| 1. |
- Bidartondo, Martin, et al.
(författare)
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Preserving accuracy in GenBank
- 2008
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Ingår i: Science. ; 319:5870
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
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| 3. |
- Kõljalg, Urmas, et al.
(författare)
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Towards a unified paradigm for sequence-based identification of fungi.
- 2013
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Ingår i: Molecular ecology. - : Wiley. - 1365-294X .- 0962-1083. ; 22:21, s. 5271-7
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
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| 4. |
- Abarenkov, Kessy, et al.
(författare)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 5. |
- Abarenkov, Kessy, et al.
(författare)
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The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
- 2024
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Ingår i: Nucleic Acids Research. - 0305-1048 .- 1362-4962. ; 52:D1, s. D791-D797
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Tidskriftsartikel (refereegranskat)abstract
- UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into similar to 2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms. Graphical Abstract
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| 6. |
- Bödeker, Inga, et al.
(författare)
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ClassII peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi
- 2009
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 3, s. 1387-1395
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Tidskriftsartikel (refereegranskat)abstract
- Fungal peroxidases (ClassII) have a key role in degrading recalcitrant polyphenolic compounds in boreal forest wood, litter and humus. To date, their occurrence and activity have mainly been studied in a small number of white-rot wood decomposers. However, peroxidase activity is commonly measured in boreal forest humus and mineral soils, in which ectomycorrhizal fungi predominate. Here, we used degenerate PCR primers to investigate whether peroxidase-encoding genes are present in the genomes of a wide phylogenetic range of ectomycorrhizal taxa. Cloning and sequencing of PCR products showed that ectomycorrhizal fungi from several different genera possess peroxidase genes. The new sequences represent four major homobasidiomycete lineages, but the majority is derived from Cortinarius, Russula and Lactarius. These genera are ecologically important, but consist mainly of non-culturable species from which little ecophysiological information is available. The amplified sequences contain conserved active sites, both for folding and substrate oxidation. In some Cortinarius spp., there is evidence for gene duplications during the evolution of the genus. ClassII peroxidases seem to be an ancient and a common feature of most homobasidiomycetes, including ectomycorrhizal fungi. Production of extracellular peroxidases may provide ectomycorrhizal fungi with access to nitrogen sequestered in complex polyphenolic sources. The ISME Journal (2009) 3, 1387-1395; doi: 10.1038/ismej.2009.77; published online 2 July 2009
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| 7. |
- Harder, Christoffer Bugge, et al.
(författare)
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Mycena species can be opportunist-generalist plant root invaders
- 2023
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Ingår i: Environmental Microbiology. - 1462-2912. ; 25:10, s. 1875-1893
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Tidskriftsartikel (refereegranskat)abstract
- Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of 13C/15N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published 13C/15N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.
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| 8. |
- Lithell, Cajsa, et al.
(författare)
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Mykorrhizasvamparnas näringsupptag : nyckeln till ökad förståelse för störningseffekter på svampsamhället?
- 2009
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Ingår i: Fakta. Skog. - 1400-7789.
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Annan publikation (populärvet., debatt m.m.)abstract
- • I svenska barrskogar är nästan alla trädens finrötter koloniserade av symbiotiska mykorrhizasvampar som hjälper träden att tillgodogöra sig näringsämnen i marken. • Vår kunskap om mykorrhizasvamparnas omsättning av kväve och fosfor i skogsmark bygger på studier av några få snabbväxande och lättodlade svamparter. Tyvärr är det inte alltid de lättodlade svamparterna som är vanligast, och därmed ekologiskt viktiga, ute i skogen. • Här visar vi att flera av de ekologiskt viktigaste arterna går att odla i renkultur. Alla svamparter som vi undersökt kan bilda enzymer som gör det möjligt för dem att utnyttja ett flertal olika kväve- och fosforkällor. Förmågan att ta upp olika näringsämnen varierade dock avsevärt mellan arterna. • Ökad kunskap om ektomykorrhizasvamparnas näringsupptag kan ge oss större möjligheter att förutse hur svamparna reagerar på störningar i miljön, t.ex. förändrat klimat och ökat kvävenedfall
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| 9. |
- Madigan, Andrew, et al.
(författare)
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Can Hymenoscyphus fraxineus infect hardy members of the Oleaceae other than ash species?
- 2015
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Ingår i: Forest Pathology. - : Wiley. - 1437-4781 .- 1439-0329. ; 45, s. 426-429
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Tidskriftsartikel (refereegranskat)abstract
- The interaction between the ash dieback fungus, Hymenoscyphus fraxineus, and two commonly grown members of the Oleaceae (Forsythiaxintermedia Lynwood' and Ligustrum vulgare) was investigated. Shoots were inoculated with three isolates of H.fraxineus and harvested after 2 and 10weeks. DNA was extracted from tissue collected at the point of inoculation, as well as 15mm below and above (distal), and analysed using fungal-specific ITS primers and specific primers for H.fraxineus. The fungus was frequently detected in tissue at the point of inoculation, but rarely in distal samples. There was no evidence that H.fraxineus was pathogenic on either of the two oleaceous species over the duration of the experiment.
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| 10. |
- Mikusinska, Anna, et al.
(författare)
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Response of ectomycorrhizal extramatrical mycelium production and isotopic composition to in-growth bag size and soil fauna
- 2013
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 66, s. 154-162
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Tidskriftsartikel (refereegranskat)abstract
- In-growth bags are increasingly used to study extramatrical mycelium (EMM) of ectomycorrhizal fungi in forest soils. In this paper we tested whether bag size and presence of soil fauna in bags influence the production, isotopic composition, carbon (C) and nitrogen (N) content of the EMM. Cylindrical in-growth mesh bags (2- or 5-cm-diameter; with or without openings - (1 or 2 mm), allowing faunal colonization or not) were harvested 37, 48, 81 and 283 days after installation in July and the EMM biomass was determined from elemental analyses of the extractable amount of mycelia. The occurrence of openings allowed animals to invade the bags but this did not affect the amount of EMM. We suggest further studies in this matter since the number of animals was low and variable. In the first harvest, mycelial biomass C was three times greater in 2-cm than in 5-cm-bags. After 81 days, mycelial biomass C was 54% greater in the 2-cm (54 kg ha(-1)) than in the 5-cm bags (35 kg ha(-1)). While total mycelial C did not change over winter, N content increased suggesting a role for the EMM in the storage of N from autumn to spring. The delta C-13 and delta N-15 of the EMM changed between the first three harvests. We hypothesize these changes to be mainly driven by changes in plant C and N sinks. The relation between the isotopic composition of sporocarp exploration type, plant roots and EMM is discussed. (C) 2013 Elsevier Ltd. All rights reserved.
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| 11. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.
- 2019
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Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 47:D1
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Tidskriftsartikel (refereegranskat)abstract
- UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer(ITS) region-and offers all ∼1 000000 public fungal ITS sequences for reference. These are clustered into ∼459000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
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| 12. |
- Parrent, Jeri Lynn, et al.
(författare)
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Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses
- 2009
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Conclusion: We found a strong signature of both ecological strategy and phylogeny on GH32 gene number in fungi. These data suggest that plant biotrophic fungi exhibit a wide range of ability to access plant-synthesized sucrose. Endophytic fungi are more similar to plant pathogens in their possession of GH32 genes, whereas most genomes of mycorrhizal taxa lack GH32 genes. Reliance on plant GH32 enzyme activity for C acquisition in these symbionts supports earlier predictions of possible plant control over C allocation in the mycorrhizal symbiosis.
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| 13. |
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| 14. |
- Vinichuk, Mykhailo, et al.
(författare)
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Accumulation of potassium, rubidium and caesium (Cs-133 and Cs-137) in various fractions of soil and fungi in a Swedish forest
- 2010
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 408, s. 2543-2548
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Tidskriftsartikel (refereegranskat)abstract
- Radiocaesium (Cs-137) was widely deposited over large areas of forest in Sweden as a result of the Chernobyl accident in 1986 and many people in Sweden eat wild fungi and game obtained from these contaminated forests. In terms of radioisotope accumulation in the food chain, it is well known that fungal sporocarps efficiently accumulate radiocaesium (Cs-137), as well as the alkali metals potassium (K), rubidium (Rb) and caesium (Cs). The fungi then enhance uptake of these elements into host plants. This study compared the accumulation of these three alkali metals in bulk soil, rhizosphere, soil-root interface, fungal mycelium and sporocarps of mycorrhizal fungi in a Swedish forest. The soil-root interface was found to be distinctly enriched in K and Rb compared with the bulk soil. Potassium concentrations increased in the order: bulk soil
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