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      The Amsterdam Declaration on Fungal Nomenclature

      research-article
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      IMA Fungus : The Global Mycological Journal
      Nationaal Herbarium Nederland & Centraallbureau voor Schimmelcultures
      Anamorph, Article 59, BioCode, Candidate species, Environmental sequences, International Code of Botanical Nomenclature, MycoCode, Pleomorphic fungi, Teleomorph

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          Abstract

          The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19–20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.

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          Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes.

          The International Committee on Systematic Bacteriology recommended that the category Candidatus, recently proposed by Murray and Schleifer (Int. J. Syst. Bacteriol. 44:174-176, 1994) to record the properties of putative taxa of procaryotes, should be implemented. This category should be used for describing procaryotic entities for which more than a mere sequence is available but for which characteristics required for description according to the International Code of Nomenclature of Bacteria are lacking. In addition to genomic information, such as sequences apt to determine the phylogenetic position of the organism, all information, including structural, metabolic, and reproductive features, should be included in the description of a provisional taxon, together with the natural environment in which the organism can be identified by in situ hybridization or other similar techniques for cell identification.
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            'Candidatus Planktophila limnetica', an actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton.

            Actinobacteria often constitute a large fraction of the bacterioplankton in freshwater systems. Cultivation-independent methods have revealed that the so-called acI lineage frequently represents the most numerous taxon among assemblages of freshwater Actinobacteria and even among total freshwater bacterioplankton. Bacteria affiliated with this uncultivated lineage have been detected in freshwater habitats located in various continents and climatic zones but have never been found among terrestrial or offshore marine systems. So far, this ecologically important lineage of freshwater Actinobacteria is not represented by a recognized taxon. In this study, we established a stable mixed culture containing a strain affiliated with the acI lineage from a freshwater lake in Austria. The proportion of the strain in the culture could be increased by manipulation of the medium composition by more than one order of magnitude, however all subsequent attempts to isolate this strain into pure culture were unsuccessful. Some of the phenotypic traits of this acI strain were determined and its taxonomic position within the Actinobacteria was analysed. Phylogenetic analysis of this organism's 16S rRNA gene revealed a distant relationship with cultivated organisms and recognized species (89 % gene sequence similarity with the latter). Furthermore, this analysis did not support a clear assignment of the strain to any of the recognized families within the phylum Actinobacteria. It is suggested that a candidate taxon, 'Candidatus Planktophila limnetica' is established to represent this strain.
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              Author and article information

              Journal
              IMA Fungus
              IMA Fungus
              IMA Fungus
              IMA Fungus : The Global Mycological Journal
              Nationaal Herbarium Nederland & Centraallbureau voor Schimmelcultures
              2210-6340
              2210-6359
              7 June 2011
              June 2011
              : 2
              : 1
              : 105-112
              Affiliations
              [1 ]Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, E-28040 Madrid, Spain; and Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK;
              [2 ]CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; p.crous@cbs.knaw.nl.
              [3 ]National Mycological Herbarium, Agriculture and Agri-Food Canada, Neatby Building, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada.
              [4 ]Herbarium, University of California Berkeley, 1001 Valley Life Sciences Building 2465, Berkeley, CA 94720-2465, USA.
              [5 ]Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
              [6 ]Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield 0028, Pretoria 0002, South Africa.
              [7 ]Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, İzmir, Turkey.
              [8 ]Department of Plant Pathology and Crop Physiology, Louisiana State University, Agricultural Center, 302 Life Sciences Building, Baton Rouge, LA 70803, USA.
              [9 ]Department of Biology, Trakya University, 22030 Edirne, Turkey.
              [10 ]State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No.3, 1st Beichen West Road, Chaoyang District, Beijing 100101, China.
              [11 ]AG Geobotanik, Ruhr-Universität Bochum, Universitätsstraße 150, D-44780 Bochum, Germany.
              [12 ]Department of Biology, Anadolu University, TR-26470 Eskisehir, Turkey.
              [13 ]Landcare Research, Private Bag 92170, Auckland 1142, New Zealand.
              [14 ]School of Biological Sciences and Biotechnology, Murdoch University, South St, Perth, 6150, Australia.
              [15 ]Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Universitaetsplatz 4, A 8010 Graz, Austria.
              [16 ]Key Laboratory of Systematic Mycology & Lichenology, Institute of Microbiology, Chinese Academy of Sciences, No.10, North 4 th Ring Road West (BeiSiHuanXiLu), HaiDian District, Beijing 100190, China.
              [17 ]CABI Europe – UK and Royal Botanic Gardens Kew, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.
              [18 ]BCCM/MUCL, Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Croix du Sud 3, bte 6, B-1348 Louvain-la-Neuve, Belgium.
              [19 ]Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, 1060 Vienna, Austria.
              [20 ]School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
              [21 ]RSMAS/University of Miami, 4600 Rickenbacker Causeway, Key Biscayne, Fl 33149, USA.
              [22 ]Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Søltofts Plads B. 221, DK-2800 Kgs. Lyngby, Denmark.
              [23 ]Fusarium Research Center, Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA.
              [24 ]National Herbarium of the Netherlands, Netherlands Centre for Biodiversity Naturalis, Leiden University, P.O. Box 9514, Einsteinweg 2, 2300 RA Leiden, The Netherlands.
              [25 ]Departament of Genetics, Federal University of Parana Curitiba – Brazil, PO Box 19071, 815310990 Brazil.
              [26 ]Grain Research Laboratory, Canadian Grain Commission, 1404-303 Main Street, Winnipeg, Manitoba R3C 3G8, Canada.
              [27 ]Plant Protection Service, P.O. Box 9102, 6700 HC Wageningen, The Netherlands.
              [28 ]5 Rue de la Huchette, 61400 Mauves sur Huisne, France.
              [29 ]Biology Department, Clark University, Worcester, MA 01610, USA.
              [30 ]National Academy of Agricultural Science, Suwon, 441-707, Korea.
              [31 ]Department of Botany, The Field Museum, 400 South Lake Shore Drive, Chicago, IL 60605-2496, USA.
              [32 ]PO Box 58, Bandoo Post Office, Muang, Chiang Rai 57100, Thailand.
              [33 ]Department of Biology, Faculty of Science, Istanbul University, 34134 Vezneciler-Istanbul, Turkey.
              [34 ]CABI - Europe, Bakeham Lane, Egham, Surrey TW20 9TY, UK.
              [35 ]Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Street, EE-51005 Tartu, Estonia.
              [36 ]National Center for Agricultural Utilization Research, ARS, USDA, 1815 North University Street, Peoria, IL 61604-3999 USA.
              [37 ]Regional Association for Health and Animal Identification, Drève du Prophète 2, B-7000 Mons, Belgium.
              [38 ]Molecular Mycology Research Laboratory, Westmead Millennium Institute, Sydney Medical School - Westmead, University of Sydney Centre for Infectious Diseases and Microbiology, ICPMR, Level 3, Room 3114A, Darcy Road, Westmead Hospital, Westmead, NSW 2145, Australia.
              [39 ]Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970, USA.
              [40 ]Cybertruffle, 4 Esk Terrace, Whitby, North Yorkshire YO21 1PA, UK; CAB InternationaI, Bakeham Lane, Egham, Surrey, TW20 9TY, UK.
              [41 ]Mashhad University of Medical Sciences, Mashhad, Iran.
              [42 ]6720 NW Skyline Boulevard, Portland, OR 97229-1309, USA.
              [43 ]All-Russian Collection of Microorganisms, G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Prospect Nauki 5, Pushchino, Russia 142290.
              [44 ]Department of Biology, Faculty of Science, Anadolu University, TR-26470 Eskişehir, Turkey.
              [45 ]Department of Microbiology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7025, SE-750 07, Uppsala, Sweden.
              [46 ]Agricultural Institute of Slovenia, Hacquetova 17, 1000 Ljubljana, Slovenia.
              [47 ]Plant Pathology Herbarium (BRIP), Ecosciences Precinct, Department of Employment, Economic Development and Innovation, 41 Boggo Road, Dutton Park, Qld 4102, Australia.
              [48 ]Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
              [49 ]Biology Department, Faculty of Arts and Sciences, Celal Bayar University, 45140 Muradiye /Manisa, Turkey.
              [50 ]Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt (Main), Germany; and Institute of Ecology, Evolution and Diversity, Goethe University, Siesmayerstrasse 70, D-60323 Frankfurt (Main), Germany.
              [51 ]Basic and Industrial Microbiology Section, Biology Department, Ege University, Bornova/Izmir, Turkey.
              [52 ]Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Közép fasor 52, Hungary.
              [53 ]Laboratorio de Taxonomía y Ecología de Hongos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, A.A.1226 Medellín, Colombia.
              [54 ]AG Geobotanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany.
              [55 ]Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA.
              Author notes
              corresponding author e-mail: d.hawksworth@ 123456nhm.ac.uk .
              [*]

              The first eight authors undertook the finalization of this text, taking into account comments and suggestions from the others listed here.

              Article
              10.5598/imafungus.2011.02.01.14
              3317370
              22679594
              06692b3f-92dd-43e2-b49c-abc7672f43e4
              © 2011 International Mycological Association

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              Categories
              Article

              Plant science & Botany
              teleomorph,pleomorphic fungi,anamorph,environmental sequences,biocode,international code of botanical nomenclature,mycocode,candidate species,article 59

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