Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota)

The phylogeny and taxonomy of Glypholecia (Acarosporaceae, lichenized Ascomycota), including a new species from northwestern China

Glypholeciaqinghaiensis An C. Yin, Q. Y. Zhong & Li S. Wang is described as new to science. It is characterized by its squamulose thallus, compound apothecia, ellipsoid ascospores, and the presence of rhizines on the lower surface of the thallus. A phylogenetic tree of Glypholecia species was constructed based on nrITS and mtSSU sequences. Two species G.qinghaiensis and G.scabra are confirmed in China.

Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Ascomycota account for about two-thirds of named fungal species.1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.3,4,5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous "orphan" ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.

Gilbertaria, a first crustose genus in the Sphaerophoraceae (Lecanoromycetes, Ascomycota) for Catillaria contristans, Toninia squalescens and related species

Lecideoid lichen-forming fungi are a large, heterogeneous group that includes many species described during the nineteenth century that are of unclear taxonomic status. We revise such a group, the species of which have previously been treated under the much-misunderstood names Catillaria contristans or Toninia squalescens, and use a seven-locus phylogeny to determine its phylogenetic position. We found strong support for a previously unrecognized monophyletic lineage within the Sphaerophoraceae, comprising five phylogenetic species, and describe the new genus Gilbertaria to accommodate them. The new genus is characterized by a crustose growth form, 1-septate ascospores, thick ((1.5–)2–3(–4) μm wide) paraphyses and asci of the Biatora-type. We revise the nomenclature and give new delimitations and descriptions of the Northern Hemisphere species Gilbertaria contristans comb. nov., G. holomeloides comb. nov., G. squalescens comb. nov. and describe the new species G. astrapeana from the Falkland Islands.

Isolation, Characterization, and Breast Cancer Cytotoxic Activity of Gyrophoric Acid from the Lichen Umbilicaria muhlenbergii

Lichens produce a large variety of secondary metabolites with diverse bioactivities, chemical structures, and physicochemical properties. For this reason, there is a growing interest in the use of lichen-derived bioactive molecules for drug discovery and development. Here, we report on the isolation, identification, and cytotoxic evaluation of gyrophoric acid (GA) from the lichen Umbilicaria muhlenbergii, a largely unexplored and scantly described lichen species. A simple purification protocol was developed for the fractionation of lichen crude extracts with silica gel column chromatography using solvents with changing polarity. GA was identified in one of the fractions with Fourier transform infrared spectroscopy (FTIR), ion trap mass spectrometry (MS), and nuclear magnetic resonance spectroscopy (1H-NMR and 13C-NMR). The FTIR spectra demonstrated the presence of aromatic and ester functional groups C=C, C-H, and C=O bonds, with the most remarkable signals recorded at 1400 cm−1 for the aromatic region, at 1400 cm−1 for the CH3 groups, and at 1650 cm−1 for the carbonyl groups in GA. The MS spectra showed a molecular ion [M-1]− at (m/z) 467 with a molecular weight of 468.4 and the molecular formula C24H20O10. that correspond to GA. The 1H-NMR and 13C-NMR spectra verified the chemical shifts that are typical for GA. GA reduced the cell viability of breast cancer cells from the MCF-7 cell line by 98%, which is indicative of the strong cytotoxic properties of GA and its significant potential to serve as a potent anticancer drug.

The circumscription and phylogenetic position of Bryonora (Lecanoraceae, Ascomycota), with two additions to the genus

Lecanoraceae is one of the largest families of the Lecanoromycetes, with about 30 accepted genera, many of which, however, have uncertain status and/or circumscriptions. We assess the phylogenetic position of the genus Bryonora and its segregate Bryodina for the first time, using a six-locus phylogeny comprising the Lecanoraceae as well as closely related families. We find strong support for the placement of Bryonora in the Lecanoraceae, whereas there is no support for treating Bryodina as a genus separate from Bryonora. Hence, we reduce Bryodina to synonymy with Bryonora. Further, we describe Bryonora microlepis as new to science and transfer Lecanora castaneoides to Bryonora and L. vicaria to Miriquidica. A world key to Bryonora is included.

Unlocking the Changes of Phyllosphere Fungal Communities of Fishscale Bamboo (Phyllachora heterocladae) under Rhombic-Spot Disease Stressed Conditions

As an important nonwood bioresource, fishscale bamboo (Phyllachora heterocladae Oliver) is widely distributed in the subtropical region of China. Rhombic-spot disease, caused by Neostagonosporella sichuanensis, is one of the most serious diseases that threatens fishscale bamboo health. However, there is limited knowledge about how rhombic-spot disease influences the diversity and structures of phyllosphere fungal communities. In this study, we investigated the phyllosphere fungal communities from stems, branches, and leaves of fishscale bamboo during a rhombic-spot disease outbreak using 18S rRNA sequencing. We found that only the phyllosphere fungal community from stems was significantly affected by pathogen invasion in terms of community richness, diversity, and structure. FUNGuild analysis revealed that the major classifications of phyllosphere fungi based on trophic modes in stems, branches, and leaves changed from symbiotroph-pathotroph, no obvious dominant trophic mode, and symbiotroph to saprotroph, saprotroph–pathotroph–symbiotroph, and saprotroph–symbiotroph, respectively, after pathogen invasion. The fungal community composition of the three tissues displayed significant differences at the genus level between healthy and diseased plants. The associations among fungal species in diseased samples showed more complex co-occurrence network structures than those of healthy samples. Taken together, our results highlight the importance of plant pathological conditions for the assembly of phyllosphere fungal communities in different tissues.

The First Finding of the Lichen Solorina saccata at an Algific Talus Slope in Korea

An algific talus slope is composed of broken rocks with vents connected to an ice cave, releasing cool air in summer and relatively warmer air in winter to maintain a more stable microclimate all year round. Such geological features create a very unusual and delicate ecosystem. Although there are around 25 major algific talus slopes in Korea, lichen ecology of these areas had not been investigated to date. In this study, we report the first exploration of lichen diversity and ecology at an algific talus slope, Jangyeol-ri, in Korea. A total of 37 specimens were collected over 2017-2018. Morphological and sequencing analysis revealed 27 species belonging to 18 genera present in the area. Of particular interest among these species was Solorina saccata, as it has previously not been reported in Korea and most members of genus Solorina are known to inhabit alpine regions of the Northern Hemisphere. We provide here a taxonomic key for S. saccata alongside molecular phylogenetic analyses and prediction of potential habitats in South Korea. Furthermore, regions in South Korea potentially suitable for Solorina spp. were predicted based on climatic features of known habitats around the globe. Our results showed that the suitable areas are mostly at high altitudes in mountainous areas where the annual temperature range does not exceed 26.6 °C. Further survey of other environmental conditions determining the suitability of Solorina spp. should lead to a more precise prediction of suitable habitats and trace the origin of Solorina spp. in Korea.

High levels of endemism and local differentiation in the fungal and algal symbionts of saxicolous lecideoid lichens along a latitudinal gradient in southern South America

Saxicolous, lecideoid lichenized fungi have a cosmopolitan distribution but, being mostly cold adapted, are especially abundant in polar and high-mountain regions. To date, little is known of their origin or the extent of their trans-equatorial dispersal. Several mycobiont genera and species are thought to be restricted to either the Northern or the Southern Hemisphere, whereas others are thought to be widely distributed and occur in both hemispheres. However, these assumptions often rely on morphological analyses and lack supporting molecular genetic data. Also unknown is the extent of regional differentiation in the southern polar regions. An extensive set of lecideoid lichens (185 samples) was collected along a latitudinal gradient at the southern end of South America. Subantarctic climate conditions were maintained by increasing the elevation of the collecting sites with decreasing latitude. The investigated specimens were placed in a global context by including Antarctic and cosmopolitan sequences from other studies. For each symbiont three markers were used to identify intraspecific variation (mycobiont: ITS, mtSSU, RPB1; photobiont: ITS, psbJ-L, COX2). For the mycobiont, the saxicolous genera Lecidea, Porpidia, Poeltidea and Lecidella were phylogenetically re-evaluated, along with their photobionts Asterochloris and Trebouxia. For several globally distributed species groups, the results show geographically highly differentiated subclades, classified as operational taxonomical units (OTUs), which were assigned to the different regions of southern South America (sSA). Furthermore, several small endemic and well-supported clades apparently restricted to sSA were detected at the species level for both symbionts.

Brazilian fungal diversity represented by DNA markers generated over 20 years

Molecular techniques using fungal DNA barcoding (ITS) and other markers have been key to identifying the biodiversity of different geographic areas, mainly in megadiverse countries. Here, we provide an overview of the fungal diversity in Brazil based on DNA markers of phylogenetic importance generated since 1996. We retrieved fungal sequences of ITS, LSU, SSU, tef1-α, β-tubulin, rpb1, rpb2, actin, chitin synthase, and ATP6 from GenBank using different field keywords that indicated their origin in Brazil. A total of 19,440 sequences were recovered. ITS is the most representative marker (11,209 sequences), with 70.1% belonging to Ascomycota, 18.6% Basidiomycota, 10.2% unidentified, 1.1% Mucoromycota, two sequences of Olpidium bornovanus (Fungi incertae sedis), one sequence of Blastocladiomycota (Allomyces arbusculus), and one sequence of Chytridiomycota (Batrachochytrium dendrobatidis). Considering the sequences of all selected markers, only the phyla Cryptomycota and Entorrhizomycota were not represented. Based on ITS, using a cutoff of 98%, all sequences comprise 3047 OTUs, with the majority being Ascomycota (2088 OTUs) and Basidiomycota (681 OTUs). Previous numbers based mainly on morphological and bibliographical data revealed 5264 fungal species from Brazil, with a predominance of Basidiomycota (2741 spp.) and Ascomycota (1881 spp.). The unidentified ITS sequences not assigned to a higher taxonomic level represent 1.61% of all ITS sequences sampled and correspond to 38 unknown class-level lineages (75% cutoff). A maximum likelihood phylogeny based on LSU illustrates the fungal classes occurring in Brazil.

Fungal diversity notes 1151–1276: taxonomic and phylogenetic contributions on genera and species of fungal taxa

Fungal diversity notes is one of the important journal series of fungal taxonomy that provide detailed descriptions and illustrations of new fungal taxa, as well as providing new information of fungal taxa worldwide. This article is the 11th contribution to the fungal diversity notes series, in which 126 taxa distributed in two phyla, six classes, 24 orders and 55 families are described and illustrated. Taxa in this study were mainly collected from Italy by Erio Camporesi and also collected from China, India and Thailand, as well as in some other European, North American and South American countries. Taxa described in the present study include two new families, 12 new genera, 82 new species, five new combinations and 25 new records on new hosts and new geographical distributions as well as sexual-asexual reports. The two new families are Eriomycetaceae (Dothideomycetes, family incertae sedis) and Fasciatisporaceae (Xylariales, Sordariomycetes). The twelve new genera comprise Bhagirathimyces (Phaeosphaeriaceae), Camporesiomyces (Tubeufiaceae), Eriocamporesia (Cryphonectriaceae), Eriomyces (Eriomycetaceae), Neomonodictys (Pleurotheciaceae), Paraloratospora (Phaeosphaeriaceae), Paramonodictys (Parabambusicolaceae), Pseudoconlarium (Diaporthomycetidae, genus incertae sedis), Pseudomurilentithecium (Lentitheciaceae), Setoapiospora (Muyocopronaceae), Srinivasanomyces (Vibrisseaceae) and Xenoanthostomella (Xylariales, genera incertae sedis). The 82 new species comprise Acremonium chiangraiense, Adustochaete nivea, Angustimassarina camporesii, Bhagirathimyces himalayensis, Brunneoclavispora camporesii, Camarosporidiella camporesii, Camporesiomyces mali, Camposporium appendiculatum, Camposporium multiseptatum, Camposporium septatum, Canalisporium aquaticium, Clonostachys eriocamporesiana, Clonostachys eriocamporesii, Colletotrichum hederiicola, Coniochaeta vineae, Conioscypha verrucosa, Cortinarius ainsworthii, Cortinarius aurae, Cortinarius britannicus, Cortinarius heatherae, Cortinarius scoticus, Cortinarius subsaniosus, Cytospora fusispora, Cytospora rosigena, Diaporthe camporesii, Diaporthe nigra, Diatrypella yunnanensis, Dictyosporium muriformis, Didymella camporesii, Diutina bernali, Diutina sipiczkii, Eriocamporesia aurantia, Eriomyces heveae, Ernakulamia tanakae, Falciformispora uttaraditensis, Fasciatispora cocoes, Foliophoma camporesii, Fuscostagonospora camporesii, Helvella subtinta, Kalmusia erioi, Keissleriella camporesiana, Keissleriella camporesii, Lanspora cylindrospora, Loratospora arezzoensis, Mariannaea atlantica, Melanographium phoenicis, Montagnula camporesii, Neodidymelliopsis camporesii, Neokalmusia kunmingensis, Neoleptosporella camporesiana, Neomonodictys muriformis, Neomyrmecridium guizhouense, Neosetophoma camporesii, Paraloratospora camporesii, Paramonodictys solitarius, Periconia palmicola, Plenodomus triseptatus, Pseudocamarosporium camporesii, Pseudocercospora maetaengensis, Pseudochaetosphaeronema kunmingense, Pseudoconlarium punctiforme, Pseudodactylaria camporesiana, Pseudomurilentithecium camporesii, Pseudotetraploa rajmachiensis, Pseudotruncatella camporesii, Rhexocercosporidium senecionis, Rhytidhysteron camporesii, Rhytidhysteron erioi, Septoriella camporesii, Setoapiospora thailandica, Srinivasanomyces kangrensis, Tetraploa dwibahubeeja, Tetraploa pseudoaristata, Tetraploa thrayabahubeeja, Torula camporesii, Tremateia camporesii, Tremateia lamiacearum, Uzbekistanica pruni, Verruconis mangrovei, Wilcoxina verruculosa, Xenoanthostomella chromolaenae and Xenodidymella camporesii. The five new combinations are Camporesiomyces patagoniensis, Camporesiomyces vaccinia, Camposporium lycopodiellae, Paraloratospora gahniae and Rhexocercosporidium microsporum. The 22 new records on host and geographical distribution comprise Arthrinium marii, Ascochyta medicaginicola, Ascochyta pisi, Astrocystis bambusicola, Camposporium pellucidum, Dendryphiella phitsanulokensis, Diaporthe foeniculina, Didymella macrostoma, Diplodia mutila, Diplodia seriata, Heterosphaeria patella, Hysterobrevium constrictum, Neodidymelliopsis ranunculi, Neovaginatispora fuckelii, Nothophoma quercina, Occultibambusa bambusae, Phaeosphaeria chinensis, Pseudopestalotiopsis theae, Pyxine berteriana, Tetraploa sasicola, Torula gaodangensis and Wojnowiciella dactylidis. In addition, the sexual morphs of Dissoconium eucalypti and Phaeosphaeriopsis pseudoagavacearum are reported from Laurus nobilis and Yucca gloriosa in Italy, respectively. The holomorph of Diaporthe cynaroidis is also reported for the first time.

A taxonomically broad metagenomic survey of 339 species spanning 57 families suggests cystobasidiomycete yeasts are not ubiquitous across all lichens

PREMISE

Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested.

METHODS

We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America.

RESULTS

Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results.

CONCLUSIONS

Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.

Phylogenetic placement of Leprariacryptovouauxii sp. nov. (Lecanorales, Lecanoromycetes, Ascomycota) with notes on other Lepraria species from South America

Leprariacryptovouauxii is described as a new semicryptic species similar to L.vouauxii, from which it differs geographically (South America) and phylogenetically; both species differ in nucleotide position characters in nucITS barcoding marker. Leprariaharrisiana is reported as new to South America and L.nothofagi as new to Antarctica, Bolivia, and Peru. Leprariaincana (South American records are referred to L.aff.hodkinsoniana) and L.vouauxii (most South American records are referred to L.cryptovouauxii) should be excluded at least temporarily from the lichen list of South America. All records previously referred to as L.alpina from Bolivia and Peru belong to L.nothofagi. Most of Bolivian records of L.pallida belong to L.harrisiana. Leprariaborealis and L.caesioalba should be included in L.neglecta. Leprariaachariana, L.impossibilis, and L.sipmaniana are sequenced for the first time.

Sharpening species boundaries in the Micarea prasina group, with a new circumscription of the type species M. prasina

Micarea is a lichenized genus in the family Pilocarpaceae (Ascomycota). We studied the phylogeny and reassessed the current taxonomy of the M. prasina group. We focused especially on the taxonomic questions concerning the type species M. prasina and, furthermore, challenges concerning type specimens that are too old for successful DNA barcoding and molecular studies. The phylogeny was reconstructed using nuc rDNA internal transcribed spacer region (ITS1-5.8S-ITS2 = ITS), mitochrondrial rDNA small subunit (mtSSU), and replication licensing factor MCM7 gene from 31 species. Fifty-six new sequences were generated. The data were analyzed using maximum parsimony and maximum likelihood methods. The results revealed four undescribed, well-supported lineages. Three lineages represent new species described here as M. fallax, M. flavoleprosa, and M. pusilla. In addition, our results support the recognition of M. melanobola as a distinct species. Micarea fallax is characterized by a vivid to olive green thallus composed of aggregated granules and whitish or brownish apothecia sometimes with grayish tinge (Sedifolia-gray pigment).Micarea flavoleprosa has a thick, wide-spreading yellowish green, whitish green to olive green sorediate thallus and lacks the Sedifolia-gray pigmentation. The species is mostly anamorphic, developing apothecia rarely. Micarea melanobola is characterized by a pale to dark vivid green granular thallus and darkly pigmented apothecia (Sedifolia-gray). Micarea pusilla is characterized by a whitish green to olive green thinly granular or membranous thallus, numerous and very small whitish apothecia lacking the Sedifolia-gray pigment, and by the production of methoxymicareic acid. Micarea fallax, M. flavoleprosa, and M. melanobola produce micareic acid. The reliability of crystalline granules as a character for species delimitation was investigated and was highly informative for linking the old type specimen of M. prasina to fresh material.

Two New Species of the Genus Candelariella from China and Korea

Candelariella is a widespread lineage of lichenized ascomycetes with ambiguous relationships among species that have not solved completely. In this study, several specimens belonging to Candelariella were collected from China and South Korea, and the internal transcribed spacer region was generated to confirm the system position of the newly collected specimens. Combined with a morphological examination and phylogenetic analysis, two new areolate species, Candelariella rubrisoli and C. subsquamulosa, are new to science. Detail descriptions of each new species are presented. In addition, C. canadensis is firstly reported from China mainland.

New species and records of Pyxine (Caliciaceae) in China

In this study, the diversity of Pyxine Fr. in China was assessed based on morphological and chemical traits and molecular data are inferred from ITS and mtSSU sequences. Nineteen species were recognised, including three that are new to science (i.e. P.flavicans M. X. Yang & Li S. Wang, P.hengduanensis M. X. Yang & Li S. Wang and P.yunnanensis M. X. Yang & Li S. Wang) and three records new to China were found (i.e. P.cognata Stirt., P.himalayensis Awas. and P.minuta Vain.). Pyxineyunnanensis is diagnosed by the small size of the apothecia, a white medulla of the stipe and the presence of lichexanthone. Pyxineflavicans is characterised by broad lobes, a pale yellow medulla of the stipe and the presence of atranorin. Pyxinehengduanensis can be distinguished by its pale yellow medulla, marginal labriform soralia and the absence of atranorin. Detailed descriptions of each new species are presented, along with a key to the known species of Pyxine in China.

A new species of Lecidea (Lecanorales, Ascomycota) from Pakistan

We describe here a new species, Lecideaaptrootii, in Lecidea sensu stricto from Swat Valley, Pakistan. It is most similar to L.fuscoatra in having an areolate thallus and black, lecideine apothecia with a persistent margin. However, L.aptrootii can be readily distinguished by having smaller ascospores (average length 8-10 µm). In phylogenetic analyses, using ITS and nuLSU rDNA sequences, L.aptrootii forms a sister-group relationship to L.grisella, which differs in having a rimose thallus.

A plant pathology perspective of fungal genome sequencing

The majority of plant pathogens are fungi and many of these adversely affect food security. This mini-review aims to provide an analysis of the plant pathogenic fungi for which genome sequences are publically available, to assess their general genome characteristics, and to consider how genomics has impacted plant pathology. A list of sequenced fungal species was assembled, the taxonomy of all species verified, and the potential reason for sequencing each of the species considered. The genomes of 1090 fungal species are currently (October 2016) in the public domain and this number is rapidly rising. Pathogenic species comprised the largest category (35.5 %) and, amongst these, plant pathogens are predominant. Of the 191 plant pathogenic fungal species with available genomes, 61.3 % cause diseases on food crops, more than half of which are staple crops. The genomes of plant pathogens are slightly larger than those of other fungal species sequenced to date and they contain fewer coding sequences in relation to their genome size. Both of these factors can be attributed to the expansion of repeat elements. Sequenced genomes of plant pathogens provide blueprints from which potential virulence factors were identified and from which genes associated with different pathogenic strategies could be predicted. Genome sequences have also made it possible to evaluate adaptability of pathogen genomes and genomic regions that experience selection pressures. Some genomic patterns, however, remain poorly understood and plant pathogen genomes alone are not sufficient to unravel complex pathogen-host interactions. Genomes, therefore, cannot replace experimental studies that can be complex and tedious. Ultimately, the most promising application lies in using fungal plant pathogen genomics to inform disease management and risk assessment strategies. This will ultimately minimize the risks of future disease outbreaks and assist in preparation for emerging pathogen outbreaks.

Lichenized Fungi and the Evolution of Symbiotic Organization

Lichen symbioses comprise a fascinating relationship between algae and fungi. The lichen symbiotic lifestyle evolved early in the evolution of ascomycetes and is also known from a few basidiomycetes. The ascomycete lineages have diversified in the lichenized stage to give rise to a tremendous variety of morphologies. Their thalli are often internally complex and stratified for optimized integration of algal and fungal metabolisms. Thalli are frequently colonized by specific nonlichenized fungi and occasionally also by other lichens. Microscopy has revealed various ways these fungi interact with their hosts. Besides the morphologically recognizable diversity of the lichen mycobionts and lichenicolous (lichen-inhabiting) fungi, many other microorganisms including other fungi and bacterial communities are now detected in lichens by culture-dependent and culture-independent approaches. The application of multi-omics approaches, refined microscopic techniques, and physiological studies has added to our knowledge of lichens, not only about the taxa involved in the lichen interactions, but also about their functions.

A Molecular Phylogeny of the Lichen Genus Lecidella Focusing on Species from Mainland China

The phylogeny of Lecidella species is studied, based on a 7-locus data set using ML and Bayesian analyses. Phylogenetic relationships among 43 individuals representing 11 Lecidella species, mainly from mainland China, were included in the analyses and phenotypical characters studied and mapped onto the phylogeny. The Lecidella species fall into three major clades, which are proposed here as three informal groups-Lecidella stigmatea group, L. elaeochroma group and L. enteroleucella group, each of them strongly supported. Our phylogenetic analyses support traditional species delimitation based on morphological and chemical traits in most but not all cases. Individuals considered as belonging to the same species based on phenotypic characters were found to be paraphyletic, indicating that cryptic species might be hidden under these names (e.g. L. carpathica and L. effugiens). Potentially undescribed species were found within the phenotypically circumscribed species L. elaeochroma and L. stigmatea. Additional sampling across a broader taxonomic and geographic scale will be crucial to fully resolving the taxonomy in this cosmopolitan genus.

Extremotolerant fungi from alpine rock lichens and their phylogenetic relationships

Fungi other than the lichen mycobiont frequently co-occur within lichen thalli and on the same rock in harsh environments. In these situations dark-pigmented mycelial structures are commonly observed on lichen thalli, where they persist under the same stressful conditions as their hosts. Here we used a comprehensive sampling of lichen-associated fungi from an alpine habitat to assess their phylogenetic relationships with fungi previously known from other niches. The multilocus phylogenetic analyses suggest that most of the 248 isolates belong to the Chaetothyriomycetes and Dothideomycetes, while a minor fraction represents Sordariomycetes and Leotiomycetes. As many lichens also were infected by phenotypically distinct lichenicolous fungi of diverse lineages, it remains difficult to assess whether the culture isolates represent these fungi or are from additional cryptic, extremotolerant fungi within the thalli. Some of these strains represent yet undescribed lineages within Chaethothyriomycetes and Dothideomycetes, whereas other strains belong to genera of fungi, that are known as lichen colonizers, plant and human pathogens, rock-inhabiting fungi, parasites and saprotrophs. The symbiotic structures of the lichen thalli appear to be a shared habitat of phylogenetically diverse stress-tolerant fungi, which potentially benefit from the lichen niche in otherwise hostile habitats.

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.

Do photobiont switch and cephalodia emancipation act as evolutionary drivers in the lichen symbiosis? A case study in the Pannariaceae (Peltigerales)

Lichen symbioses in the Pannariaceae associate an ascomycete and either cyanobacteria alone (usually Nostoc; bipartite thalli) or green algae and cyanobacteria (cyanobacteria being located in dedicated structures called cephalodia; tripartite thalli) as photosynthetic partners (photobionts). In bipartite thalli, cyanobacteria can either be restricted to a well-delimited layer within the thallus ('pannarioid' thalli) or spread over the thallus that becomes gelatinous when wet ('collematoid' thalli). We studied the collematoid genera Kroswia and Physma and an undescribed tripartite species along with representatives of the pannarioid genera Fuscopannaria, Pannaria and Parmeliella. Molecular inferences from 4 loci for the fungus and 1 locus for the photobiont and statistical analyses within a phylogenetic framework support the following: (a) several switches from pannarioid to collematoid thalli occured and are correlated with photobiont switches; the collematoid genus Kroswia is nested within the pannarioid genus Fuscopannaria and the collematoid genus Physma is sister to the pannarioid Parmeliella mariana group; (b) Nostoc associated with collematoid thalli in the Pannariaceae are related to that of the Collemataceae (which contains only collematoid thalli), and never associated with pannarioid thalli; Nostoc associated with pannarioid thalli also associate in other families with similar morphology; (c) ancestors of several lineages in the Pannariaceae developed tripartite thalli, bipartite thalli probably resulting from cephalodia emancipation from tripartite thalli which eventually evolved and diverged, as suggested by the same Nostoc present in the collematoid genus Physma and in the cephalodia of a closely related tripartite species; Photobiont switches and cephalodia emancipation followed by divergence are thus suspected to act as evolutionary drivers in the family Pannariaceae.