| 1. |
- Crous, P. W., et al.
(author)
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Fusarium : more than a node or a foot-shaped basal cell
- 2021
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In: Studies in mycology. - : CENTRAALBUREAU SCHIMMELCULTURE. - 0166-0616 .- 1872-9797. ; :98
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Journal article (peer-reviewed)abstract
- Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
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| 2. |
- Weslien, Per, 1963, et al.
(author)
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Carrot cropping on organic soil is a hotspot for nitrous oxide emissions
- 2012
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In: Nutrient Cycling in Agroecosystems. - : Springer Science and Business Media LLC. - 1385-1314 .- 1573-0867. ; 94:2-3, s. 249-253
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Journal article (peer-reviewed)abstract
- The emissions of the greenhouse gas nitrous oxide (N2O) were measured from a non nitrogen fertilized carrot (Daucus carota ssp. sativa) field on an organic soil in Sweden during one cropping and post-harvest season. The cumulative emission during the measuring period of 149 days was 41 (±2.8) kg N2O ha−1. Dividing the measuring period into a cropping and a post-harvest period revealed that the presence of carrots strongly stimulated N2O emissions, as the emission during the cropping period was one order of magnitude higher compared to the post-harvest period. The N2O emission from the carrot field were higher than fluxes reported from cereal crop and grass production, but in the same order as reported fluxes from vegetable cropping on organic soils. In conclusion, our results indicate that the cultivation of root vegetable, such as carrots, on organic soil can be a high point source for N2O emissions.
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| 3. |
- Abarenkov, Kessy, et al.
(author)
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Protax-fungi: A web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences
- 2018
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 220:2, s. 517-525
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Journal article (peer-reviewed)abstract
- © 2018 New Phytologist Trust. Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax-fungi, a general tool for taxonomic placement of fungal internal transcribed spacer (ITS) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. With empirical data on root- and wood-associated fungi, Protax-fungi reliably identified (with at least 90% identification probability) the majority of sequences to the order level but only around one-fifth of them to the species level, reflecting the current limited coverage of the databases. Protax-fungi outperformed the Sintax and Rdb classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. We applied Protax-fungi to examine the internal consistencies of the Index Fungorum and UNITE databases. This revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. Protax-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships.
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| 4. |
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| 5. |
- Götmark, Frank, 1955, et al.
(author)
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Factors influencing presence-absence of oak (Quercus spp.) seedlings after conservation-oriented partial cutting of high forests in Sweden
- 2011
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In: Scandinavian Journal of Forest Research. - : Informa UK Limited. - 0282-7581 .- 1651-1891. ; 26, s. 136-145
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Journal article (peer-reviewed)abstract
- We studied occurrence of oak seedlings (Quercus robur L. and Q. petraea Liebl.) in 11 semi-natural oak-rich temperate forests in south Sweden after partial cutting (mean harvest; 26% of basal area). Earlier studies show that canopy openness is positively correlated with oak seedling performance. We used 20 pairs of subplots in each forest, with and without oak seedlings and matched with respect to canopy openness, to analyse other factors associated with seedling establishment and growth. The height of the ground layer (herbs and woody plants) had negative influence, i.e. higher height was associated with reduced probability of seedling occurrence. Higher soil water content had positive influence on seedling occurrence. Protection of seedlings by e.g. Rubus spp., twigs or dead wood was associated with lower seedling occurrence, but seedlings that did establish there tended to be taller. Type of ground vegetation and species composition did not differ between subplots with and without oak seedling. Thus, after conservation-oriented partial cutting of closed canopy high forests, increasing height of the ground vegetation disfavours oak seedlings (independent of canopy openness). High soil moisture favours oak seedlings, as does protected microsites for seedlings that can maintain high growth rate among their competitors.
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| 6. |
- Jayasiri, Subashini C., et al.
(author)
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The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
- 2015
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In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18
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Journal article (peer-reviewed)abstract
- Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
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| 7. |
- Jensen, Anna M, et al.
(author)
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Shrubs protect oak seedlings against ungulate browsing in temperate broadleaved forests of conservation interest: A field experiment
- 2012
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In: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 266, s. 187-193
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Journal article (peer-reviewed)abstract
- In many oak-rich temperate broadleaved forests of conservation value, high ungulate browsing pressure restricts oak regeneration. We examined the protection of oak (Quercus sp.) seedlings from browsing provided by naturally occurring shrubs in 10 forests across southern Sweden over 3 years. We planted oak seedlings in four plots in each forest; two with naturally regenerated shrubs and two with no shrubs. Ungulate browsers were excluded from two plots at each site, one with and one without shrubs. Fencing provided the best protection against ungulate browsers for the seedlings. The probability of a seedling being browsed (browsing frequency) was approximately 20% units lower for individuals growing among shrubs than for individuals growing in the absence of shrubs. When browsing did occur, the intensity (measured as a reduction in height growth) was significantly lower for seedlings in shrubs. Regression analyses showed that browsing frequency increased on seedlings in tall shrubs, and decreased on seedlings that had been browsed previously. Browsing intensity decreased if the seedling grew in tall and dense shrubs. Browsing frequency and intensity increased on oak seedlings that over topped the shrub canopy. Increased abundance of the prickled Rubus idaeus and Rubus fruticosus coll. in plots with shrubs did not affect browsing frequency and intensity. Two and a half years after planting, oak seedling mortality increased by the presence of shrubs. Although shrubs restricted oak seedling growth, we conclude that shrubs initially facilitated oak regeneration by concealment, and subsequently by numeric dilution. Shrubs may be used to reduce browsing damages if long-term evaluation indicates a net positive outcome for oak survival and growth.
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| 8. |
- Klemedtsson, Åsa Kasimir, 1956
(author)
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Lustgasavgång från jordbruksmark
- 2009
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Reports (other academic/artistic)abstract
- Regeringen fattade den 26 juni 2008 beslut om ändring av Jordbruksverkets regleringsbrev rörande uppdraget ”Åtgärdsprogram för minskade växtnäringsförluster” vilket ersätts av uppdraget; ”Jordbruksverket ska efter samråd med berörda myndigheter och organisationer lämna förslag till ett handlingsprogram för minskade växtnärings- och växthusgasförluster från jordbruket för perioden 2011 till och med 2016 med utblick till 2020.” Framtagandet av ett handlingsprogram inom jordbruksverket bedrivs som ett projekt vilket ska utgöra underlag för vidare beslut och genomförande. Föreslagna åtgärder och styrmedel ska vara realistiska, genomförbara och kostnadseffektiva. Förslag till nytt handlingsprogram ska vara färdigt våren 2010. Som ett led i projektet gavs ett uppdrag till Åsa Kasimir Klemedtsson att utreda och ge förslag till möjliga åtgärder i jordbruket som kan minska lustgasavgången från jordbruksmark. Rapporteringen följer de anvisningar som gavs.
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| 9. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Top 50 most wanted fungi
- 2016
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 12, s. 29-40
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Journal article (peer-reviewed)abstract
- Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond “Fungi”. There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.
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| 10. |
- Tedersoo, Leho, et al.
(author)
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Novel soil-inhabiting clades fill gaps in the fungal tree of life
- 2017
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In: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5
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Journal article (peer-reviewed)abstract
- Background - Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. Results - We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. Conclusions - This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
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