Symbiotic systems of photosynthetic microorganisms and fungi are widespread in terrestrial biomes and lichens are probably the most advanced and complex. Conversely, the least complex systems are "green biofilms" with a completely unexplored mycobiome. We describe here a new system intermediate between green biofilms and lichens - semilichens. Light and fluorescence microscopy, eDNA sequencing, molecular phylogeny, Chlorophyll a fluorescence and 13C labelling/metabolomics were used to study algal and fungal identity, morphology and physiology of the symbiosis. Tight contact between algae and a single predominant fungus (mycobiont) is revealed in semilichens. The algae are from the symbiotic lineages of Trebouxiophyceae and Ulvophyceae, the fungi belong to Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Lecanoromycetes and Lichinomycetes. Algae are alive and perform substantial photosynthetic activity. 13C labelled photosynthates are partially converted into specific fungal polyols (arabitol, mannitol) demonstrating the C-flow from algae to fungi. The new symbiotic system was defined and compared with other terrestrial algal-fungal symbioses. It is characterized by minimalist environmental requirements and extremely low production of biomass. As a result, it also inhabits environments unfavourable for lichens. Our research supports the hypothesis that the long-term existence of algae and fungi in terrestrial conditions affected by frequent and repeated drying is likely dependent on their mutual coexistence.

Aims: To revise the syntaxonomy of epiphytic lichen communities on Fagus sylvatica from old-growth beech forests in the Carpathians and adjacent uplands, in particular (1) to identify the main syntaxonomic units and reveal their ecologіcal, structural, and compositional peculiarities; (2) to assign the associations to higher-rank syntaxa; (3) to define the position of the resulting syntaxonomic units in the system of syntaxa of lichen communities of Europe; and (4) to evaluate the potential use of epiphytic lichen communities on beech trees as indicators of the ecological integrity of forest habitats. Study area: Ukrainian Carpathians, Roztochchia, Podillia, and Khotyn uplands. Methods: 230 relevés of lichen communities from western Ukraine and data from literary sources (reference data) were classified using the modified TWINSPAN algorithm implemented in JUICE software in two steps, identifying units of higher and then lower rank consecutively. Results: The first step of the analysis resulted in seven clusters which were mainly interpreted as classes or orders. The second step of the analysis resulted in 20 units of association or unranked community level. 12 of these were recorded in the study area and included 267 lichen species. Conclusions: Epiphytic lichen communities on Fagus sylvatica in the old-growth beech forests of Western Ukraine are divided into five classes: Agonimietea repletae (a new class encompassing lichen communities occurring on exposed roots and the bases of old tree trunks with smooth bark), Arthonio radiatae-Lecidelletea elaeochromae, Hypogymnietea physodis, Neckeretea complanatae and Physcietea, and 12 assocations or unranked communities. The order Agonimietalia repletae, the alliances Biatorion radicicolae and Dictyocatenulation albae, and five associations are newly described here. The provisional alliance Biatorion vernalis is proposed for epiphytic lichens on mosses. Taxonomic reference: Nimis et al. (2018). Abbreviations: EUNIS = European Nature Information System; EVC = EuroVegChecklist; ICPN = International Code of Phytosociological Nomenclature; UNESCO = United Nations Educational, Scientific and Cultural Organization; OD = Original diagnosis.

Gyalolechia fruticum , a new epiphytic species with a Mediterranean-Macaronesian distribution, is described. It differs in molecular data and in ecology from two closely related calcicolous species, G. luteococcinea and G. marmorata , both formerly called Caloplaca subochracea auct. The new species grows on coastal shrubs (rarely on wood), accompanied by species-rich communities of maritime epiphytic lichens. The typical habitat is undisturbed sand dunes, under dry conditions with frequent spells of humid air from the sea. The species is so far known from Greece, Italy, Tunisia, the Canary Islands and probably mainland Spain. We consider this conspicuous lichen an umbrella species of endangered and declining epiphytic communities of ancient shrub vegetation on well-developed sand dunes along Mediterranean coasts affected by touristic overexploitation.

Sequencing of environmental samples has great potential for biodiversity research, but its application is limited by the lack of reliable DNA barcode databases for species identifications. Such a database has been created for epiphytic lichens of Europe, allowing us to compare the results of environmental sequencing with standard taxonomic surveys. The species undetected by taxonomic surveys (what we term the ghost component) amount to about half of the species actually present in hectare plots of Central European forests. Some of these, which currently occur only as diaspores or weakly developed thalli, are likely to be favoured in the course of global change. The ghost component usually represents a larger fraction in managed forests than in old-growth unmanaged forests. The total species composition of different plots is much more similar than suggested by taxonomic surveys alone. On a regional scale, this supports the well-known statement that “everything is everywhere, but, the environment selects”.

Four days of lichenological excursions in the surroundings of Sajathutte and Eisseehutte (Pragraten, High Tauern) resulted in the list of 428 lichen taxa, 13 lichenicolous fungi and 2 lichen-associated fungi. Five species (Catillaria cf. nigroisidiata, Micarea fennica, Microcalicium loraasii, Placynthium pulvinatum and Rinodina cf. calcigena) are first records for the Alps. In addition to the taxa mentioned, a further ten lichens are new to Austria: Caloplaca approximata, C. fuscorufa, Candelariella aggregata, Halecania spodomela, Lempholemma cladodes, L. isidioides, Porina rosei, Protoparmelia leproloma, Protoparmeliopsis bolcana, and Stereocaulon capitellatum. The area harbours an extraordinarily rich lichen diversity. The combination of high-mountain elements with continental or even xerothermic species is remarkable.

Micarea (Ascomycota, Pilocarpaceae) is a large cosmopolitan genus of crustose lichens. We investigated molecular systematics and taxonomy of the poorly known Micarea melaeniza group focussing on M. melaeniza, M. nigella and M. osloensis. A total of 54 new sequences were generated and using Bayesian and maximum likelihood analysis of two markers (nuITS and mtSSU), we discovered two previously unrecognized phylogenetic lineages, one of which is described here as Micarea eurasiatica Kantelinen & G. Thor, sp. nov., morphologically characterized by pycnidia that are sessile to emergent, cylindrically shaped, with greenish-black K+ olive green, wall pigmentation and containing large mesoconidia up to 6 µm in length. The species is known from Japan and Finland. In addition, we show that the reproduction biology of M. osloensis has been poorly understood and that the species often occurs as an anamorph with stipitate pycnidia. We present a species synopsis and notes on pigments. Our research supports previous results of asexuality being an important reproductive strategy of species growing on dead wood.

Ecological science aims for general principles that are transferable, predictive and widely applicable across different local situations. However, natural history, in contrast to ecology, is rife with examples of the particular. In this study, we reject the validity of the general expectation that diversity hot-spots contribute to overall species diversity accordingly to their species richness. In eleven 1-hectare forest plots in four distinct areas across Great Britain, we recorded 550 epiphytic and epixylic lichen species, i.e. 73 % of the presently known British epiphytic flora. Species richness per site was regionally stratified and mirrored by functional diversity, but species composition differed among sites, and was unrelated to the distance between sites. Rare species and species restricted to a single site consistently represented a high proportion of the local species richness. This demonstrated that each site contributed substantially and evenly to the regional and national biodiversity of epiphytic lichens in Britain. Several functional attributes are quite specific to rare species, so further disappearance of rare species would lead to disproportionately high loss of overall functional diversity.

Sequencing of environmental DNA is increasingly used to estimate biodiversity at various taxonomic and spatial levels. However, most such studies tend to deal with abstract numbers not linked to species names, which hampers evaluation and downstream use of the results. In our survey of epiphytic lichens in the Czech Republic, we managed to link sequences from environmental DNA with species names, using an existing reference database of DNA barcodes. On 1-ha sites in various types of central-European forests, we were able to compare DNA data from environmental samples with (i) results of a parallel taxonomic survey and (ii) species abundance data on a country-wide scale. In the environmental DNA data, we detected a large number of species strongly under-recorded in taxonomic surveys and in previous distributional data from the Czech Republic. Most of these species are either very small or poorly known microlichens notoriously overlooked by taxonomists. Some are rare species with specific ecological requirements, but many are relatively abundant. Numerous species apparently new to science were detected, of which 12 species and two genera are newly described and Xylopsora diffissa. In the descriptions, eDNA data are, for the first time in lichenology, utilized for characterizing ecology and distribution of the new species. In addition, 43 species detected by eDNA are new to the Czech Republic (23 of them confirmed by the parallel taxonomic survey). Absconditella amabilis and Chaenotheca nitidula are new to Europe.

Habitat loss, fragmentation and degradation are major causes of the ongoing decline of epiphytic and epixylic lichen species in temperate forests throughout Europe. We investigated how extant species richness and composition of epiphytic and epixylic lichen communities in ten hot-spots of lichen diversity in the Czech Republic reflected the occurrence and properties of potentially suitable microhabitats and habitats. At each hot-spot, we surveyed a pair of 1-ha square plots, one in (over-)mature managed and the second in unmanaged forest. In total, we recorded 513 epiphytic and epixylic lichen species which represent a substantial part of lichen biota in Central Europe. Species richness and composition of lichen communities were explained by microhabitat heterogeneity, and also by the area of near-natural forest habitats (habitat extent) at the landscape scale. In addition, lichen species richness and number of red-listed species were explained by a categorial variable distinguishing mature managed and unmanaged plots, used as a proxy of temporal continuity of natural succession. This finding illustrates that temporal continuity of natural succession in unmanaged forests likely had an extra stimulus for lichen communities that may not be reflected by observed aspects of forest habitats. Hence, we confirmed indispensable positive effects of (micro)habitat heterogeneity, and spatial and temporal continuity for preserved hot-spots of lichen diversity in Central Europe. Due to generally slow colonization-extinction dynamics of epiphytic and epixylic lichens we call for strengthening microhabitat heterogeneity, and the spatial and temporal continuity of European temperate forests at the landscape scale.

The new species Caloplaca tswaluensis is described from Tswalu Kalahari Reserve, Northern Cape Province, South Africa. Caloplaca tswaluensis occurs on the trunks of Vachellia erioloba (camelthorn) trees and is characterized by its 3-septate to quadrilocular ascospores. Molecular data indicate that the new species is placed in the subfamily Teloschistoideae but cannot be assigned to any existing genus and, because its systematic position is unclear, we choose to describe it in Caloplaca s. lat. Caloplaca tswaluensis is compared with other crustose Teloschistaceae species with plurilocular ascospores.

Alcobiosis, the symbiosis of algae and corticioid fungi, frequently occurs on bark and wood. Algae form a layer in or below fungal basidiomata reminiscent of the photobiont layer in lichens. Identities of algal and fungal partners were confirmed by DNA barcoding. Algal activity was examined using gas exchange and chlorophyll fluorescence techniques. Carbon transfer from algae to fungi was detected as 13 C, assimilated by algae, transferred to the fungal polyol. Nine fungal partners scattered across Agaricomycetes are associated with three algae from Trebouxiophycae: Coccomyxa sp. with seven fungal species on damp wood, Desmococcus olivaceus and Tritostichococcus coniocybes , both with a single species on bark and rain-sheltered wood, respectively. The fungal partner does not cause any obvious harm to the algae. Algae enclosed in fungal tissue exhibited a substantial CO 2 uptake, but carbon transfer to fungal tissues was only detected in the Lyomyces-Desmococcus alcobiosis where some algal cells are tightly enclosed by hyphae in goniocyst-like structures. Unlike lichen mycobionts, fungi in alcobioses are not nutritionally dependent on the algal partner as all of them can live without algae. We consider alcobioses to be symbioses in various stages of co-evolution, but still quite different from true lichens.

AbstractOur floristic work in British ancient forests resulted in a description of a frequently reported but misidentified species, Coenogonium nimisii. Its thallus is very similar to Porina rosei, but the apothecia and pycnidia correspond with C. luteum. Sterile collections are not easy to distinguish but the new species differs from P. rosei in several microscopic characters of the isidia. Coenogonium nimisii is so far known from bark and epiphytic bryophytes, rarely mossy rocks, in ancient humid forests of Great Britain and Ireland. The genus Coenogonium is poorly represented by molecular data in the GenBank database. Our preliminary results revealed distinct genetic lineages within two traditionally circumscribed species, C. luteum and C. pineti, which may represent cryptic species.

ABSTRACTTaxonomists consider species as discrete units of biological organization, which are subject to a continuous process of evolutionary change and are connected through their shared ancestry. However, the continuous nature of evolutionary change is difficult to reconcile with the discrete outcome of speciation, especially where species boundaries are permeable. A good example of this inconsistency is the lichen genusPyrenodesmia, which shows a high morphologic and genetic diversity that that defies systematization by taxonomic or phylogenetic methods. Here we show that hybridization explains the presence of discordant morphs and that European species are interconnected through cross-mating in a single reproductive network, a syngameon, despite which species remain largely distinct and distinguishable. Whole genome data reflect the important role played by genome defense mechanisms in the genomic stabilization of fungal hybrids. The recurrence of Repeat Induced Point mutations (RIP) shapes genomes with islands of suppressed recombination and loss of gene content, which in turn generates a feedback loop reinforcing the lack of reproductive isolation through the loss of heterokaryon incompatibility and a tendency towards morphological reduction.

A unique crustose lichen species was recently documented from various types of preserved forests across boreal and temperate Europe (Norway, Ukraine, the Czech Republic) and the Caucasus (Russia). It is formally described here as the new species Biatora amylacea. A phylogeny based on ITS and mtSSU sequences demonstrates that it belongs to an isolated group within the core of Biatora s. lat., together with the recently described B. radicicola. It is a distinctive taxon within the genus on account of its amyloid exciple, otherwise known only from members of the Biatora rufidula group. The new species is also characterized by amyloid thalline hyphae and the production of soredia with a blue-green pigment. This microlichen may serve as a bioindicator species of old-growth forests.

Molecular identification of organisms is now a common practice and, increasingly, species are identified from environmental samples.However, for most organisms, we still lack comprehensive reference databases of DNA barcodes to identify the sequences produced.We present a near-complete database of ITS and mtSSU barcodes, named Martin7, for accurate molecular identification of epiphytic lichens (mycobionts) of central Europe.New data were obtained by Sanger and PacBio sequencing.We obtained 907 ITS sequences from 603 species and 844 mtSSU sequences from 546 species and supplemented our dataset with sequences from other reliable sources.In total, 1,172 species are included in the database, 1,004 for the ITS barcode and 906 for mtSSU.ITS was newly sequenced for 224 species and mtSSU for 234 species.For 45 genera these are the first ITS or mtSSU (or both) barcodes ever obtained.In most cases, these barcodes distinguish species as currently circumscribed, but we detected 82 groups or pairs of species where at least one of the barcodes (mostly mtSSU) does not clearly discriminate between species.We revealed diverging genotypes, possibly representing cryptic taxa, within 37 traditionally conceived species.By sequencing phenotypically unidentifiable lichens, we detected numerous "known-unknowns" (presumed undescribed species), especially in the genera Bacidina and Micarea.Five species of sorediate crustose lichens are newly described in the genera Bacidina (two species), Chrysothrix, Japewia and Lecanora.We provide a number of taxonomic novelties, for example that Lecidea betulicola and L. coriacea are teleomorphs of Cheiromycina, and Dictyocatenulata is an anamorph of Thelenella.

Molecular identification of organisms is now a common practice and, increasingly, species are identified from environmental samples. However, for most organisms, we still lack comprehensive reference databases of DNA barcodes to identify the sequences produced. We present a near-complete database of ITS and mtSSU barcodes, named Martin7, for accurate molecular identification of epiphytic lichens (mycobionts) of central Europe. New data were obtained by Sanger and PacBio sequencing. We obtained 907 ITS sequences from 603 species and 844 mtSSU sequences from 546 species and supplemented our dataset with sequences from other reliable sources. In total, 1,172 species are included in the database, 1,004 for the ITS barcode and 906 for mtSSU. ITS was newly sequenced for 224 species and mtSSU for 234 species. For 45 genera these are the first ITS or mtSSU (or both) barcodes ever obtained. In most cases, these barcodes distinguish species as currently circumscribed, but we detected 82 groups or pairs of species where at least one of the barcodes (mostly mtSSU) does not clearly discriminate between species. We revealed diverging genotypes, possibly representing cryptic taxa, within 37 traditionally conceived species. By sequencing phenotypically unidentifiable lichens, we detected numerous "known-unknowns" (presumed undescribed species), especially in the genera Bacidina and Micarea. Five species of sorediate crustose lichens are newly described in the genera Bacidina (two species), Chrysothrix, Japewia and Lecanora. We provide a number of taxonomic novelties, for example that Lecidea betulicola and L. coriacea are teleomorphs of Cheiromycina, and Dictyocatenulata is an anamorph of Thelenella.

Recent lichenological fieldwork in the Czech Republic resulted in the discovery of two previously unrecognized entities in the genus Psilolechia which are described below as new species: the saxicolous P. cretacea and the lignicolous P. torii . Both taxa regularly produce a hyphomycetous anamorph in the form of erect, elongate conidiogenous cells on the thallus surface, and both contain unidentified specific secondary metabolites. The placement of the two new species within the genus is primarily based on morphology and chemistry. In addition, three barcodes were received for P. cretacea (ITS, mtSSU) and P. torii (ITS). A key to the five species of Psilolechia currently known from Europe is included.

We surveyed epiphytic and epixylic lichens in eleven 1-hectare forest plots located in representative old-forest stands in four distinct regions of Great Britain that are well-known centres of lichen biodiversity. We aimed to analyse the patterns of lichen biodiversity in these important biodiversity hotspots from a British perspective. In total, we recorded 550 lichen species in 11 ha, i.e. 73% of the presently known British epiphytic and epixylic lichen flora. Species richness per site was regionally stratified and varied from 126 to 235 species. Although the presence of frequent species coincided with total species richness in the respective hotspot, rare species (those with <50 records in Great Britain since 2000) were more balanced among hotspots and relatively independent of species richness. Species turnover contributed significantly and evenly to the species composition regardless of species richness so that hotspots did not have nested structure, typical for the hotspots in Central Europe. Although British hotspots generally shared more species within regions than between regions, geographic distances between regions did not correspond with the differences in species composition. The results document the importance and irreplaceability of the surveyed hotspots for lichen diversity in Great Britain, notwithstanding their current species richness and past depletion due to long-term acid deposition and habitat degradation.

Biodiversity is a key criterion in nature protection and often indicates habitats and localities rich in endangered species. Our research, using 48 one-man one-day field trips, located an exceptional lichen diversity hotspot and refugium for rare species, the Tyrov National Nature Reserve (Czech Republic, central Bohemia). Within its 410 hectares, we detected 787 species of lichens and related taxa (675 lichens, 35 semilichens, 58 lichenicolous fungi and 19 bark microfungi). This is more species of these organisms than has ever been recorded from such a small area, up to 10 km(2), anywhere in Europe (and probably anywhere in the world). The species richness is positively correlated with the habitat heterogeneity within Tyrov, which is very far from uniform. In most of the reserve, the species richness is fairly typical for the broader region, and only three sites, with an overall area of a mere 80 hectares, have distinctly higher species richnesses. The most species-rich site, with 502 species, is only about 25 hectares and is distinctly more diverse in habitats than other sites. The enormous importance of Tyrov for biodiversity protection is emphasized by the nine species described as new to science: Acarospora fissa, Bacidia hyalina, Buellia microcarpa, Micarea substipitata, Microcalicium minutum, Rufoplaca griseomarginata, Verrucaria substerilis, V. tenuispora and V. teyrzowensis. Three species are new to Europe, 55 to the Czech Republic and 191 species are included in the national Red-list.