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Rock-inhabiting fungi (RIF) are adapted to thrive in oligotrophic environments and to survive under conditions of abiotic stress. Under these circumstances, they form biocoenoses with other tolerant organisms, such as lichens, or with less specific phototrophic consortia of aerial algae or cyanobacteria. RIF are phylogenetically diverse, and their plastic morphological characters hamper the straightforward species delimitation of many taxa. Here, we present a phylogenetic study of two RIF genera, Lichenothelia and Saxomyces. Representatives of both genera inhabit rather similar niches on rocks, but their phylogenetic relationships are unknown so far. The cosmopolitan genus Lichenothelia is recognized by characters of fertile ascomata and includes species with different life strategies. In contrast, Saxomyces species were described exclusively by mycelial characters found in cultured isolates from rock samples collected at high alpine elevations. Here, we use an extended taxon sampling of Dothideomycetes to study the phylogenetic relationships of both Lichenothelia and Saxomyces. We consider environmental samples, type species, and cultured isolates of both genera and demonstrate their paraphyly, as well as the occurrence of teleomorphs in Saxomyces. We applied three species delimitation methods to improve species recognition based on molecular data. We show the distinctiveness of the two main lineages of Lichenothelia (Lichenotheliales s. str.) and Saxomyces and discuss differences in species delimitation depending on molecular markers or methods. We revise the taxonomy of the two genera and describe three new taxa, Lichenothelia papilliformis, L. muriformis, and Saxomyces americanus, and the teleomorph of S. penninicus.

Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces , that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

Rock-inhabiting fungi (RIF) are melanized, meristematic fungi which dwell on and within rocks and have adapted to withstand harsh conditions in extreme habitats worldwide. Their morphological and genetic diversity remained unknown for a long time, but in the past few years culture-dependent and molecular phylogenetic approaches have contributed to uncovering the species richness of these otherwise very inconspicuous fungi. Only a few taxa of RIF develop both sexual reproductive structure (fertile stromata and/or pycnidia) and show multiple life styles, interacting with algae and lichen thalli in different ways. The genus Lichenothelia is one of these: It is characterized by fertile stromata and pycnidia and by species which can grow on and within exposed rocks, optionally associating with algae, with some species also being lichenicolous. The genus Lichenothelia includes up to now 25 species and form a monotypic family (Lichenotheliaceae) and order (Lichenotheliales) in Dothideomycetes. Here we focused on a group of Lichenothelia taxa distributed in the hot arid region of the Sonoran and Mojave Deserts in the Joshua Tree National Park in California. We performed molecular and morphological analyses and culture isolation and considered the ecology of the environmental samples to disentangle five species. We present the revision of two species already described, Lichenothelia calcarea and L. convexa, and introduce three new taxa to science, L. arida, L. umbrophila and L. umbrophila var. pullata.

The fungal mitochondrial small subunit (mtSSU) ribosomal DNA is one of the most commonly used loci for phylogenetic analysis of lichen-forming fungi, but their primer specificity to mycobionts has not been evaluated. The current study aimed to design mycobiont-specific mtSSU primers and highlights their utility with an example from the saxicolous lichen-forming fungal genus Melanelia Essl. in Iceland. The study found a 12.5% success rate (3 out of 24 specimens with good-quality mycobiont mtSSU sequences) using universal primers (i.e. mrSSU1 and mrSSU3R), not including off-target amplification of environmental fungi, e.g. Cladophialophora carrionii and Lichenothelia convexa . New mycobiont-specific primers (mt-SSU-581-5’ and mt-SSU-1345-3’) were designed by targeting mycobiont-specific nucleotide sites in comparison with environmental fungal sequences, and assessed for mycobiont primer specificity using in silico PCR. The new mycobiont-specific mtSSU primers had a success rate of 91.7% (22 out of 24 specimens with good-quality mycobiont mtSSU sequences) on the studied Melanelia specimens. Additional testing confirmed the specificity and yielded amplicons from 79 specimens of other Parmeliaceae mycobiont lineages. This study highlights the effectiveness of designing mycobiont-specific primers for studies on lichen identification, barcoding and phylogenetics.

In this contribution, new data concerning algae, bryophytes, fungi, and lichens of the Italian flora are presented. It includes new records and confirmations for the algae genus Chara , the bryophyte genera Cephalozia , Conardia , Conocephalum , Didymodon , Sphagnum , Tetraplodon , and Tortula , the fungal genera Endophyllum , Gymnosporangium , Microbotryum , Phragmidium , and Pluteus , and the lichen genera Candelariella , Cladonia , Flavoplaca , Lichenothelia , Peltigera , Placolecis , Rinodina , Scytinium , and Solenopsora .

Many black meristematic fungi persist on rock surfaces—hostile and exposed habitats where high doses of radiation and periods of desiccation alternate with rain and temperature extremes. To cope with these extremes, rock-inhabiting black fungi show phenotypic plasticity and produce melanin as cell wall pigments. The rather slow growth rate seems to be an additional prerequisite to oligotrophic conditions. At least some of these fungi can undergo facultative, lichen-like associations with photoautotrophs. Certain genera presenting different lifestyles are phylogenetic related among the superclass Dothideomyceta. In this paper, we focus on the genus Lichenothelia , which includes border-line lichens, that is, associations of melanised fungi with algae without forming proper lichen thalli. We provide a first phylogenetic hypothesis to show that Lichenothelia belongs to the superclass Dothideomyceta. Further, culture experiments revealed the presence of co-occurring fungi in Lichenothelia thalli. These fungi are related to plant pathogenic fungi (Mycosphaerellaceae) and to other rock-inhabiting lineages (Teratosphaeriaceae). The Lichenothelia thallus-forming fungi represent therefore consortia of different black fungal strains. Our results suggest a common link between rock-inhabiting meristematic and lichen-forming lifestyles of ascomycetous fungi.

Two new species of Lichenothelia, both from Iran, are described. Lichenothelia iranica is characterized by a black thallus with often finely lobate, slightly effigurate, not areolate margins, eight non-amyloid spores per ascus and 1–3-septate ascospores with 1–2 longitudinal or oblique septa. Lichenothelia ilamensis is distinguished by a black areolate, fissured, slightly effigurate or rarely lobulate thallus. The areoles are confluent and aggregated in the centre, becoming dispersed towards the margin, and the asci contain (4–)6(–8) non-amyloid, 1-septate spores.

Lichenostigma saxicola, growing on silicate rocks and lichens, is described from southern California from both the Sonoran and Mojave deserts as well as from the Santa Monica Mountains on the coast. The species belongs to the subgenus Lichenostigma, has a non-amyloid centrum, and dark one-septate ascospores, 10–12 × 5–6 µm, cells equal or not, constricted at the septum, the walls of over-mature ascospores becoming granular-verrucose. The species is considered facultatively lichenicolous, not host specific, and is pathogenic.

Microcolonial rock fungi occur most typically in conditions of high temperature, sparse water, and low nutrients. This study was designed to assess their growth and survival under various conditions of temperature and relative humidity. In one set of experiments, rocks containing microcolonial fungi (MCF) from Arizona and Oregon deserts were exposed in the laboratory to different temperatures and humidities, and the survival of MCF was tested by transferring them to growth medium. The survival of MCF from Oregon and Arizona rocks was similar: many survived at 70 and 80⚬C even after 21 d of exposure. Those from the Sonoran Desert in Arizona which were exposed to 100⚬C were dead after 4 d. Low humidity favoured tolerance to high temperatures. Pure cultures of MCF from these locales in the USA as well as from Australia and Egypt were tested for growth at various temperatures and relative humidities. No isolates were able to grow at water activities below 0.95. Some strains grew at temperatures as low as 4⚬C, but none grew at 50⚬C or higher. These results indicate that these MCF are not able to grow during the hot periods encountered on desert rock surfaces regardless of the humidity, but they are able to survive for extended periods under these conditions.

In this study of rocks in eastern Oregon, air and rock temperatures and moisture were monitored, along with the abundance and distribution of micro-colonial fungi (MCF) and lichens, for 2 yr. Conditions were suitable for MCF growth during all but the winter months with the most favorable conditions occurring in spring and autumn. In these seasons moisture was frequent and the absorption of solar irradiation by rocks increased the surface temperatures considerably above the very cool air temperatures. Distributions of MCF and lichens were studied in detail on ten granite rocks at one site. While MCF were most numerous on southern rock exposures, this appeared to be because this exposure was least favorable for lichen growth. MCF appeared to precede lichens in colonizing recently fractured, exposed rock surfaces. The ability of the MCF to grow in the dark as well as the light may be an important factor favouring growth of MCF relative to lichens, especially in the summer when daytime air and rock temperatures were too high to permit growth. However, conditions on some areas of the rocks were especially favourable for lichen growth and in these places lichens effectively dominated the MCF for surface area. A list of lichen species observed at this and nearby locations is provided.14CO2release from [14C]acetate was used as a measure of MCF activity at 10-12⚬C and 25⚬C under different conditions of moisture. Moderate respiration was found at 10-12⚬C and respiration occurred with a 2 h period of air drying. In contrast, MCF on rocks air dried for several weeks and subsequently dried for 18 h over H2SO4did not become active during incubation for 2 h following wetting.