Lichen-forming fungi are symbiotic organisms forming a thallus with autotrophic green algae and/or cyanobacteria. Protoparmeliopsis muralis (Schreb.) Choisy is a green-algal lichen-forming fungus associating with Trebouxia photobionts. It is known as one of the most successful urban lichens in the world. In this paper, the development of microsatellite markers specific for the mycobiont of Protoparmeliopsis muralis is reported. In order to avoid algal contaminations, the pure mycobiont culture was obtained and subsequently used for DNA isolation. For DNA enrichment, the Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) method was applied. Of the 380 clones sequenced, 62 contained repeats. In total, 38 primer pairs were designed and tested, and finally 7 primer pairs were polymorphic based on 21 specimens of P. muralis.

The new species Pyrenula reginae and P. rubromamillana are described from NE Brazil. Both have a conspicuous red or orange thallus, an inspersed hamathecium and relatively small ascospores, but they differ clearly in colour and ascoma organization.

As part of a phylogenetic and taxonomic revision of the lichenized genus Sticta in Colombia, six new species with apotheciate thalli but lacking vegetative propagules are described: Sticta atroandensis Moncada & Lücking sp. nov., S. brevior Moncada & Lücking sp. nov., S. lumbschiana Moncada & Lücking sp. nov., S. macrocyphellata Moncada & Coca sp. nov., S. parahumboldtii Moncada & Lücking sp. nov., and S. pseudohumboldtii Moncada & Lücking sp. nov. The last two are related to S. humboldtii but phylogenetically distinct and differ in details of cyphellae morphology and spot reactions. Sticta atroandensis is similar to S. andensis but has a dark lower tomentum, whereas S. brevior belongs in the S. kunthii group, being characterized by mainly laminal apothecia with tomentose margins and a rather stout thallus. Both S. lumbschiana and S. macrocyphellata form part of the S. dilatata group and can be characterized by their lobe surface structure and cyphellae anatomy. Keys to species of the S. dilatata and S. humboldtii groups are presented.

The relationship of Aspicilia uxoris within Megasporaceae is assessed within a phylogenetic context. ‘Aspicilia’ uxoris and other related species are recovered as sister to the genus Lobothallia s. str. and described here as a new genus. Teuvoa (Ascomycota, Megasporaceae) is erected based on nuclear ITS and LSU sequence data and morphological characters. In addition to Teuvoa uxoris, a second species, T. junipericola, is added to the new genus based on material collected from North America. Teuvoa junipericola, T. uxoris and T. tibetica form a group with 8-spored asci, absence of extrolites, rather short-sized conidia and ascospores, lack of a subhypothecial algal layer, and different substratum preferences (on organic substratum) with a sister relationship to genus Lobothallia s. lat. (Aspicilia subgenus Pachyothallia Clauzade & C. Roux). Based on spore measurements of the holotypes, Lecanora ferganensis Tomin from central Asia (Kyrgyzstan, Tajikistan and Uzbekistan), Lecanora atrodiscata Gintovt, from Tajikistan and Lecanora takyroides Dzhur. from Turkmenistan are new synonyms to T. uxoris. A lectotype for Lecanora ferganensis is designated, expanding the known distribution of T. uxoris from Algeria, Morocco and Spain, into Central Asia.

Dermatocarpon luridum is a subaquatic lichen which is distributed within temperate climatic zones around the world. It colonizes rock substrata along the shoreline of lakes and rivers of watersheds that regularly experience water level fluctuations. The mycobiont produces perithecia with small, simple spores that are thought to be wind dispersed. The photobiont, Diplosphaera chodatii, occurs both free-living and lichenized but little is known about its distribution and dispersal. The goal of this study was to compare the population structure of the photobiont from lakes and rivers in central North America with those of Europe. Specimens were collected in Manitoba, Canada and Austria. Population structure of the algal symbiont was assessed using the internal transcribed spacer (ITS) of ribosomal DNA (rDNA) and actin gene sequences. Results showed that genetic diversity and gene flow was high within local populations, but gene flow was low between continental populations. Low levels of gene flow between the most distant populations support the isolation-by-distance theory. The photobiont on both continents is also reported to be the photobiont for other lichen species contributing to photobiont availability for D. luridum.

A quantitative cluster analysis of lichen distribution data demonstrates that the main biogeographical subdivision in the world's lichen biota is into a Gondwanan and a Laurasian element. Patterns at smaller scales mainly reflect local climate. Wallace's line is not a significant boundary for lichens. The Gondwana / Laurasia split also applies to lichenicolous fungi. To a considerable extent, it applies to many of the larger families and orders of lichens too, though at these ranks the affinities of the lichen biota of eastern Asia and temperate North America are sometimes ambiguous.

The generic classification of Lobariaceae based on a three-gene phylogeny of mtSSU, nuLSU and ITS data, with special reference to the genus Lobariella, is reassessed. Twelve well-supported clades are recognized within Lobariaceae, which correlate with morpho-chemical and ecological features and are suggested to represent distinct generic lineages within the family. Lobaria s. lat. forms at least six lineages: Lobaria s. str. (type L. pulmonaria), the Pseudocyphellaria anomala group, for which the genus Anomalobaria is introduced (type A. anomala), Lobarina (type L. scrobiculata), Ricasolia (type R. amplissima; syn.: Dendriscocaulon), the Sticta wrightii group, for which the genus Dendriscosticta is introduced (type D. wrightii), the Lobaria peltigera group, for which the genus Yoshimuriella is introduced (type Y. fendleri), and Lobariella (type L. crenulata; syn: Durietzia nom. illeg.). Pseudocyphellaria s. lat. comprises four lineages, each of which having genus-level names available: Crocodia (type C. aurata), Parmostictina (type P. hirsuta), Podostictina (type P. endochrysoides), and Pseudocyphellaria (type P. crocata). The Pseudocyphellaria anomala group (Anomalobaria) comes out sister to Lobaria s. str., whereas Sticta s. lat. forms two unrelated lineages, Sticta s. str. (type S. sylvatica) and the S. wrightii group (Dendriscosticta), which is closely related to Lobariella and the Lobaria peltigera group (Yoshimuriella). Although these twelve clades can be organized into three larger clades that largely correspond to the traditional genera Lobaria, Pseudocyphellaria, and Sticta, the clade support for Pseudocyphellaria s. lat., as well as the distribution of morpho-chemical characters over the topology, does not favour such a conclusion. In particular, the most relevant characters traditionally used to separate these genera, pseudocyphellae and/or cyphellae, are found in at least two of the three larger clades (some species of Sticta having pseudocyphellae rather than cyphellae). The strongly supported Lobaria s. lat. clade includes species with and without cyphellae and pseudocyphellae (both on the lower side), which defies the traditional classification using these characters. Based on an expanded ITS phylogeny, Lobariella itself is emended to include 26 species, and a key is presented to all species. The following three genera and 19 species are described as new: Anomalobaria B. Moncada & Lücking gen. nov., Dendriscosticta B. Moncada & Lücking gen. nov., Yoshimuriella B. Moncada & Lücking gen. nov., Lobariella angustata B. Moncada & Lücking sp. nov., L. auriculata B. Moncada & Lücking sp. nov., L. ecorticata B. Moncada & Lücking sp. nov., L. flavomedullosa B. Moncada, Betancourt-Macuase & Lücking sp. nov., L. isidiata B. Moncada & Lücking sp. nov., L. nashii B. Moncada & Lücking sp. nov., L. olivascens B. Moncada & Lücking sp. nov., L. pallidocrenulata B. Moncada & Lücking sp. nov., L. papillifera B. Moncada & Lücking sp. nov., L. parmelioides B. Moncada & Lücking sp. nov., L. peltata B. Moncada & Lücking sp. nov., L. pseudocrenulata B. Moncada & Lücking sp. nov., L. reticulata B. Moncada & Lücking sp. nov., L. rugulosa B. Moncada & Lücking sp. nov., L. soredians B. Moncada, Betancourt-Macuase & Lücking sp. nov., L. spathulifera B. Moncada & Lücking sp. nov., L. stenroosiae B. Moncada & Lücking sp. nov., L. subcorallophora B. Moncada & Lücking sp. nov., and L. subcrenulata B. Moncada & Lücking sp. nov. Further, the following 15 new combinations are proposed: Anomalobaria anomala (Brodo & Ahti) B. Moncada & Lücking comb. nov. [Pseudocyphellaria anomala Brodo & Ahti], A. anthraspis (Ach.) B. Moncada & Lücking comb. nov. [Sticta anthraspis Ach.; Pseudocyphellaria anthraspis (Ach.) H. Magn.], Dendriscosticta platyphylla (Trevis.) B. Moncada & Lücking comb. nov. [Lobaria platyphylla Trevis.; Sticta nylanderiana Zahlbr.], D. platyphylloides (Nyl.) B. Moncada & Lücking comb. nov. [Sticta platyphylloides Nyl.], D. oroborealis (Goward & Tønsberg) B. Moncada & Lücking comb. nov. [Sticta oroborealis Goward & Tønsberg], D. praetextata (Räsänen) B. Moncada & Lücking comb. nov. [Sticta platyphylla var. praetextata Räsänen; S. praetextata (Räsänen) D. D. Awasthi], D. wrightii (Tuck.) B. Moncada & Lücking comb. nov. [Sticta wrightii Tuck.], Lobariella corallophora (Yoshim.) B. Moncada & Lücking comb. et stat. nov. [Lobaria exornata var. corallophora Yoshim.], Yoshimuriella carassensis (Vain.) B. Moncada & Lücking comb. nov. [Lobaria carassensis Vain.], Y. corrosa (Ach.) B. Moncada & Lücking comb. nov. [Sticta dissecta var. corrosa Ach.; Lobaria corrosa (Ach.) Vain.], Y. deplanata (Nyl.) B. Moncada & Lücking comb. nov. [Ricasolia subdissecta f. deplanata Nyl.; Lobaria deplanata (Nyl.) Yoshim.], Y. dissecta (Sw.) B. Moncada & Lücking comb. nov. [Lichen dissectus Sw.; Lobaria dissecta (Sw.) Raeusch], Y. fendleri (Tuck. & Mont.) B. Moncada & Lücking comb. nov. [Sticta fendleri Tuck. & Mont.; Lobaria fendleri (Tuck. & Mont.) Lindau], Y. subcorrosa (Nyl.) B. Moncada & Lücking comb. nov. [Ricasolia subcorrosa Nyl.; Lobaria subcorrosa (Nyl.) Vain.], and Y. subdissecta (Nyl.) B. Moncada & Lücking comb. nov. [Ricasolia subdissecta Nyl.; Lobaria subdissecta (Nyl.) Vain.].

The widespread and ubiquitous lichen-forming fungus Protoparmeliopsis muralis is able to form a thallus with Trebouxia species. In this study, several photobiont strains were isolated from different specimens of P. muralis and cultured in vitro. The compatibility of Trebouxia spp. and Asterochloris algae with P. muralis were investigated in in vitro resynthesis experiments and the re-lichenized bionts were observed with the scanning electron microscope. It was found that, in addition to compatible photobionts, also a presumably incompatible Asterochloris sp. was able to interact with the mycobiont. The life strategy that enables the mycobiont to form associations with a wider range of photobionts could be advantageous for the survival of the lichen and successful colonization of new habitats.

Cephalodia were investigated on young and mature thalli of Lobaria pulmonaria. Cephalodia originate from contact between hyphae and cyanobacteria on the upper or lower cortex or, less frequently, in the apical zone. Young thalli were found to associate with cyanobacteria even in the anchoring zone. Cephalodia formed on the young thalli or the anchoring hyphae share the same phenotypic characteristics. In spite of being composed of paraplectenchymatous hyphae, the cortex of mature thalli preserves a considerable plasticity, enabling the formation of cephalodia. The cyanobacterial incorporation process begins with cortical hyphae growing out towards adjacent cyanobacterial colonies, enveloping them and incorporating them into the thallus. The incorporation process is the same on the upper and the lower cortex. Early stages of cephalodia are usually found in young lobes, whereas in the older parts of the thallus only mature cephalodia are found.

In the face of changing environments, conservation is tending towards an adaptive framework which accounts for the movement of species in the landscape. This makes it necessary to quantify population dynamics of species of concern. We studied the nationally scarce Cladonia botrytes, a priority Biodiversity Action Plan species in Britain, examining population dynamics at two scales: first, we studied the demography for two populations over a period of 13 years. The monitored populations declined to complete absence, starting from 77 mats on 19 stumps. Individual mats persisted maximally for up to 7 years, but over 78% of more than 290 individual cases persisted only 1 year, and more than 93% of mats disappeared within 3 years. Secondly, we performed a targeted regional survey of more than 800 stumps across an additional 27 sites in the centre of the lichen's distribution in Britain in 2006. The largest populations known from 1998 were revisited and found to no longer support the species; only 9 stumps in 5 sites supported C. botrytes in 2006. We show that C. botrytes in Britain is characterized by short individual and population persistence times, probably locally dependent upon vegetative succession including overgrowth and shading, and the degree of stump decay. The species' transient nature poses a particular challenge to conservation, though we identify comparable systems from which lessons may be learned.

The new species Cryptothecia fabispora and C. lichexanthonica are described from NE Brazil. The first has domed asci with two large, reniform ascospores and the thallus contains psoromic acid. The second contains lichexanthone and has globose asci. Cryptothecia fabispora was found at the Serra de Itabaiana National Park which represents one of the few rainforest remnants in the state, and is a transitional area with Mata Atlantica influence and also open vegetation spots like Caatinga. It was also found in Caxiuaná in Amazonian Para and may well occur elsewhere. Cryptothecia lichexanthonica was collected at Vale do Catimbau National Park in Pernambuco, which is in a Caatinga area.

Two new species of the small genus Crypthonia are described from the Chapada do Araripe, an isolated table mountain in the state of Ceará, in NE Brazil. Both share the thallus and ascoma organization with the other known species of the genus, and are mainly characterized by differences in ascospores and chemistry. Crypthonia lichexanthonica A. A. Menezes, M. Cáceres & Aptroot has 7-septate ascospores and contains lichexanthone in the thallus, and C. submuriformis A. A. Menezes, M. Cáceres & Aptroot has (sub)muriform ascospores and also contains lichexanthone, but only in the ascigerous areas. A key to all known species of the genus Crypthonia is provided, in which Crypthonia olivacea Frisch & G. Thor is newly reported from Argentina. The new species Syncesia byssolomoides A. A. Menezes, M. Cáceres & Aptroot is described from the same area. It also has a thin byssoid thallus, but differs by the narrowly fusiform ascospores and by containing psoromic acid. It differs from all Syncesia species by the absence of carbonization and the presence of psoromic acid. The epiphytic lichen flora in this Caatinga forest area is dominated by crustose lichens, with Graphis and Polymeridium as the most speciose genera.

Bird colonies affect all elements of inhabited ecosystems, such as the soil, floristic composition and phytocoenosis structure, including the lichen biota. To date, the few papers focusing on changes in the composition of lichen vegetation caused by bird colonies are concerned with saxicolous ornithocoprophilous communities. The aim of this study was to define the impact of the grey heron in two breeding colonies on epiphytic lichens on Scots pines presently inhabited by birds, as well as those recently abandoned. Analysis of the lichen biota showed that the species composition and number of lichens were significantly modified in the functioning colony and the post-colony areas when compared with the control plots never inhabited by grey heron. Within the functioning and post-colony areas, mainly species with a wide ecological amplitude and those characteristic of fertile habitats dominated, while acidophilous and ubiquitous taxa occurred in the control plots. Multivariate analyses (for species abundance and ecological characteristics) showed that lichens growing within the functioning colony and post-colony areas differed significantly from those in the control area in their habitat requirements, as they demanded nutrient-rich, low or moderately moist and deacidified bark. Within the control plots, lichens preferring a relatively acidic and slightly nitrified substratum occurred. The direct impact of bird excrement and the fertilized bark could cause significant modifications in qualitative and quantitative species composition compared to the epiphytic lichen biota usually occurring on Scots pines.

In our earlier work, we demonstrated that the oxidases tyrosinase and laccase occur widely in lichens from the Peltigerales. Recently, we discovered the occurrence of another oxidoreductase, a heme peroxidase, in the Peltigeralean ‘jelly lichens’ Leptogium and Collema. Here we present the results of a survey of peroxidase activity in a range of lichens. In addition to the jelly lichens, strong peroxidase activity also occurs within the Peltigeralean genera Lobaria, Pseudocyphellaria and Sticta. Significant activity occurs in the cell wall, and, unlike laccase activity, peroxidase activity increases considerably following the rehydration of dry thalli. However, activity is absent from Peltigera and from the non-Peltigeralean species tested here. Electrophoretic investigation showed that lichen peroxidases are oligomeric. Possible roles for peroxidases in lichen biology are discussed.

The epiphytic lichen Evernia prunastri is sensitive to air pollution and reacted by total retreat to the worsening of air quality during the peak of SO2 pollution in Central Europe (1950s–1990). Since 1990, after a significant decrease in air pollution, epiphytic lichens recolonized previously polluted areas, including E. prunastri. We investigated the physiological status of E. prunastri, transplanted for six months in 34 sites in the urban area of Bratislava (Slovakia) under current conditions. The content of chlorophylls, cortical and medullar secondary metabolites and soluble proteins were explored. We then examined the relationship of these parameters with the environmental quality status, reflected by the diversity of epiphytic lichens. The results showed that the physiological status of E. prunastri did not change significantly after exposure. Positive correlations were found between lichen diversity in the sampling sites and physiological parameters (photosynthetic pigments and phaeophytinization quotient) in the transplants. Transplants from sampling sites with a greater proportion of nitrophilous lichens displayed a decrease in photosynthetic pigments. Sites where E. prunastri naturally occurred had a lower proportion of nitrophilous species in comparison to sites where E. prunastri was not present. This suggests that the indicator species E. prunastri may also recolonize sites with low eutrophication in urban environments under decreased air pollution, and the information on its presence can help to assess the pressure caused by nitrogen excess.

Zeorin-containing red-fruited Cladonia species, the so-called C. coccifera group, are widespread terrestrial lichens which share most of their secondary substances but differ morphologically. The main objective of this study was to explore whether the current delimitation of these species is supported by molecular data. A total of 52 European and North American specimens of C. coccifera, C. deformis, C. diversa, and C. pleurota were examined. The internal transcribed spacer regions of the nuclear ribosomal DNA and the β-tubulin gene loci were sequenced for phylogenetic analyses. Traditional morphological species circumscriptions in zeorin-containing members of the C. coccifera group are not supported by molecular data. Cladonia coccifera, C. deformis, and C. pleurota were recovered as polyphyletic in both gene topologies; C. diversa formed a lineage in the ITS phylogeny but this was not statistically supported. We detected chemical patterns of the presence/absence of porphyrilic and/or isousnic acid which may help to characterize two lineages. Our results also show incongruence between the two molecular markers studied. Therefore, we focused on possible explanations of this phenomenon. Five major evolutionary mechanisms can potentially result in phylogenetic discordance between genes: presence of pseudogenes, horizontal gene transfer, gene paralogy, incomplete lineage sorting, and hybridization. These mechanisms are briefly discussed. We consider incomplete lineage sorting and/or hybridization to best explain the incongruence.

The new species Eugeniella nigrodisca is described from Fazenda Cafuz, Serra de Itabaiana, Sergipe, NE Brazil, where it was found on bark. It is characterized by the clavate, consistently 7-septate ascospores.

Photobiont diversity within populations of Xanthoria parietina was studied at the species level by means of ITS analyses and at the subspecific level with fingerprinting techniques (RAPD-PCR) applied to sterile cultured algal isolates. Populations from coastal, rural and urban sites from NW, SW and central France and from NE Switzerland were investigated. Between 8 and 63 samples per population, altogether 150 isolates, were subjected to phenetic and ordination analyses. Epiphytic samples of X. parietina associated with different genotypes of Trebouxia decolorans but saxicolous samples contained T. arboricola. For comparison the T. gelatinosa photobiont of a small population of Teloschistes chrysophthalmus (4 samples) was investigated. ITS sequences of T. decolorans isolates from different geographic locations were largely similar. In all populations a surprisingly high diversity of genotypes was observed in Trebouxia isolated from lichen thalli growing side by side. As Trebouxia spp. are assumed to be asexually reproducing haplonts, the genetic background of this diversity is discussed. Fingerprinting techniques are a powerful tool for obtaining valuable insights into the genetic diversity within the algal partner of lichen-forming fungi at the population level, provided that sterile cultured isolates are available.