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      Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)

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      1 , 2 , 3 , 4 , 5 , 6 , 1 , 2 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 12 , 13 , 14 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 1 , 2 , 27 , 19 , 20 , 28 , 29 , 30 , 1 , 2 , 31 , 19 , 20 , 5 , 32 , 32
      MycoKeys
      Pensoft Publishers
      Indoor mycobiome, built environment, molecular identification, fungi, taxonomy, systematics, sequence annotation, metadata, open data

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          Abstract

          Abstract

          Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi – whether transient visitors or more persistent residents – may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions – such as country and host/substrate of collection – are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10–11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes – including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences – were implemented in the UNITE database for molecular identification of fungi ( https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium , Talaromyces , Cladosporium , Acremonium , and Alternaria , all of them of significant importance in both culture-based and culture-independent surveys of the built environment.

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          Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances

          The indoor microbiome is a complex system that is thought to depend on dispersal from the outdoor biome and the occupants' microbiome combined with selective pressures imposed by the occupants' behaviors and the building itself. We set out to determine the pattern of fungal diversity and composition in indoor air on a local scale and to identify processes behind that pattern. We surveyed airborne fungal assemblages within 1-month time periods at two seasons, with high replication, indoors and outdoors, within and across standardized residences at a university housing facility. Fungal assemblages indoors were diverse and strongly determined by dispersal from outdoors, and no fungal taxa were found as indicators of indoor air. There was a seasonal effect on the fungi found in both indoor and outdoor air, and quantitatively more fungal biomass was detected outdoors than indoors. A strong signal of isolation by distance existed in both outdoor and indoor airborne fungal assemblages, despite the small geographic scale in which this study was undertaken (<500 m). Moreover, room and occupant behavior had no detectable effect on the fungi found in indoor air. These results show that at the local level, outdoor air fungi dominate the patterning of indoor air. More broadly, they provide additional support for the growing evidence that dispersal limitation, even on small geographic scales, is a key process in structuring the often-observed distance–decay biogeographic pattern in microbial communities.
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            Identification and nomenclature of the genus Penicillium

            Penicillium is a diverse genus occurring worldwide and its species play important roles as decomposers of organic materials and cause destructive rots in the food industry where they produce a wide range of mycotoxins. Other species are considered enzyme factories or are common indoor air allergens. Although DNA sequences are essential for robust identification of Penicillium species, there is currently no comprehensive, verified reference database for the genus. To coincide with the move to one fungus one name in the International Code of Nomenclature for algae, fungi and plants, the generic concept of Penicillium was re-defined to accommodate species from other genera, such as Chromocleista, Eladia, Eupenicillium, Torulomyces and Thysanophora, which together comprise a large monophyletic clade. As a result of this, and the many new species described in recent years, it was necessary to update the list of accepted species in Penicillium. The genus currently contains 354 accepted species, including new combinations for Aspergillus crystallinus, A. malodoratus and A. paradoxus, which belong to Penicillium section Paradoxa. To add to the taxonomic value of the list, we also provide information on each accepted species MycoBank number, living ex-type strains and provide GenBank accession numbers to ITS, β-tubulin, calmodulin and RPB2 sequences, thereby supplying a verified set of sequences for each species of the genus. In addition to the nomenclatural list, we recommend a standard working method for species descriptions and identifications to be adopted by laboratories working on this genus.
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              Towards an integrated phylogenetic classification of the Tremellomycetes

              Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained.
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                Author and article information

                Journal
                MycoKeys
                MycoKeys
                MycoKeys
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2018
                8 January 2018
                : 28
                : 65-82
                Affiliations
                [1 ] Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
                [2 ] Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
                [3 ] The James Hutton Institute and University of Aberdeen, Aberdeen, United Kingdom
                [4 ] Plant and Microbial Biology, University of California, 94720 Berkeley, California, USA
                [5 ] Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
                [6 ] Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
                [7 ] Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
                [8 ] Department of Plant Pathology & Microbiology and Institute of Integrative Genome Biology, University of California, Riverside, Riverside 92501, CA, USA
                [9 ] Université catholique de Louvain, Earth and Life Institute, Applied Microbiology, BCCM/MUCL, Louvain-la-Neuve, Belgium
                [10 ] Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA
                [11 ] Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo Japan 184-8584
                [12 ] Sydney Medical School-Westmead Hospital, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney, Australia
                [13 ] University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia
                [14 ] Westmead Institute for Medical Research, Westmead, Australia
                [15 ] Institute of Botany, Nature Research Centre, Žaliųjų ežerų Str. 49, 08406 Vilnius, Lithuania
                [16 ] Bundesanstalt für Materialforschung und -prüfung (BAM), Department 4. Materials & Environment, Unter den Eichen 87, 12205 Berlin, Germany
                [17 ] School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
                [18 ] UCIBIO-REQUIMTE, DCV, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
                [19 ] Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
                [20 ] Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
                [21 ] Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
                [22 ] Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i, Prague, Czech Republic
                [23 ] BCCM/IHEM, Scientific Institute of Public Health WIV-ISP, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
                [24 ] ATCC, 10801 University Blvd., Manassas, Virginia 20110, USA
                [25 ] Sporometrics, 219 Dufferin Street, Suite 20C, Toronto, Ontario Canada, M6K 1Y9
                [26 ] Dalla Lana School of Public Health, University of Toronto, Health Sciences Building, 155 College Street, 6th floor, Toronto, Ontario Canada, M5T 3M7
                [27 ] Evangelisches Schulzentrum Martinschule, Max-Planck-Str. 7, 17491 Greifswald, Germany
                [28 ] Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood 0121, Pretoria, South Africa
                [29 ] Steinbeis-Innovationszentrum, Organismische Mykologie und Mikrobiologie, Vor dem Kreuzberg 17, 72070 Tübingen, Germany
                [30 ] Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
                [31 ] Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, D-16775 Stechlin, Germany
                [32 ] University of Tartu, Tartu, Estonia
                Author notes
                Corresponding author: R. Henrik Nilsson ( henrik.nilsson@ 123456bioenv.gu.se )

                Academic editor: J. Geml

                Article
                10.3897/mycokeys.28.20887
                5804120
                474a31fa-e13f-4cab-8d73-e374b4d000db
                R. Henrik Nilsson, Andy F. S. Taylor, Rachel I. Adams, Christiane Baschien, Johan Bengtsson-Palme, Patrik Cangren, Claudia Coleine, Heide-Marie Daniel, Sydney I. Glassman, Yuuri Hirooka, Laszlo Irinyi, Reda Iršėnaitė, Pedro M. Martin-Sanchez, Wieland Meyer, Seung-Yoon Oh, Jose Paulo Sampaio, Keith A. Seifert, Frantisek Sklenář, Dirk Stubbe, Sung-Oui Suh, Richard Summerbell, Sten Svantesson, Martin Unterseher, Cobus M. Visagie, Michael Weiss, Joyce HC Woudenberg, Christian Wurzbacher, Silke Van den Wyngaert, Neriman Yilmaz, Andrey Yurkov, Urmas Kõljalg, Kessy Abarenkov

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 9 September 2017
                : 12 November 2017
                Funding
                Alfred P. Sloan Foundation Stiftelsen Olle Engkvist Byggmästare Stiftelsen Lars Hiertas Minne Kapten Carl Stenholms Donationsfond Birgit och Birger Wålhströms Minnesfond European Research Council
                Categories
                Research Article

                indoor mycobiome,built environment,molecular identification,fungi,taxonomy,systematics,sequence annotation,metadata,open data

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