Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500\uffc2\uffa0bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large\uffe2\uff80\uff90scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungs\uffc3\uffa4ngen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic\uffe2\uff80\uff90dry part that has a species rich grass\uffe2\uff80\uff90dominated plant community including a high frequency of F.\uffc2\uffa0meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%\uffe2\uff80\uff9340% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.
", "keywords": ["580", "species hypothesis", "Ekologi", "0301 basic medicine", "0303 health sciences", "Ecology", "rDNA", "Biological Systematics", "15. Life on land", "03 medical and health sciences", "14. Life underwater", "ITS", "Research Articles", "clustering"]}, "links": [{"href": "https://pub.epsilon.slu.se/27699/1/eshghi-sahraei-s-et-al-220505.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.8676"}, {"href": "https://doi.org/10.1002/ece3.8676"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology%20and%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ece3.8676", "name": "item", "description": "10.1002/ece3.8676", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ece3.8676"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-01T00:00:00Z"}}, {"id": "10.3389/ffunb.2021.716385", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:21:37Z", "type": "Journal Article", "created": "2021-09-29", "title": "In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies", "description": "Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.
", "keywords": ["0301 basic medicine", "Evolutionary Biology", "0303 health sciences", "Biologisk systematik", "topology", "572", "Plant culture", "Biological Systematics", "15. Life on land", "single nuclei sequencing", "SB1-1110", "Evolutionsbiologi", "03 medical and health sciences", "genomics", "General Earth and Planetary Sciences", "Fungal Biology", "phylogenetic", "Glomeromycota", "General Environmental Science"]}, "links": [{"href": "https://pub.epsilon.slu.se/26757/1/montoliu-nerin_m_et_al_220120.pdf"}, {"href": "https://doi.org/10.3389/ffunb.2021.716385"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Fungal%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/ffunb.2021.716385", "name": "item", "description": "10.3389/ffunb.2021.716385", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/ffunb.2021.716385"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-11T00:00:00Z"}}, {"id": "10.5943/mycosphere/14/1/23", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:25:23Z", "type": "Journal Article", "created": "2024-03-21", "title": "Global consortium for the classification of fungi and fungus-like taxa", "description": "The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. 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For example, \u2018to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation\u2019, or \u2018are there too many genera in the Boletales?\u2019 and even more importantly, \u2018what should be done with the tremendously diverse \u2018dark fungal taxa?\u2019 There are undeniable differences in mycologists\u2019 perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others\u2019 work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. 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The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, \u2018to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation\u2019, or \u2018are there too many genera in the Boletales?\u2019 and even more importantly, \u2018what should be done with the tremendously diverse \u2018dark fungal taxa?\u2019 There are undeniable differences in mycologists\u2019 perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others\u2019 work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.", "keywords": ["[SDE] Environmental Sciences", "570", "Biologisk systematik", "scientific criticism", "Evolution", "[SPI] Engineering Sciences [physics]", "[SDV]Life Sciences [q-bio]", "0607 Plant Biology", "Plant Science", "Biological Systematics", "Mycology", "FATTY-ACID-COMPOSITION", "[SPI]Engineering Sciences [physics]", "taxonomy", "Behavior and Systematics", "DNA-SEQUENCE DATA", "taksonomia", "Biowissenschaften; Biologie", "NOMENCLATURE", "INCORPORATING ANAMORPHIC FUNGI", "NATURAL CLASSIFICATION", "TREE", "580", "Science & Technology", "Ecology", "IDENTIFICATION", "klasyfikacja", "classification", " nomenclature", " scientific criticism", " taxonomy", "Botany", "Botanik", "15. 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