BACKGROUND: Denitrification is a microbial process that has received considerable attention during the past decade since it can result in losses of added nitrogen fertilisers from agricultural soils. Paddy soil has been known to have strong denitrifying activity, but the denitrifying microorganisms responsible for fertilisers in paddy soil are not well known. The objective of this study was to explore the impacts of 17\uffe2\uff80\uff90year application of inorganic and organic fertiliser (rice straw) on the abundance and composition of a nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Soil samples were collected from CK plots (no fertiliser), N (nitrogen fertiliser), NPK (nitrogen, phosphorus and potassium fertilisers) and NPK + OM (NPK plus organic matter). The nitrous oxide reductase gene (nosZ) community composition was analysed using terminal restriction fragment length polymorphism, and the abundance was determined by quantitative PCR.
RESULTS: Both the largest abundance of nosZ\uffe2\uff80\uff90denitrifier and the highest potential denitrifying activity (PDA) occurred in the NPK + OM treatment with about four times higher than that in the CK and two times higher than that in the N and NPK treatments (no significant difference). Denitrifying community composition differed significantly among fertilisation treatments except for the comparison between CK and N treatments. Of the measured abiotic factors, total organic carbon was significantly correlated with the observed differences in community composition and abundance (P < 0.01 by Monte Carlo permutation).
CONCLUSION: This study shows that the addition of different fertilisers affects the size and composition of the nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Copyright \uffc2\uffa9 2011 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Nitrogen", "0402 animal and dairy science", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Carbon", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "Denitrification", "0405 other agricultural sciences", "Fertilizers", "Oxidoreductases", "Monte Carlo Method", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.4533"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.4533", "name": "item", "description": "10.1002/jsfa.4533", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.4533"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-27T00:00:00Z"}}, {"id": "10.1007/s00248-003-0229-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:14:49Z", "type": "Journal Article", "created": "2005-06-17", "title": "Methanogen Communities In A Drained Bog: Effect Of Ash Fertilization", "description": "Forestry practises such has drainage have been shown to decrease emissions of the greenhouse gas methane (CH(4)) from peatlands. The aim of the study was to examine the methanogen populations in a drained bog in northern Finland, and to assess the possible effect of ash fertilization on potential methane production and methanogen communities. Peat samples were collected from control and ash fertilized (15,000 kg/ha) plots 5 years after ash application, and potential CH(4) production was measured. The methanogen community structure was studied by DNA isolation, PCR amplification of the methyl coenzyme-M reductase (mcr) gene, denaturing gradient gel electrophoresis (DGGE), and restriction fragment length polymorphism (RFLP) analysis. The drained peatland showed low potential methane production and methanogen diversity in both control and ash-fertilized plots. Samples from both upper and deeper layers of peat were dominated by three groups of sequences related to Rice cluster-I hydrogenotroph methanogens. Even though pH was marginally greater in the ash-treated site, the occurrence of those sequences was not affected by ash fertilization. Interestingly, a less common group of sequences, related to the Fen cluster, were found only in the fertilized plots. The study confirmed the depth related change of methanogen populations in peatland.", "keywords": ["0301 basic medicine", "0303 health sciences", "Bacteria", "tuhkalannoitus", "metanogeeniset mikrobit", "Biodiversity", "15. Life on land", "03 medical and health sciences", "Genes", " Bacterial", "ojitetut suot", "Fertilizers", "Methane", "Ecosystem", "Phylogeny", "Polymorphism", " Restriction Fragment Length"]}, "links": [{"href": "https://doi.org/10.1007/s00248-003-0229-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-003-0229-2", "name": "item", "description": "10.1007/s00248-003-0229-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-003-0229-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-02-01T00:00:00Z"}}, {"id": "10.1007/s00248-010-9727-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:14:50Z", "type": "Journal Article", "created": "2010-08-03", "title": "Soil Microbial Abundance And Diversity Along A Low Precipitation Gradient", "description": "The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while \u223c2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (\u223c9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem.", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "0301 basic medicine", "Salinity", "0303 health sciences", "Bacteria", "Mediterranean Region", "Climate", "Rain", "Water", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Soil", "03 medical and health sciences", "Phospholipids", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-010-9727-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-010-9727-1", "name": "item", "description": "10.1007/s00248-010-9727-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-010-9727-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-08-01T00:00:00Z"}}, {"id": "10.1007/s11274-011-0809-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:15:36Z", "type": "Journal Article", "created": "2011-06-15", "title": "Soil Bacterial Community Composition And Diversity Respond To Cultivation In Karst Ecosystems", "description": "Soil microorganisms play vital roles in recovering and maintaining the health of ecosystems, particularly in fragile Karst ecosystems that are easily degraded after cultivation. We investigated the composition and diversity of soil bacterial communities, based on RFLP and 16S rDNA sequencing, in a cropland, a naturally revegetated land with former cultivation disturbance and a primeval forest in the subtropical Karst of southwest China. Our results illustrated that Proteobacteria accounted for 44.8% of the 600 tested clones, making it the most dominant phylum observed. This phylum was followed by Acidobacteria and Planctomycetes for the three Karst soils analyzed. Compared with the primeval forest soil, the proportions of Proteobacteria were decreased by 30.2 and 37.9%, while Acidobacteria increased by 93.9 and 87.9%, and the Shannon-Wiener diversity indices and the physicochemical parameters declined in the cropland and the revegetated land, respectively. Among the three soils, the proportion of dominant bacterial phyla and the diversity indices in the revegetated land were similar to the cropland, implying the bacterial community in the cropland was relatively stable, and the after-effects of cultivation were difficult to eliminate. However, similar distributions of the four Proteobacteria subphyla were observed between the revegetated land and the primeval forest soil. Furthermore, the proportion of Rhizobiales belonging to \u03b1-Proteobacteria was sharply decreased with cultivation compared to the primeval forest soil, while a small cluster of Rhizobiales recurred with vegetation recovery. These results indicated that although the subphyla of the dominant bacterial phylum had some positive responses to 20\u00a0years of vegetation recovery, it is a slow process. Our results suggest that priority should be given to conserve the primeval forest and inoculation of functional microorganisms on the basis of vegetation recovery may be more effective for the restoration of Karst ecosystems after cultivation.", "keywords": ["2. Zero hunger", "0301 basic medicine", "China", "0303 health sciences", "Bacteria", "Agriculture", "Biodiversity", "15. Life on land", "Trees", "RNA", " Bacterial", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Metagenome", "Ecosystem", "Phylogeny", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"], "contacts": [{"organization": "Xiangbi Chen, Ya-wei Wei, Wenxue Wei, Jinshui Wu, Yirong Su, Xunyang He,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s11274-011-0809-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/World%20Journal%20of%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11274-011-0809-0", "name": "item", "description": "10.1007/s11274-011-0809-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11274-011-0809-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-15T00:00:00Z"}}, {"id": "10.1016/j.xgen.2024.100639", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:53Z", "type": "Journal Article", "created": "2024-08-30", "title": "ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers", "description": "The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.", "keywords": ["330", "Bioinformatics", "Genome", " Human", "610", "Genomics", "Medical Oncology", "Somatic variant calling", "Polymorphism", " Single Nucleotide", "Article", "Benchmarking", "Oncology", "INDEL Mutation", "\u00c0rees tem\u00e0tiques de la UPC::Inform\u00e0tica::Aplicacions de la inform\u00e0tica::Bioinform\u00e0tica", "Neoplasms", "Cancer genomics", "Humans", "Benchmarking data", "Precision Medicine", "Software"]}, "links": [{"href": "https://doi.org/10.1016/j.xgen.2024.100639"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Cell%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.xgen.2024.100639", "name": "item", "description": "10.1016/j.xgen.2024.100639", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.xgen.2024.100639"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-09-01T00:00:00Z"}}, {"id": "10.1038/ismej.2009.136", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:18:15Z", "type": "Journal Article", "created": "2009-12-24", "title": "Biogeography Of Soil Archaea And Bacteria Along A Steep Precipitation Gradient", "description": "AbstractFor centuries, biodiversity has spellbound biologists focusing mainly on macroorganism's diversity and almost neglecting the geographic mediated dynamics of microbial communities. We surveyed the diversity of soil bacteria and archaea along a steep precipitation gradient ranging from the Negev Desert in the south of Israel (<100\uffe2\uff80\uff89mm annual rain) to the Mediterranean forests in the north (>900\uffe2\uff80\uff89mm annual rain). Soil samples were retrieved from triplicate plots at five long-term ecological research stations, collected from two types of patches: plant interspaces and underneath the predominant perennial at each site. The molecular fingerprint of each soil sample was taken using terminal restriction length polymorphism of the 16S rRNA gene to evaluate the bacterial and archaeal community composition and diversity within and across sites. The difference in community compositions was not statistically significant within sites (P=0.33 and 0.77 for bacteria and archaea, respectively), but it differed profoundly by ecosystem type. These differences could largely be explained by the precipitation gradient combined with the vegetation cover: the archaeal and bacterial operational taxonomic units were unique to each climatic region, that is, arid, semiarid and Mediterranean (P=0.0001, for both domains), as well as patch type (P=0.009 and 0.02 for bacteria and archaea, respectively). Our results suggest that unlike macroorganisms that are more diverse in the Mediterranean ecosystems compared with the desert sites, archaeal and bacterial diversities are not constrained by precipitation. However, the community composition is unique to the climate and vegetation cover that delineates each ecosystem.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Geography", "Biodiversity", "15. Life on land", "Archaea", "DNA Fingerprinting", "DNA", " Ribosomal", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Cluster Analysis", "Israel", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2009.136"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2009.136", "name": "item", "description": "10.1038/ismej.2009.136", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2009.136"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-12-24T00:00:00Z"}}, {"id": "10.1038/ismej.2007.89", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:18:15Z", "type": "Journal Article", "created": "2007-10-25", "title": "The Effect Of Experimental Warming On The Root-Associated Fungal Community Of Salix Arctica", "description": "AbstractThe effect of experimental warming on the root-associated fungal community of arctic willow (Salix arctica) was studied in three distinct habitats at a tundra site in the Canadian High Arctic. Plots were passively warmed for 5\uffe2\uff80\uff937 years using open-top chambers and compared to control plots at ambient temperature. Fungal communities were assessed using terminal restriction fragment length polymorphisms. We found the following: (1) the root-associated fungal community in these high arctic tundra habitats is highly diverse; (2) site and soil characteristics are the most important drivers of community structure and (3) warming increased the density of different genotypes on individual root sections but has not (yet) affected the composition, richness or evenness of the community. The change in genotype density in the warmed plots was associated with an increase in PCR amplification efficiency, suggesting that increased C allocation belowground is increasing the overall biomass of the fungal community.
", "keywords": ["0106 biological sciences", "0301 basic medicine", "Canada", "Fungi", "Salix", "15. Life on land", "Plant Roots", "01 natural sciences", "Heating", "03 medical and health sciences", "Cluster Analysis", "DNA", " Fungal", "Ecosystem", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"], "contacts": [{"organization": "Gregory H. R. Henry, Keith N. Egger, Kei E. Fujimura,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1038/ismej.2007.89"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2007.89", "name": "item", "description": "10.1038/ismej.2007.89", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2007.89"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-10-25T00:00:00Z"}}, {"id": "10.1038/s41467-019-14197-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:18:19Z", "type": "Journal Article", "created": "2020-01-24", "title": "High-quality genome sequence of white lupin provides insight into soil exploration and seed quality", "description": "AbstractWhite lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n\uffe2\uff80\uff89=\uffe2\uff80\uff8950, 451\uffe2\uff80\uff89Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.
", "keywords": ["Repetitive Sequences", " Nucleic Acid/genetics", "0301 basic medicine", "[SDV]Life Sciences [q-bio]", "Plant Roots/genetics", "Gene Dosage", "Plant Science", "Crop", "Alkaloids/chemistry", "Plant Roots", "Gene", "Repetitive Sequences", "630", "Agricultural and Biological Sciences", "Domestication", "Soil", "Models", "Symbiotic Nitrogen Fixation in Legumes", "Gene Duplication", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_3224", "Plant Proteins/metabolism", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Genome", "Q", "http://aims.fao.org/aos/agrovoc/c_27583", "Life Sciences", "Transcriptome/genetics", "http://aims.fao.org/aos/agrovoc/c_92382", "Polymorphism", " Single Nucleotide/genetics", "Lupinus", "[SDV] Life Sciences [q-bio]", "Protein Crop", "Seeds", "http://aims.fao.org/aos/agrovoc/c_5956", "White (mutation)", "Single Nucleotide/genetics", "Sequence Analysis", "Genome", " Plant", "expression des g\u00e8nes", "http://aims.fao.org/aos/agrovoc/c_4464", "Synteny/genetics", "Evolution", "Lupin Seeds", "Science", "Centromere", "Lupinus/genetics", "Polymorphism", " Single Nucleotide", "Article", "g\u00e9nomique", "Evolution", " Molecular", "Evolution and Nutritional Properties of Lupin Seeds", "physiologie v\u00e9g\u00e9tale", "03 medical and health sciences", "Alkaloids", "Genetic", "Nucleic Acid/genetics", "Seeds/physiology", "Centromere/genetics", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Polymorphism", "Biology", "Ecology", " Evolution", " Behavior and Systematics", "Repetitive Sequences", " Nucleic Acid", "Sequence assembly", "http://aims.fao.org/aos/agrovoc/c_25189", "Ecotype", "Models", " Genetic", "g\u00e9nome", "Botany", "Molecular", "Genetic Variation", "Molecular Sequence Annotation", "Plant", "DNA", "Sequence Analysis", " DNA", "s\u00e9quence nucl\u00e9otidique", "15. Life on land", "http://aims.fao.org/aos/agrovoc/c_27527", "Agronomy", "Plant Leaves", "Evolution and Ecology of Endophyte-Grass Symbiosis", "Lupinus albus", "FOS: Biological sciences", "Genomic Structural Variation", "Plant Leaves/metabolism", "Gene expression", "Transcriptome", "am\u00e9lioration des plantes"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-14197-9.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-14197-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-14197-9", "name": "item", "description": "10.1038/s41467-019-14197-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-14197-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-24T00:00:00Z"}}, {"id": "10.1098/rstb.2018.0243", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:19:07Z", "type": "Journal Article", "created": "2019-06-03", "title": "Convergent evolution inArabidopsis halleriandArabidopsis arenosaon calamine metalliferous soils", "description": "It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species,Arabidopsis halleriandArabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in severalA. hallerigenes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.
This article is part of the theme issue \uffe2\uff80\uff98Convergent evolution in the genomics era: new insights and directions\uffe2\uff80\uff99.MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in plant genomes. While some miRNA genes are deeply conserved, the majority appear to be species-specific, raising the question of how they emerge and integrate into cellular regulatory networks. To address this question, we first performed a detailed annotation of miRNA genes in the closely related Arabidopsis halleri and A. lyrata, then evaluated their phylogenetic conservation across 87 plant species. We then characterized the process by which newly emerged miRNA genes progressively acquire the properties of \uffe2\uff80\uff9ccanonical\uffe2\uff80\uff9d miRNA genes, in terms of size and stability of the hairpin precursor, loading of their cleavage products into Argonaute proteins, and potential to regulate downstream target genes. Analysis of nucleotide polymorphism distribution along the hairpin sequence (stem, mature miRNA, terminal loop) revealed that the selective constraints on recently emerged miRNA genes were initially weak, gradually increasing toward evolutionarily conserved miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary progression toward canonical miRNAs by which a small fraction of de novo formed miRNA genes eventually integrate into \uffe2\uff80\uff9ccore\uffe2\uff80\uff9d biological processes.Plant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated byermresistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.
", "keywords": ["DNA", " Bacterial", "Nitrogen", "Molecular Sequence Data", "Colony Count", " Microbial", "104004 Chemical biology", "Soil", "Cluster Analysis", "Organic Chemicals", "Chromatography", " High Pressure Liquid", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Bacteria", "Fungi", "Biodiversity", "Methyltransferases", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Plants", "15. Life on land", "Bacterial Load", "Carbon", "104004 Chemische Biologie", "0401 agriculture", " forestry", " and fisheries", "Polymorphism", " Restriction Fragment Length"]}, "links": [{"href": "https://doi.org/10.1128/aem.00527-11"}, {"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.00527-11", "name": "item", "description": "10.1128/aem.00527-11", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.00527-11"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-11-01T00:00:00Z"}}, {"id": "10.1128/aem.69.3.1800-1809.2003", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:19:56Z", "type": "Journal Article", "created": "2003-03-06", "title": "Soil Type Is The Primary Determinant Of The Composition Of The Total And Active Bacterial Communities In Arable Soils", "description": "ABSTRACTDegradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.
", "keywords": ["Polymerase Chain Reaction", "geography", "630", "1000 Technology", "Soil", "soil type", "RNA", " Ribosomal", " 16S", "C500 - Microbiology", "genetic polymorphism", "soil analysis", "Bacteria (microorganisms)", "Soil Microbiology", "2. Zero hunger", "article", "Agriculture", "Fabaceae", "Biodiversity", "legume", "04 agricultural and veterinary sciences", "Bacterial Typing Techniques", "microbial community", "Polymorphism", " Restriction Fragment Length", "0605 Microbiology", "Electrophoresis", "16S", "570", "Conservation of Natural Resources", "productivity", "RNA 16S", "soil microorganism", "0600 Biological Sciences", "DNA", " Ribosomal", "0700 Agricultural And Veterinary Sciences", "controlled study", "community composition", "Polymorphism", "Pisum sativum", "Ecosystem", "Ribosomal", "nonhuman", "Bacteria", "bacterial flora", "land use", "DNA", "15. Life on land", "bacterial disease", "Restriction Fragment Length", "C180 - Ecology", "physiology", "RNA", "Soils", "0401 agriculture", " forestry", " and fisheries", "bioavailability"]}, "links": [{"href": "https://doi.org/10.1128/aem.69.3.1800-1809.2003"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.69.3.1800-1809.2003", "name": "item", "description": "10.1128/aem.69.3.1800-1809.2003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.69.3.1800-1809.2003"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-03-01T00:00:00Z"}}, {"id": "10.1128/aem.71.5.2713-2722.2005", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:19:56Z", "type": "Journal Article", "created": "2005-05-03", "title": "Changes In Nitrogen-Fixing And Ammonia-Oxidizing Bacterial Communities In Soil Of A Mixed Conifer Forest After Wildfire", "description": "ABSTRACTThis study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant nifH sequence types was greater in fire-impacted soils, and nifH sequences that were most closely related to those from the spore-forming taxa Clostridium and Paenibacillus were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing amoA cluster 1, 2, or 4 Nitrosospira spp. were dominant (80 to 90%) in unburned soils, while TRFs representing amoA cluster 3A Nitrosospira spp. dominated (65 to 95%) in fire-impacted soils. The dominance of amoA cluster 3A Nitrosospira spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH 3 -N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Base Sequence", "Molecular Sequence Data", "15. Life on land", "Polymerase Chain Reaction", "Fires", "Trees", "Soil", "03 medical and health sciences", "Ammonia", "Nitrogen Fixation", "Oxidoreductases", "Oxidation-Reduction", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"], "contacts": [{"organization": "Chris M. Yeager, Diana E. Northup, Susan M. Barns, Cheryl R. Kuske, Christy C. Grow,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1128/aem.71.5.2713-2722.2005"}, {"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.71.5.2713-2722.2005", "name": "item", "description": "10.1128/aem.71.5.2713-2722.2005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.71.5.2713-2722.2005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-05-01T00:00:00Z"}}, {"id": "10.1371/journal.pone.0076447", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:20:16Z", "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": "20.500.11850/345383", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:26:37Z", "type": "Journal Article", "created": "2019-06-03", "title": "Convergent evolution inArabidopsis halleriandArabidopsis arenosaon calamine metalliferous soils", "description": "It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa , which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in several A. halleri genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.
This article is part of the theme issue \uffe2\uff80\uff98Convergent evolution in the genomics era: new insights and directions\uffe2\uff80\uff99.