Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

Andrey Yurkov; Artur Alves; Feng-Yan Bai; Kyria Boundy-Mills; Pietro Buzzini; Neža Čadež; Gianluigi Cardinali; Serge Casaregola; Vishnu Chaturvedi; Valérie Collin; Jack W Fell; Victoria Girard; Marizeth Groenewald; Ferry Hagen; Chris Todd Hittinger; Aleksey V Kachalkin; Markus Kostrzewa; Vassili Kouvelis; Diego Libkind; Xinzhan Liu; Thomas Maier; Wieland Meyer; Gábor Péter; Marcin Piątek; Vincent Robert; Carlos A Rosa; Jose Paulo Sampaio; Matthias Sipiczki; Marc Stadler; Takashi Sugita; Junta Sugiyama; Hiroshi Takagi; Masako Takashima; Benedetta Turchetti; Qi-Ming Wang; Teun Boekhout

doi:10.1186/s43008-021-00067-x

Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

IMA Fungus. 2021 Jul 13;12(1):18. doi: 10.1186/s43008-021-00067-x.

Authors

Andrey Yurkov¹, Artur Alves², Feng-Yan Bai³, Kyria Boundy-Mills⁴, Pietro Buzzini⁵, Neža Čadež⁶, Gianluigi Cardinali⁷, Serge Casaregola⁸, Vishnu Chaturvedi⁹, Valérie Collin¹⁰, Jack W Fell¹¹, Victoria Girard¹⁰, Marizeth Groenewald¹², Ferry Hagen¹², Chris Todd Hittinger¹³, Aleksey V Kachalkin^{14

15}, Markus Kostrzewa¹⁶, Vassili Kouvelis¹⁷, Diego Libkind¹⁸, Xinzhan Liu³, Thomas Maier¹⁶, Wieland Meyer^{19

20

21

22}, Gábor Péter²³, Marcin Piątek²⁴, Vincent Robert¹², Carlos A Rosa²⁵, Jose Paulo Sampaio^{26

27}, Matthias Sipiczki²⁸, Marc Stadler²⁹, Takashi Sugita³⁰, Junta Sugiyama^{31

32}, Hiroshi Takagi³³, Masako Takashima³⁴, Benedetta Turchetti⁵, Qi-Ming Wang^{3

35}, Teun Boekhout^{12

36}

Affiliations

¹ Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany. andrey.yurkov@dsmz.de.
² Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
³ State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China.
⁴ Department of Food Science and Technology, Phaff Yeast Culture Collection, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
⁵ Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
⁶ Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ul. 101, 1000, Ljubljana, Slovenia.
⁷ Department of Pharmaceutical Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
⁸ Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
⁹ Mycology Laboratory, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA.
¹⁰ BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
¹¹ Emeritus Professor, Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Key Biscayne, FL, 33149, USA.
¹² Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
¹³ Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 1552 University Avenue, Madison, WI, 53726-4084, USA.
¹⁴ Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1-12, 119991, Moscow, Russia.
¹⁵ All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms (IBPM RAS), Russian Academy of Sciences, Prospect Nauki 5, 142290, Puschino, Russia.
¹⁶ Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359, Bremen, Germany.
¹⁷ Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701, Athens, Greece.
¹⁸ Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) CONICET - Universidad Nacional del Comahue, Quintral 1250, San Carlos de Bariloche, Rio Negro, Argentina.
¹⁹ Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia.
²⁰ Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, 2006, Australia.
²¹ Westmead Institute for Medical Research, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia.
²² Westmead Hospital (Research and Education Network), Darcy Rd, Westmead, NSW, 2145, Australia.
²³ National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, Budapest, H-1118, Hungary.
²⁴ Department of Mycology, W. Szafer Institute of Botany of the Polish Academy of Sciences, Lubicz ul. 46, 31-512, Kraków, Poland.
²⁵ Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, 31270-901, Brazil.
²⁶ UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Largo da Torre, 2825-149, Caparica, Portugal.
²⁷ Departamento de Ciências da Vida, PYCC - Portuguese Yeast Culture Collection, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Largo da Torre, 2825-149, Caparica, Portugal.
²⁸ Department of Genetics and Applied Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4010, Hungary.
²⁹ Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
³⁰ Department of Microbiology, Meiji Pharmaceutical University, 2 Chome-522-1 Noshio, Kiyose, Tokyo, 204-8588, Japan.
³¹ Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan.
³² TechnoSuruga Laboratory Co., Ltd., 388-1, Nagasaki, Shimuzu, Shizuoka, 424-0065, Japan.
³³ Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
³⁴ Laboratory of Yeast Systematics, Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
³⁵ College of Life Sciences, Hebei University, 180 Wusi Dong Road, Lian Chi District, Baoding City, Hebei Province, 071002, People's Republic of China.
³⁶ Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, The Netherlands.

Abstract

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.

Keywords: Culture collection; Metabolically inactive; Nomenclatural type; Typification; Viable strains.