus simple and 27\uffe2\uff80\uff9338 \uffc2\uffb5m or 1.4\uffe2\uff80\uff931.9 body diameters long, vulva (V = 53\uffe2\uff80\uff9356) longitudinal, tail convex conoid to subcylindrical (24\uffe2\uff80\uff9334 \uffc2\uffb5m, c = 31\uffe2\uff80\uff9338, c\uffe2\uff80\uff99 = 1.8\uffe2\uff80\uff932.1), spicules strongly curved ventrad and 23\uffe2\uff80\uff9325 \uffc2\uffb5m long, and four ventromedian supplements. Morphological and molecular data support the retrieval of Capitellus as a valid genus, its taxonomy being updated, including the transference of Dorylaimellus neocapitatus to it.Gypsum soils in the Mediterranean Basin house large numbers of edaphic specialists that are adapted to stressful environments. The evolutionary history and standing genetic variation of these taxa have been influenced by the geological and paleoclimatic complexity of this area and the long\uffe2\uff80\uff90standing effect of human activities. However, little is known about the origin of Mediterranean gypsophiles and the factors affecting their genetic diversity and population structure.

METHODS

Using phylogenetic and phylogeographic approaches based on microsatellites and sequence data from nuclear and chloroplast regions, we evaluated the divergence time, genetic diversity, and population structure of 27 different populations of the widespread Iberian gypsophile Lepidium subulatum throughout its entire geographic range.

RESULTS

Lepidium subulatum diverged from its nearest relatives ~3 million years ago, and ITS and psbA/matK trees supported the monophyly of the species. These results suggest that both geological and climatic changes in the region around the Plio\uffe2\uff80\uff90Pleistocene promoted its origin, compared to other evolutionary processes. We found high genetic diversity in both nuclear and chloroplast markers, but a greater population structure in the chloroplast data. These results suggest that while seed dispersal is limited, pollen flow may be favored by the presence of numerous habitat patches that enhance the movement of pollinators.

CONCLUSIONS

Despite being an edaphic endemic, L. subulatum possesses high genetic diversity probably related to its relatively old age and high population sizes across its range. Our study highlights the value of using different markers to fully understand the phylogeographic history of plant species.A new belondirid, dorylaimid taxon, Oleaxonchium olearumgen. et sp. nov., collected from an olive grove in the Andalusia region of Spain, is characterised, including its morphological description, morphometrics, SEM study, and molecular (18S-, 28S-rDNA) analyses. The new genus displays a unique combination of traits that distinguishes it from its closest genera: a rectangular lip region with sclerotized margins when observed in lateral view and visibly hexagonal in face view under SEM; a comparatively long cheilostom with thickened walls at its anterior part; a short isthmus-like section separating both pharyngeal regions; a mono-opistho-ovarian didelphic female genital system without pars refringens vaginae; and a short and rounded tail. The new species is characterised by its 2.44\uffe2\uff80\uff932.87 mm long body, lip region 7\uffe2\uff80\uff937.5 \uffc2\uffb5m wide, odontostyle 10\uffe2\uff80\uff9310.5 \uffc2\uffb5m long, neck 723\uffe2\uff80\uff93973 \uffc2\uffb5m long, pharyngeal expansion occupying 63\uffe2\uff80\uff9372% of the total neck length, female anterior genital branch 4\uffe2\uff80\uff936% of body length, tripartite posterior uterus 1.9\uffe2\uff80\uff932.6 body diameters long, with a short intermediate section bearing sclerotized elements, vulva (V = 58\uffe2\uff80\uff9361) a transverse slit, caudal region 29\uffe2\uff80\uff9335 \uffc2\uffb5m long (c = 74\uffe2\uff80\uff9389, c\uffe2\uff80\uff99 = 0.9\uffe2\uff80\uff931.1), and male unknown. As derived from an integrative approach combining morphological and molecular data, the new genus is close to Metaxonchium, the polyphyly of Belondiridae is confirmed, and support is provided in favour of the monophyly of Axonchiinae.

The analysis of plant elemental composition and the underlying factors affecting its variation are a current hot topic in ecology. Ecological adaptation to atypical soils may shift plant elemental composition. However, no previous studies have evaluated its relevance against other factors such as phylogeny, climate or individual soil conditions.

We evaluated the effect of the phylogeny, environment (climate, soil), and affinity to gypsum soils on the elemental composition of 83 taxa typical of Iberian gypsum ecosystems. We used a new statistical procedure (multiple phylogenetic variance decomposition, MPVD) to decompose total explained variance by different factors across all nodes in the phylogenetic tree of target species (covering 120\uffe2\uff80\uff89million\uffe2\uff80\uff89years of Angiosperm evolution).

Our results highlight the relevance of phylogeny on the elemental composition of plants both at early (with the development of key preadaptive traits) and recent divergence times (diversification of the Iberian gypsum flora concurrent with Iberian gypsum deposit accumulation). Despite the predominant phylogenetic effect, plant adaptation to gypsum soils had a strong impact on the elemental composition of plants, particularly on sulphur concentrations, while climate and soil effects were smaller.

Accordingly, we detected a convergent evolution of gypsum specialists from different lineages on increased sulphur and magnesium foliar concentrations.

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe\u2013plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant\u2013growth\u2013promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

", "keywords": ["0301 basic medicine", "570", "plant\u2013growth\u2013promotion (PGP)", "metagenomically-assembled-genomes (MAGs)", "Article", "03 medical and health sciences", "carbon dioxide fixation", "Ammonia", "metagenomic binning", "Germany", "soil microbiome", "Proteobacteria", "Humans", "biocontrol", "secondary metabolite synthesis", "suppressive soil", "Phylogeny", "Soil Microbiology", "soil microbiome; suppressive soil; biocontrol; plant\u2013growth\u2013promotion (PGP); metagenomic binning; metagenomically-assembled-genomes (MAGs); secondary metabolite synthesis; carbon dioxide fixation; carbohydrate-active enzymes; differentially abundant features (DAFs)", "2. Zero hunger", "Bacteria", "Bacteroidetes", "Agriculture", "differentially abundant features (DAFs)", "15. Life on land", "Archaea", "Actinobacteria", "13. Climate action", "carbohydrate-active enzymes", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://doi.org/2946862318"}, {"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": "2946862318", "name": "item", "description": "2946862318", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2946862318"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-03T00:00:00Z"}}, {"id": "10045/97692", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:22:12Z", "type": "Journal Article", "created": "2019-06-27", "title": "Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands", "description": "Abstract

Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.

Comparable data is essential to understand biodiversity patterns. While assemblage or community inventorying requires comprehensive sampling, monitoring focuses on as few components as possible to detect changes. Quantifying species, their evolutionary history, and the way they interact requires studying changes in taxonomic (TD), phylogenetic (PD) and functional diversity (FD). Here we propose a method for the optimization of sampling protocols for inventorying and monitoring assemblages or communities across these three diversity dimensions taking sampling costs into account. We used Iberian spiders and Amazonian bats as two case-studies. The optimal combination of methods for inventorying and monitoring required optimizing the accumulation curve of \u03b1-diversity and minimizing the difference between sampled and estimated \u03b2-diversity (bias), respectively. For Iberian spiders, the optimal combination for TD, PD and FD allowed sampling at least 50% of estimated diversity with 24 person-hours of fieldwork. The optimal combination of six person-hours allowed reaching a bias below 8% for all dimensions. For Amazonian bats, surveying all the 12 sites with mist-nets and 0 or 1 acoustic recorders was the optimal combination for almost all diversity types, resulting in >89% of the diversity and <10% bias with roughly a third of the cost. Only for phylogenetic \u03b1-diversity, the best solution was less clear and involved surveying both with mist nets and acoustic recorders. The widespread use of optimized and standardized sampling protocols and regular repetition in time will radically improve global inventory and monitoring of biodiversity. We strongly advocate for the global adoption of sampling protocols for both inventory and monitoring of taxonomic, phylogenetic and functional diversity.

", "keywords": ["0106 biological sciences", "chiroptera", "Science", "Q", "R", "Spiders", "Biodiversity", "15. Life on land", "phylogeny", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "01 natural sciences", "Environmental sciences", "Ecology", " evolutionary biology", "Chiroptera", "Medicine", "Animals", "Phylogeny", "biodiversity", "Research Article"]}, "links": [{"href": "https://repositorio.ulisboa.pt/bitstream/10400.5/96634/1/journal.pone.0307156%20%281%29.pdf"}, {"href": "https://www.biorxiv.org/content/10.1101/060400v1.full.pdf"}, {"href": "https://doi.org/10138/586547"}, {"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": "10138/586547", "name": "item", "description": "10138/586547", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10138/586547"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-23T00:00:00Z"}}, {"id": "10261/184998", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:22:16Z", "type": "Journal Article", "created": "2017-09-19", "title": "Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles", "description": "Abstract

Dispersal is a critical factor determining the spatial scale of speciation, which is constrained by the ecological characteristics and distribution of a species\uffe2\uff80\uff99 habitat and the intrinsic traits of species. Endogean taxa are strongly affected by the unique qualities of the below\uffe2\uff80\uff90ground environment and its effect on dispersal, and contrasting reports indicate either high dispersal capabilities favoured by small body size and mediated by passive mechanisms, or low dispersal due to restricted movement and confinement inside the soil. We studied a species\uffe2\uff80\uff90rich endogean ground beetle lineage, Typhlocharina, including three genera and more than 60 species, as a model for the evolutionary biology of dispersal and speciation in the deep soil. A time\uffe2\uff80\uff90calibrated molecular phylogeny generated from >400 individuals was used to delimit candidate species, to study the accumulation of lineages through space and time by species\uffe2\uff80\uff93area\uffe2\uff80\uff93age relationships and to determine the geographical structure of the diversification using the relationship between phylogenetic and geographic distances across the phylogeny. Our results indicated a small spatial scale of speciation in Typhlocharina and low dispersal capacity combined with sporadic long distance, presumably passive dispersal events that fuelled the speciation process. Analysis of lineage growth within Typhlocharina revealed a richness plateau correlated with the range of distribution of lineages, suggesting a long\uffe2\uff80\uff90term species richness equilibrium mediated by density dependence through limits of habitat availability. The interplay of area\uffe2\uff80\uff90 and age\uffe2\uff80\uff90dependent processes ruling the lineage diversification in Typhlocharina may serve as a general model for the evolution of high species diversity in endogean mesofauna.Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.

The analysis of plant elemental composition and the underlying factors affecting its variation are a current hot topic in ecology. Ecological adaptation to atypical soils may shift plant elemental composition. However, no previous studies have evaluated its relevance against other factors such as phylogeny, climate or individual soil conditions.

We evaluated the effect of the phylogeny, environment (climate, soil), and affinity to gypsum soils on the elemental composition of 83 taxa typical of Iberian gypsum ecosystems. We used a new statistical procedure (multiple phylogenetic variance decomposition, MPVD) to decompose total explained variance by different factors across all nodes in the phylogenetic tree of target species (covering 120\uffe2\uff80\uff89million\uffe2\uff80\uff89years of Angiosperm evolution).

Our results highlight the relevance of phylogeny on the elemental composition of plants both at early (with the development of key preadaptive traits) and recent divergence times (diversification of the Iberian gypsum flora concurrent with Iberian gypsum deposit accumulation). Despite the predominant phylogenetic effect, plant adaptation to gypsum soils had a strong impact on the elemental composition of plants, particularly on sulphur concentrations, while climate and soil effects were smaller.

Accordingly, we detected a convergent evolution of gypsum specialists from different lineages on increased sulphur and magnesium foliar concentrations.

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": "10871/134717", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:22:27Z", "type": "Journal Article", "created": "2023-10-27", "title": "Shifts in soil ammonia\u2010oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions", "description": "Abstract

Anthropogenic nitrogen (N) loading alters soil ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize\uffc2\uffa068 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N\uffe2\uff80\uff90stimulation of nitrification, but does so via climate\uffe2\uff80\uff90related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N\uffe2\uff80\uff90availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate\uffe2\uff80\uff90related shifts in soil ammonia\uffe2\uff80\uff90oxidizing community maintain the N\uffe2\uff80\uff90stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.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.Feedback between plants and soil microbial communities can be a powerful driver of vegetation dynamics. Plants elicit changes in the soil microbiome that either promote or suppress conspecifics at the same location, thereby regulating population density\uffe2\uff80\uff90dependence and species co\uffe2\uff80\uff90existence. Such effects are often attributed to the accumulation of host\uffe2\uff80\uff90specific antagonistic or beneficial microbiota in the rhizosphere. However, the identity and host\uffe2\uff80\uff90specificity of the microbial taxa involved are rarely empirically assessed. Here we review the evidence for host\uffe2\uff80\uff90specificity in plant\uffe2\uff80\uff90associated microbes and propose that specific plant\uffe2\uff80\uff93soil feedbacks can also be driven by generalists. We outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plant\uffe2\uff80\uff93soil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities. Identifying factors that promote specialization or generalism in plant\uffe2\uff80\uff93microbial interactions and thereby modulate the impact of microbiota on plant performance will advance our understanding of the mechanisms underlying plant\uffe2\uff80\uff93soil feedback and the ways it contributes to plant co\uffe2\uff80\uff90existence.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.

There is strong evidence for a phylogenetic signal in the degree to which species share co\uffe2\uff80\uff90evolved biotic partners and in the outcomes of biotic interactions. This implies there should be a phylogenetic signal in the outcome of feedbacks between plants and the soil microbiota they cultivate. However, attempts to identify a phylogenetic signal in plant\uffe2\uff80\uff93soil feedbacks have produced mixed results.

Here we clarify how phylogenetic signals could arise in plant\uffe2\uff80\uff93soil feedbacks and use a recent compilation of data from feedback experiments to identify: whether there is a phylogenetic signal in the outcome of plant\uffe2\uff80\uff93soil feedbacks; and whether any signal arises through directional or divergent changes in feedback outcomes with evolutionary time.

We find strong evidence for a divergent phylogenetic signal in feedback outcomes. Distantly related plant species show more divergent responses to each other\uffe2\uff80\uff99s soil microbiota compared with closely related plant species. The pattern of divergence implies occasional co\uffe2\uff80\uff90evolutionary shifts in how plants interact with soil microbiota, with strongly contrasting feedback responses among some plant lineages.

Our results highlight that it is difficult to predict feedback outcomes from phylogeny alone, other than to say that more closely related species tend to have more similar responses.

Despite having key functions in terrestrial ecosystems, information on the dominant soil fungi and their ecological preferences at the global scale is lacking. To fill this knowledge gap, we surveyed 235 soils from across the globe. Our findings indicate that 83 phylotypes (<0.1% of the retrieved fungi), mostly belonging to wind dispersed, generalist Ascomycota, dominate soils globally. We identify patterns and ecological drivers of dominant soil fungal taxa occurrence, and present a map of their distribution in soils worldwide. Whole-genome comparisons with less dominant, generalist fungi point at a significantly higher number of genes related to stress-tolerance and resource uptake in the dominant fungi, suggesting that they might be better in colonising a wide range of environments. Our findings constitute a major advance in our understanding of the ecology of fungi, and have implications for the development of strategies to preserve them and the ecosystem functions they provide.N fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answered is whether such a fundamental process would still be that important in an over-fertilized world, as the long-term effects of fertilization on N fixation and associated diazotrophic communities remain to be tested. Here, we used a 35-year fertilization experiment, and investigated the changes in N fixation rates and the diazotrophic community in response to long-term inorganic and organic fertilization.

Results

It was found that N fixation was drastically reduced (dropped by 50%) after almost four decades of fertilization. Our results further indicated that functionality losses were associated with reductions in the relative abundance of keystone and phylogenetically clustered N fixers such as Geobacter spp.

Conclusions

Our work suggests that long-term fertilization might have selected against N fixation and specific groups of N fixers. Our study provides solid evidence that N fixation and certain groups of diazotrophic taxa will be largely suppressed in a more and more fertilized world, with implications for soil biodiversity and ecosystem functions.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Diazotrophs", "0303 health sciences", "Nitrogen", "Research", "QR100-130", "Agriculture", "Biodiversity", "15. Life on land", "Microbial ecology", "03 medical and health sciences", "13. Climate action", "Nitrogen Fixation", "XXXXXX - Unknown", "Long-term fertilization", "Ecological clusters", "Fertilizers", "Ecosystem", "Phylogeny", "Soil Microbiology", "Nitrogen fixation rates"]}, "links": [{"href": "https://doi.org/1959.7/uws:67551"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1959.7/uws:67551", "name": "item", "description": "1959.7/uws:67551", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1959.7/uws:67551"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-31T00:00:00Z"}}, {"id": "20.500.11850/506000", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:22:49Z", "type": "Journal Article", "created": "2021-06-23", "title": "Limitation of Microbial Processes at Saturation-Level Salinities in a Microbial Mat Covering a Coastal Salt Flat", "description": "

Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even on Earth, the limitations imposed on microbial processes by saturation-level salinity have rarely been studied in situ . Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

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