Author
Judd M. Curtis
Bio: Judd M. Curtis is an academic researcher from Clark University. The author has contributed to research in topics: Agaricomycotina & Fungal genetics. The author has an hindex of 3, co-authored 3 publications receiving 2294 citations.
Topics: Agaricomycotina, Fungal genetics, Monophyly, Paraphyly, Marine fungi
Papers
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Duke University1, Oregon State University2, Clark University3, Natural History Museum4, University of Minnesota5, Field Museum of Natural History6, Kaiserslautern University of Technology7, University of Arizona8, New York Botanical Garden9, University of Iowa10, Technische Universität Darmstadt11, University of Maine12, United States Department of Agriculture13, University of Georgia14, University of Alabama15, University of California, Berkeley16, University of Kansas17, Aberystwyth University18, West Virginia University19, Washington State University20, Harvard University21, University of North Carolina at Chapel Hill22, Centraalbureau voor Schimmelcultures23, University of Tennessee24, Okayama University25, University of Kassel26, Brandon University27, Pennsylvania State University28, Leibniz Association29, University of Hamburg30, Royal Botanic Garden Edinburgh31
TL;DR: It is indicated that there may have been at least four independent losses of the flagellum in the kingdom Fungi, and the enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.
Abstract: The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.
1,682 citations
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Clark University1, Duke University2, Agricultural Research Service3, University of Toronto4, Chinese Academy of Sciences5, University of Washington6, State University of New York at Cortland7, Department of Environment and Conservation8, University of Tennessee9, United States Forest Service10, National University of Cordoba11, San Francisco State University12, Utah State University13, University of California, Berkeley14
TL;DR: An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix, with at least 11 origins of the ectomycorrhizal habit appear to have evolved in the AgARicales.
Abstract: An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes re- covered six major clades, which are recognized informally and labeled the Agaricoid, Tricholoma- toid, Marasmioid, Pluteoid, Hygrophoroid and Plica- turopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families,
473 citations
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Clark University1, University of British Columbia2, University of Gothenburg3, University of Tennessee4, Duke University5, University of Washington6, Oregon State University7, University of Kassel8, University of Minnesota9, University of Copenhagen10, Chinese Academy of Sciences11, State University of New York at Cortland12, Okayama University13, University of Turku14
TL;DR: Strong boostrap support and significant posterior probabilities for the first time for the following monophyletic groups are produced, particularly for deep internodes of Basidiomycota, which have been difficult to resolve with confidence using nrDNA data alone.
351 citations
Cited by
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Conrad L. Schoch1, Keith A. Seifert, Sabine M. Huhndorf2, Vincent Robert3 +157 more•Institutions (59)
TL;DR: Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation.
Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
4,116 citations
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TL;DR: An enhanced understanding of the skin microbiome is necessary to gain insight into microbial involvement in human skin disorders and to enable novel promicrobial and antimicrobial therapeutic approaches for their treatment.
Abstract: The skin is the human body's largest organ, colonized by a diverse milieu of microorganisms, most of which are harmless or even beneficial to their host. Colonization is driven by the ecology of the skin surface, which is highly variable depending on topographical location, endogenous host factors and exogenous environmental factors. The cutaneous innate and adaptive immune responses can modulate the skin microbiota, but the microbiota also functions in educating the immune system. The development of molecular methods to identify microorganisms has led to an emerging view of the resident skin bacteria as highly diverse and variable. An enhanced understanding of the skin microbiome is necessary to gain insight into microbial involvement in human skin disorders and to enable novel promicrobial and antimicrobial therapeutic approaches for their treatment.
2,279 citations
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TL;DR: It is shown that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts, and key questions for future work in endophyte biology are highlighted.
Abstract: Summary 1 Summary All plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 yr of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups (clavicipitaceous (C) and nonclavicipitaceous (NC)) have been discriminated based on phylogeny and life history traits. Here, we show that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology.
2,278 citations
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Clark University1, National Institutes of Health2, Louisiana State University3, CABI4, Umeå University5, Field Museum of Natural History6, Duke University7, University of Minnesota8, University of Alabama9, Oregon State University10, Centraalbureau voor Schimmelcultures11, United States Department of Agriculture12, University of Tübingen13, Max Planck Society14, University of Florida15, Pennsylvania State University16, Aberystwyth University17, Complutense University of Madrid18, University of Oslo19, University of Hong Kong20, University of Tartu21, University of Gothenburg22, University of Kansas23, University of Maine24, University of Illinois at Urbana–Champaign25, Royal Ontario Museum26, Georgia State University27, Estonian University of Life Sciences28, Washington State University29, Nova Southeastern University30, Ludwig Maximilian University of Munich31, University of Western Ontario32, Uppsala University33, Brandon University34, Royal Botanic Garden Edinburgh35, State University of New York at Purchase36, Boise State University37, Cornell University38
TL;DR: A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community.
2,096 citations
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Clark University1, United States Department of Energy2, University of Minnesota3, Aix-Marseille University4, Spanish National Research Council5, Oregon State University6, University of Cincinnati Academic Health Center7, Utrecht University8, University of Zaragoza9, Duke University10, United States Department of Agriculture11, University of Warsaw12, University of Tokyo13, Nancy-Université14, University of Göttingen15, Pontifical Catholic University of Chile16, University of Helsinki17, Concordia University Wisconsin18, Vanderbilt University19, University of Wisconsin-Madison20, Swedish University of Agricultural Sciences21, Universidad Pública de Navarra22, Swansea University23
TL;DR: Comparative analyses of 31 fungal genomes suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species.
Abstract: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
1,396 citations