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Lichens are the archetypal symbiosis and the one for which the term was coined. Although application of shotgun sequencing techniques has shown that many lichen symbioses can harbour more symbionts than the canonically recognized fungus and photobiont, no global census of lichen organismal composition has been undertaken. Here, we analyze the genome content of 437 lichen metagenomes from six continents, and show that four bacterial lineages occur in the majority of lichen symbioses, at a frequency on par with algal photobionts. A single bacterial genus,Lichenihabitans, occurs in nearly one-third of all lichens sampled. Genome annotations from the most common lichen bacterial symbionts suggest they are aerobic anoxygenic photoheterotrophs and produce essential vitamins, but do not fix nitrogen. We also detected secondary basidiomycete symbionts in about two-thirds of analyzed metagenomes. Our survey suggests a core set of four to seven microbial symbionts are involved in forming and maintaining lichen symbioses.

The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex and symbiotic lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal inLetharia. Here, we used genomic data from a pure culture and from thalli, together with a PCR survey of the MAT locus, to infer the genome organization and reproduction inLetharia. We found that the read count variation in the fourLethariaspecimens, including the pure culture derived from a single sexual spore ofL. lupina, is consistent with haploidy. By contrast, theL. lupinaread counts from a thallus’ metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America forL. vulpinaandL. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe forL. vulpina, consistent with predominant asexuality. Taken together, we propose thatLethariafungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are rare hybrids betweenL. lupinaand an unknownLetharialineage, reconciling classic systematic and genetic studies with recent genomic observations.

Tropical mountains and especially their forests are hot spots of biodiversity threatened by human population pressure and climate change. The diversity of lichens in tropical Africa is especially poorly known. Here we use the mtSSU and nuITS molecular markers together with morphology and ecology to assess Leptogium (Peltigerales, Ascomycota) diversity in the tropical mountains of Taita Hills and Mt. Kasigau in Kenya and Mt. Kilimanjaro in Tanzania. The sampled habitats cover a wide range of ecosystems from savanna to alpine heath vegetation and from relatively natural forests to agricultural environments and plantation forests. We demonstrate that Leptogium diversity in Africa is much higher than previously known and provide preliminary data on over 70 putative species, including nine established species previously known from the area and over 60 phylogenetically, morphologically, and/or ecologically defined Operational Taxonomic Units (OTUs). Many traditional species concepts are shown to represent morphotypes comprised of several taxa. Many of the species were only found from specific ecosystems and/or restricted habitats and are thus threatened by ongoing habitat fragmentation and degradation of the natural environment. Our results emphasize the importance of molecular markers in species inventories of highly diverse organism groups and geographical areas.

Dimorphism is a widespread feature of tremellalean fungi in general, but a little-studied aspect of the biology of lichen-associated Tremella. We show that Tremella macrobasidiata and Tremella variae have an abundant and widespread yeast stage in their life cycles that occurs in Lecanora lichens. Their sexual filamentous stage is restricted to a specific lichen: T. macrobasidiata only forms basidiomata on Lecanora chlarotera hymenia and T. variae only on Lecanora varia thalli. However, the yeast stage of T. macrobasidiata is less specific and can occur in L. varia lichens, whilst all life stages of T. variae may be specific to L. varia. Contrary to the hyphal stages, the yeasts are distributed across the thalli and hymenia of Lecanora lichens, and not limited to specimens with basidiomata. Tremella macrobasidiata was present in all studied L. chlarotera, and in 59% of L. varia specimens. Only in 8% of the L. varia thalli could none of the two Tremella species be detected. Our results indicate that lichen-associated Tremella may be much more abundant and widespread than previously assumed leading to skewed estimations about their distribution ranges and lichen specificity, and raise new questions about their biology, ecology and function in the symbiosis.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN. Publisher’s Note A first version of this text was prepared by the first eight authors and the last one, given here. The other listed co-authors in the article PDF support the content, and their actual contributions varied from only support to additions that substantially improved the content. The full details of all co-authors, with their affiliations, are included in Supplementary Table 1 after p.175 of the article for reasons of clarity and space. Slavomír Adamčík Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Teuvo Ahti Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland M. Catherine Aime Purdue University, 915 W. State St., West Lafayette, Indiana 47907, U.S.A. A. Martyn Ainsworth Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom László Albert Hungarian Mycological Society, 1087 Könyves Kálmán krt. 40, Budapest, Hungary Edgardo Albertó Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, Universidad Nacional de San Martin-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina Alberto Altés García Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Dmitry Ageev SIGNATEC Ltd., 630090, Novosibirsk, Akademgorodok (Novosibirsk Scientific Center), Inzhenernaya str., 22, Russia Reinhard Agerer Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany Begona Aguirre-Hudson Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom Joe Ammirati University of Washington, Seattle, Washington 98195-1800, U.S.A. Harry Andersson Eichhahnweg 29a, 38108 Braunschweig, Germany Claudio Angelini Jardín Botánico Nacional Dr. Rafael Ma. Moscoso, Apartado 21-9, Santo Domingo, Dominican Republic Vladimír Antonín Moravian Museum, Zeny trh 6, 659 37 Brno, Czech Republic Takayuki Aoki Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan André Aptroot ABL Herbarium, G.v.d.Veenstraat 107, 3762 XK Soest, The Netherlands Didier Argaud 40 rue du Justemont, 57290 Fameck, France Blanca Imelda Arguello Sosa Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Ciudad Victoria, Tamaulipas, Mexico Arne Aronsen Torødveien 54, 3135 Torød, Norway Ulf Arup Biological Museum, Lund University, Box 117, 221 00 Lund, Sweden Bita Asgari Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, Tehran, Iran Boris Assyov Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Str., 1113 Sofia, Bulgaria Violeta Atienza Facultad de Ciencias Biológicas, Universitat de València, C/Dr Moliner 50, 46100, Burjasot, Valencia, Spain Ditte Bandini Panoramastr 47, 69257 Wiesenbach, Germany João Luís Baptista-Ferreira Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal Hans-Otto Baral Blaihofstr. 42, 72074 Tübingen, Germany Tim Baroni The State University of New York, 340 Bowers Hall, P.O. Box 2000, Cortland, New York 13045, U.S.A. Robert Weingart Barreto Universidade Federal de Viçosa, 36570-000, Viçosa, Minas Gerais, Brazil Henry Beker (1) Royal Holloway, University of London, United Kingdom; (2) Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Ann Bell 45 Gurney Road, Lower Hutt, New Zealand Jean-Michel Bellanger CEFE UMR5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, INSERM, 1919 Route de Mende, 34293 Montpellier Cédex 5, France Francesco Bellù Naturmusem of Bolzano, CP 104, 39100, Bolzano, Italy Martin Bemmann Kleingemünderstraße 111, 69118 Heidelberg, Germany Mika Bendiksby NTNU, University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway Egil Bendiksen Norwegian Institute for Nature Research, Gaustadalleen 21, 0349 Oslo, Norway Katriina Bendiksen Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway Lajos Benedek Szent Istvan University, Hungary Anna Bérešová-Guttová Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Franz Berger University of Salzburg, Salzburg, Austria Reinhard Berndt Herbaria Z+ZT, ETH Zürich, CHN D37, Universitätstr. 16, 8092 Zürich, Switzerland Annarosa Bernicchia Via A. Guidotti 39, 40134 Bologna, Italy Alona Yu. Biketova Institute of Biochemistry, BRC-HAS, 6726 Szeged, Temesvari krt. 62, 6726 Szeged, Hungary Enrico Bizio Società Veneziana di Micologia, Società Veneziana di Scienze Naturali, Fontego dei Turchi, Santa Croce 1730, 30135 Venice, Italy Curtis Bjork UBC Herbarium, Beaty Biodiversity Museum, University of British Columbia, Canada Teun Boekhout (1) Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands; (2) Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands David Boertmann Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark Tanja Böhning AG Geobotanik Schleswig-Holstein & Hamburg, c/o University of Kiel, Olshausenstraße 75, 24098 Kiel, Germany Florent Boittin Ascomycete.org, 36 rue de la Garde, 69005 Lyon, France Carlos G. Boluda Conservatoire et Jardin botaniques de la Ville de Genève, 1292 Genève, Switzerland Menno W. Boomsluiter T.v.Lohuizenstraat 34, 8172xl, Vaassen, The Netherlands Jan Borovička Institute of Geology, Czech Academy of Sciences, Rozvojova 269, 165 00 Prague 6, Czech Republic Tor Erik Brandrud Norwegian Institute for Nature Research, Gaustadalleen 21, 0349 Oslo, Norway Uwe Braun Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik, und Botanischer Garten, Herbarium, Neuwerk 21, 06099 Halle, Germany Irwin Brodo Canadian Museum of Nature, 240 McLeod Street, Ottawa, Ontario, Canada Tatiana Bulyonkova A.P. Ershov Institute of Informatics Systems, Russian Academy of Sciences, Siberian Branch, 6 Acad. Lavrentjev pr., Novosibirsk 630090, Russia Harold H. Burdsall Jr. Fungal & Decay Diagnostics, LLC, 9350 Union Valley Road, Black Earth, Wisconsin 53515, U.S.A. Bart Buyck Muséum National d’Histoire Naturelle, CP 39, ISYEB, UMR 7205 CNRS MNHN UPMC EPHE, 12 rue Buffon, 75005 Paris, France Ana Rosa Burgaz Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain Vicent Calatayud Fundación CEAM, c/ Charles R. Darwin, 14, Parque Tecnológico, 46980 Paterna, Valencia, Spain Philippe Callac INRA, MycSA, CS 20032, 33882 Villenave d’Ornon, France Emanuele Campo Associazione Micologica Bresadola, Via Alessandro Volta 46, 38123 Trento, Italy Massimo Candusso Via Ottone Primo 90, 17021, Alassio, Savona, Italy Brigitte Capoen Queffioec, rue de Saint Gonval, 22710 Penvenan, France Joaquim Carbó Roser, 60, 17257 Torroella de Montgrí, Girona, Spain Matteo Carbone Via Don Luigi Sturzo 173 16148 Genova, Italy Rafael F. Castañeda-Ruiz Instituto de Investigaciones Fundamentales en Agricultura, Tropical ‘Alejandro de Humboldt’, OSDE, Grupo Agrícola, Calle 1 Esq. 2, Santiago de Las Vegas, C. Habana 17200, Cuba Michael A. Castellano USDA, Forest Service, Northern Research Station, Corvallis, Oregon 97330, U.S.A. Jie Chen Mae Fah Luang University, Chang Wat Chiang Rai 57100, Thailand Philippe Clerc Conservatoire et Jardin botaniques de la Ville de Genève, 1292 Genève, Switzerland Giovanni Consiglio Via C. Ronzani 61, 40033 Casalecchio Bologna, Italy Gilles Corriol National Botanical Conservatory for Pyrenees and Midi-Pyrénées Region of France and BBF Herbarium, Vallon de Salut. B.P. 315. 65203 Bagnères-de-Bigorre, France Régis Courtecuisse Université Lille, Fac. Pharma. Lille, EA4483 IMPECS, 59000 Lille, France Ana Crespo Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain Cathy Cripps Plant Sciences & Plant Pathology, 119 Plant Biosciences Building, Montana State University, Bozeman, Montana 59717, U.S.A. Pedro W. Crous Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands Gladstone Alves da Silva Universidade Federal de Pernambuco, Centro de Biociências, Avenida da Engenharia, S/N, Cidade Universitária, Recife, Pernambuco, Brazil Meiriele da Silva Universidade Federal de Viçosa, 36570-000, Viçosa, Minas Gerais, Brazil Marjo Dam Hooischelf 13, 6581 SL Malden, The Netherlands Nico Dam Hooischelf 13, 6581 SL Malden, The Netherlands Frank Dämmrich The Bavarian Natural History Collections (SNSB Munich), Menzinger Strasse 71, 80638, München, Germany Kanad Das Botanical Survey of India, Cryptogamic Unit, P.O. Botanic Garden, Howrah 711103, W.B., India Linda Davies Centre for Environmental Policy, Imperial College London, SW7 2AZ, United Kingdom Eske De Crop Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Andre De Kesel Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Ruben De Lange Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium Bárbara De Madrignac Bonzi Instituto de Botánica del Nordeste, Universidad Nacional de Nordeste-Consejo Nacional de Investigaciones Científicas y Técnicas, Sargento Cabral 2131, CC 209, Corrientes Capital, Argentina Thomas Edison E. dela Cruz University of Santo Tomas, Espana 1008 Manila, Philippines Lynn Delgat Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium Vincent Demoulin Institut de Botanique, B.22, Université de Liège, 4000 Liège I, Belgium Dennis E. Desjardin HD Thiers Herbarium (SFSU), San Francisco State University, 1600 Holloway Ave, San Francisco, California 94132, U.S.A. Paul Diederich Musée national d’histoire naturelle, 25 rue Münster, 2160 Luxembourg, Luxembourg Bálint Dima (1) Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary; (2) Viikki Plant Science Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland Maria Martha Dios Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Catamarca, Av Belgrano 300, 4700 San Fernando del Valle de Catamarca, Argentina Pradeep Kumar Divakar Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain Clovis Douanla-Meli Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Messeweg 11-12, 38104 Braunschweig, Germany Brian Douglas Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom Elisandro Ricardo Drechsler-Santos Universidade Federal de Santa Catarina, Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, Santa Catarina CEP 88040-900, Brazil Paul S. Dyer School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom Ursula Eberhardt Abt. Botanik, Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany Damien Ertz Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Fernando Esteve-Raventós Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Javier Angel Etayo Salazar Navarro Villoslada 16, 3º dcha., 31003 Pamplona, Navarra, Spain Vera Evenson Sam Mitchel Herbarium of Fungi, Denver Botanic Gardens, 1007 York Street, Denver, Colorado 80206, U.S.A. Guillaume Eyssartier Muséum national d’histoire naturelle, Jardin des plantes, 57 rue Cuvier, 75005 Paris, France Edit Farkas Institute of Ecology and Botany, MTA Centre for Ecological Research, 2163 Vácrátót, Hungary Alain Favre Fédération Mycologique et Botanique Dauphiné Savoie, Le Prieuré, 144 Place de l’Eglise, 74320 Sevrier, France Anna G. Fedosova Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Mario Filippa Regione Monsarinero 36, 14041 Agliano Terme, Italy Péter Finy 8000 Székesfehérvár, Zsombolyai u. 56, Hungary Adam Flakus W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Krakow, Poland Simón Fos Facultad de Ciencias Biológicas, Universitat de València, C/Dr Moliner 50, 46100, Burjasot, Valencia, Spain Jacques Fournier Las Muros, F. 09420 Rimont, France André Fraiture Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Paolo Franchi Associazione Micologica Bresadola, Via Alessandro Volta 46, 38123 Trento, Italy Ana Esperanza Franco Molano Escuela de Microbiología, Universidad de Antioquia, AA1226, Fundación Biodiversa Colombia, Medellín, Colombia Gernot Friebes Centre of Natural History, Botany & Mycology, Universalmuseum Joanneum, Weinzöttlstraße 16, 8045 Graz, Austria Andreas Frisch NTNU, University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway Alan Fryday Michigan State University, East Lansing, Michigan 48824, U.S.A. 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García Otálora Herbaria Z+ZT, ETH Zürich, CHN D37, Universitätstr. 16, 8092 Zürich, Switzerland Dania García Sánchez Universitat Rovira i Virgili, C/ Sant Llorenç 21, 43201 Reus, Tarragona, Spain Alain Gardiennet 14 rue Roulette, 21260 Véronnes, France Sigisfredo Garnica Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Isla Teja Campus, Casilla 567, Valdivia, Chile Isaac Garrido Benavent Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain Genevieve Gates Tasmanian Institute of Agriculture, Private Bag 54, Hobart, Tasmania 7001, Australia Alice da Cruz Lima Gerlach Conservatoire et Jardin Botaniques de la ville de Genève, Genève, Switzerland Masoomeh Ghobad-Nejhad Iranian Research Organization for Science and Technology, P.O. Box 15815-3538, Tehran 15819, Iran Tatiana B. 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Kovács Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary Martin Kříž Faculty of Science, Charles University, Benátská 2, 128 01 Praha 2, Czech Republic Åsa Kruys Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden Viktor Kučera Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Linas Kudzma 37 Maple Ave. Annandale, New Jersey 08801, U.S.A. Francisco Kuhar Instituto Multidisciplinario de Biología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba, Casilla de Correo 495, 5000 Córdoba, Argentina Martin Kukwa Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland T. K. Arun Kumar The Zamorin’s Guruvayurappan College, Kozhikode, Kerala 673014, India Vladimír Kunca Technical University in Zvolen, Ul. T. G. 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Lendemer (1) Institute of Systematic Botany, New York Botanical Garden, 2900 Southern Blvd, Bronx, New York 10458-5126, U.S.A.; (2) Graduate Center, City University of New York, 365 5th Ave, New York, New York 10016, U.S.A. Laura Levin University of Buenos Aires, Junin 956, 1113, Buenos Aires, Argentina Uwe Lindemann Landesmuseum für Naturkunde, Münster, Germany Håkan Lindström Östansjö 150, 840 64 Kälarne, Sweden Xingzhong Liu Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Road, Chaoyang District, Beijing 100101, China Regulo Carlos Llarena Hernandez Facultad de Ciencias Biológicas y Agropecuarias, Peñuela, Universidad Veracruzana, Amatlán de los Reyes, Ver., Mexico Esteve Llop Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain Csaba Locsmándi Hungarian Natural History Museum, 1087 Budapest, Hungary Deborah Jean Lodge USDA Forest Service, NRS, P.O. Box 1377, Luquillo, Puerto Rico 00773-1377, U.S.A. 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Zhurbenko Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia The following institutions are also supporting the present text (institutional support means that committees from the mentioned) Asociación Micológica Carlos Spegazzini (Argentina) Austrian Mycological Society (Austria) Croatian Mycological Society (Croatia) Committee of the Czech Scientific Society for Mycology (Czech Republic) The Netherlands Mycological Society (The Netherlands) Sociedad Española de Liquenología (Portugal/Spain) Iberian Mycological Society (which is under constitution, Portugal/Spain) Federación de Asociaciones Micológicas Andaluzas (FAMA) (Spain) Asociación Botánica y Micológica de Jaén (Spain) Asociación Micológica Hispalense Muscaria (Spain) Societat Micològica Valenciana (Spain)

Stable, long-term interactions between fungi and algae or cyanobacteria, collectively known as lichens, have repeatedly evolved complex architectures with little resemblance to their component parts. Lacking any central scaffold, the shapes they assume are casts of secreted polymers that cement cells into place, determine the angle of phototropic exposure and regulate water relations. A growing body of evidence suggests that many lichen extracellular polymer matrices harbor unicellular, non-photosynthesizing organisms (UNPOs) not traditionally recognized as lichen symbionts. Understanding organismal input and uptake in this layer is key to interpreting the role UNPOs play in lichen biology. Here, we review both polysaccharide composition determined from whole, pulverized lichens and UNPOs reported from lichens to date. Most reported polysaccharides are thought to be structural cell wall components. The composition of the extracellular matrix is not definitively known. Several lines of evidence suggest some acidic polysaccharides have evaded detection in routine analysis of neutral sugars and may be involved in the extracellular matrix. UNPOs reported from lichens include diverse bacteria and yeasts for which secreted polysaccharides play important biological roles. We conclude by proposing testable hypotheses on the role that symbiont give-and-take in this layer could play in determining or modifying lichen symbiotic outcomes., Polysaccharide composition of lichens is reviewed with an emphasis on extracellular matrix and potential input and uptake by organismal components of the matrix.

Since the late 1800s, mycologists have been detecting fungi above and beyond the assumed single fungus in lichen thalli [1-6]. Over the last century, these fungi have been accorded roles ranging from commensalists to pathogens. Recently, Cyphobasidiales yeasts were shown to be ubiquitous in the cortex layer of many macrolichens [7], but for most species, little is known of their cellular distribution and constancy beyond visible fruiting structures. Here, we demonstrate the occurrence of an additional and distantly related basidiomycete, Tremella, in 95% of studied thalli in a global sample of one of the most intensively studied groups of lichens, the wolf lichens (genus Letharia). Tremella species are reported from a wide range of lichen genera [8], but until now, their biology was deduced from fruiting bodies (basidiomata) formed on lichen thalli. Based on this, they have been thought to be uncommon to rare, to occur exclusively in a hyphal form, and to be parasitic on the dominant fungal partner [9, 10]. We show that, in wolf lichens, Tremella occurs as yeast cells also in thalli that lack basidiomata and infer that this is its dominant stage in nature. We further show that the hyphal stage, when present in Letharia, is in close contact with algal cells, challenging the assumption that lichen-associated Tremella species are uniformly mycoparasites. Our results suggest that extent of occurrence and cellular interactions of known fungi within lichens have historically been underestimated and raise new questions about their function in specific lichen symbioses.

Lichens are tremendously diverse physical outcomes of symbiotic relationships involving fungi, algae and bacteria. This thesis aims to give insight into the functionality, composition and reproduction of lichens from the fungal perspective. When previous results from a barcoding study were re-evaluated, no support for a free-living life phase of Cladonia mycobionts could be found. Genomic and transcriptomic data were used to identify the fungal partners in thalli, and a fluorescent in situ hybridization (FISH) method for the simultaneous visualization of the different fungi was developed. This approach led to the discovery of previously unknown basidiomycetes, Cyphobasidium spp., which are widespread components of the cortex of lichens in Parmeliaceae. In some cases, the abundance of Cyphobasidium correlates with previously unexplained phenotypic variation of the lichens. In the case example Bryoria capillaris, Cyphobasidium yeasts are the dominant cells in the cortex and hence the fungus that meets the eye when looking at the lichen. With the help of hologenomic data and FISH, it could also be shown that Tremella lethariae, a lichenicolous heterobasidiomycete known to induce galls on Letharia, is dimorphic and frequently occupies the cortex of asymptomatic Letharia thalli in its anamorphic state. Finally, genomic and transcriptomic data was used to investigate the mating system of the genus Letharia, which includes species with different reproductive strategies. All studied Letharia species have a heterothallic mating system, meaning they need to find a compatible mate in order to sexually reproduce. Thus, the variation of reproduction strategies within the genus cannot be explained only by the mating system of the Letharia mycobiont. Our data on the mating-type ratios indicates that no potential for sexual reproduction exists for the red-listed L. vulpina in Sweden, as only one mating type is found in the populations. The roles the secondary fungi have in the symbiosis is not yet fully understood. However, the results indicate that we should not automatically assume that some of the organisms are negligible for the function of the holobiont, or that all functions assigned to fungal origin are conducted by the primary mycobiont. Altogether, the findings presented in this thesis support the view of lichens as a community of bionts with complex interactions and calls for a more holistic approach for the study of the symbiosis.

Lichens assemble in three parts Lichen growth forms cannot be recapitulated in the laboratory by culturing the plant and fungal partners together. Spribille et al. have discovered that the classical binary view of lichens is too simple. Instead, North American beard-like lichens are constituted of not two but three symbiotic partners: an ascomycetous fungus, a photosynthetic alga, and, unexpectedly, a basidiomycetous yeast. The yeast cells form the characteristic cortex of the lichen thallus and may be important for its shape. The yeasts are ubiquitous and essential partners for most lichens and not the result of lichens being colonized or parasitized by other organisms. Science , this issue p. 488

Tree hollows often harbor animals and microorganisms, thereby storing nutritive resources derived from their biological activities. The outflows from tree hollows can create unique microenvironments, which may affect communities of epiphytic organisms on trunk surfaces below the hollows. In this study, we tested whether the species richness and composition of epiphytic bryophytes (liverworts and mosses) and lichens differ above and below tree hollows of Aria japonica and Cercidiphyllum japonicum in a Japanese temperate forest. The species richness of epiphytic bryophytes and lichens did not differ above and below hollows; however, the species composition of bryophytes differed significantly above and below hollows. Indicator species analyses showed that the moss species Anomodon tristis and the liverwort species Porella vernicosa were significantly more common below than above hollows, while the liverwort species Radula japonica and four lichen species, including Leptogium cyanescens, occurred more frequently above than below hollows. Our results highlight that tree hollows can produce unique microenvironments on trunk surfaces that potentially contribute to the maintenance of epiphytic diversity on a local scale.