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opencc-zeroAug 2019View details →

Supplementary material 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557

Supplementary material 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557

opencc-zeroAug 2019View details →

Supplementary material 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557

Supplementary material 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557

opencc-by-4.0Mar 2024View details →

AN ANALYTICAL INVESTIGATION OF FLORISTICTIC DIVERSITY FOR BIOPROSPECTING LICHENS

From ancient times, lichens have been considered a veritable "treasure chest" of natural goods due to their wide variety of applications. Traditions of using lichens in the kitchen, as medicine, in the perfume and dying industries, in brewing and distilling, and as decorative accents date back centuries.In nature, lichen metabolites serve a wide variety of purposes, including but not limited to: weathering rocks; protecting the photobiont from harmful UV rays; recycling nutrients; limiting herbivore damage; and maintaining the symbiotic balance.In addition to providing nutrition for animals, lichens are also used as human food by several societies. Certain lichen species are eaten only in times of hunger, while others are eaten as a staple meal or even as a delicacy due to their high nutrient content. Researchers looking into the matter have found that the high carbohydrate content of lichens is what makes them so appealing as a food source. Lichens, despite their low protein concentration, have some potential as a protein replacement. Because of their low fat content and high crude fiber content, lichens are an excellent dietary source

opencc-by-4.0Mar 2024View details →

A STUDY OF DISTRIBUTION OF LICHEN BIODIVERSITY FROM BIOPROSPECTION

Formed by the symbiotic relationship of representatives of as many as three kingdoms—fungi and a protista or a monera—lichens are a distinct class of perennial cryptogamic creatures. Theophrastus, the "father of botany," used the name "lichen" in 300 B.C. to describe the thin layer of lichens that forms on the outer layer of olive tree bark. When first characterized, lichens were classified with other algae and mosses based on their outward appearance. On the other hand, de Tournefort (1700) classified "lichens" as a distinct genus within the plant kingdom. Erik Acharius, the "father of lichenology," invented various words based on the unusual structures of lichens, and he classified many new genera and species based on exterior morphology in his enormous works. After the invention of the microscope, the dualistic theory of lichens was discovered, and since then, other definitions have been developed for use in modern writings. Until the publication of "Introductory Mycology," lichens were understood to be any relationship between a fungus and an alga in which the two organisms were so entangled as to form a single thallus. Nevertheless, lichens were properly characterized by Kirk et al. (2001) as an ecologically obligatory, persistent mutualism between an exhabitant fungal partner and a resident population of extracellularly situated unicellular or filamentous algal or cyanobacterial cells.

opencc-by-4.0Nov 2024View details →

Collated reference lichen genomes

Reference genomes concatenated into files for each lichen family - sourced from NCBI and JGI.  Details on how databases were created fully available on the main <a href="https://github.com/Kamouyiaraki/DEFRALichens/tree/main/databases">project github</a>

opencc-zeroNov 2021View details →

Gene expression responses to thermal shifts in the endangered lichen Lobaria pulmonaria

Anthropogenic climate change has led to unprecedented shifts in temperature across many ecosystems. In a context of rapid environmental changes, acclimation is an important process as it may influence the capacity of organisms to survive under novel thermal conditions. Mechanisms of acclimation could involve upregulation of stress response genes involved in protein folding, DNA damage repair and the regulation of signal transduction genes, along with a simultaneous downregulation of genes involved in growth or cell cycle, in order to maintain cellular functions and equilibria. We transplanted Lobaria pulmonaria lichens originating from different forests to determine the relative effects of long-term acclimation and genetic factors on the variability in expression of mycobiont and photobiont genes. We found a strong response of mycobiont and photobiont to high temperatures, regardless of sample origin. The green-algal photobiont had an overall lower response than the mycobiont. The gene expression of both symbionts was also influenced by acclimation to transplantation sites and by genetic factors. Lobaria pulmonaria seems to have evolved powerful molecular pathways to deal with environmental fluctuations and stress and can acclimate to new habitats by transcriptomic convergence. Although L. pulmonaria has the molecular machinery to counteract short-term thermal stress, survival of lichens like L. pulmonaria depends mostly on their long-term positive carbon balance, which can be compromised by warmer temperatures and reduced precipitation, and both these outcomes have been predicted for Central Europe in connection with global climate change.

FIGURE 5 in The genus Siphula Fr. (Icmadophilaceae, Lichenized Fungi) in Venezuela

FIGURE 5. Siphula carassana. Specimen showing dichotomously branched lobes and wrinkled surface (V. Marcano CHU–07–05); scale = 0.5 cm

FIGURE 4 in The genus Siphula Fr. (Icmadophilaceae, Lichenized Fungi) in Venezuela

FIGURE 4. Characteristic substrates of Siphula species in Venezuela. A. S. carassana associated with cyanobacteria on quartzite rock, Churí tepui, Chimantá massif, 2350 m, Guayana Highlands. B. S. decumbens associated with Neuropogon and Usnea on granitic rock, Paramo La Victoria, Sierra Nevada de Mérida, 3200 m, Venezuelan Andes.

FIGURE 3 in The genus Siphula Fr. (Icmadophilaceae, Lichenized Fungi) in Venezuela

FIGURE 3. Typical habitats of Siphula species on Venezuela. A. Humid sandstone tableland, top of Churí tepui, Chimantá massif, 2350 m, Guayana Highlands. B. Exposed rock surfaces, Paramo Los Conejos, Sierra La Culata, 3200 m, Venezuelan Andes.

FIGURE 6. Siphula chimantensis. A in The genus Siphula Fr. (Icmadophilaceae, Lichenized Fungi) in Venezuela

FIGURE 6. Siphula chimantensis. A. ventral surface; scale = 0.5cm. B. dorsal surface (V. Marcano CHU–06–05 holotype); scale = 0.4 cm.

FIGURE 1 in The genus Siphula Fr. (Icmadophilaceae, Lichenized Fungi) in Venezuela

FIGURE 1. Morphological details and chemical relationships in Siphula species from Guayana Highlands. Meta-depsides and chromone: A, S. carassana, wrinkled and branched lobe (thamnolic and decarboxythamnolic acids, siphulin), scale = 0.4 cm; meta-depsides: B, S. chimantensis, flabellate lobes (thamnolic and hypothamnolic acids), scale = 0.5 cm; para-depsides: C, S. subsimplex, short terete and erect lobes with truncate or concave apices (squamatic acid), scale = 2 mm; D, S. subpteruloides, long terete lobe with concave, truncate, not eroded apices (squamatic and baeomycesic acids), scale = 0.5 cm.

opencc-zeroJun 2022View details →

Data from: Species boundaries in the messy middle – testing the hypothesis of micro-endemism in a recently diverged lineage of coastal fog desert lichen fungi

Species delimitation among closely related species is challenging because traditional phenotype-based approaches, e.g., morphology, ecological, or chemical characteristics, often produce conflicting results. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, e.g., hybridization/introgression and incomplete lineage sorting, and computational limitations. Here we investigate species boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, Niebla Rundel & Bowler in the family Ramalinaceae. The species delimitation models tend to support more specious groupings, but were unable to infer robust, consistent species delimitations. The results of our study highlight the problem of delimiting species, particularly in groups such as Niebla, with complex, recent phylogeographic histories.

FIGURE 2 in On the status of Umbilicaria aprina var. halei and U. canescens (Umbilicariaceae, lichenized Ascomycota)

FIGURE 2. Umbilicaria aprina var. halei (MIN-664956—lectotype). Individual 3-, 4-celullar thallocondia (light microscopy). Scale=10μm

FIGURE 4 in On the status of Umbilicaria aprina var. halei and U. canescens (Umbilicariaceae, lichenized Ascomycota)

FIGURE 4. Umbilicaria canescens (LE-L266—holotype). Non-septate and one-septate thallocondia (light microscopy). Scale=10μm

opencc-zeroFeb 2022View details →

Supplementary material 1 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431

Table S1. List of specimens used for this study, including their voucher information, plate location, indexing, amplicon concentration and sequencing results, both as an output from SMRT tools (CCSs) and as an output from DADA2 (sequence variants). Table S2. List of the 64 barcode sequences used to index the samples. Used barcode pairs are listed in Table S1

FIGURE 2 in Umbilicaria platyrhiza-a new Mediterranean endemic species of the subgenus Papillophora (Umbilicariaceae, lichenized Ascomycota)

FIGURE 2. Umbilicaria platyrhiza: (A) strap-like unbranched and branched rhizinomorphs; (B) simple, branched, slightly flattened to strap-like rhizinomorphs; (C) branched rhizimomorphs on the upper surface; (D) Apothecia with single prominent gyrus; (E) Section of apothecium; (F) Ascospores. Bars: A–D=1 mm; E=50 µm; F=20 µm.

FIGURE 1 in Umbilicaria platyrhiza-a new Mediterranean endemic species of the subgenus Papillophora (Umbilicariaceae, lichenized Ascomycota)

FIGURE 1. Umbilicaria platyrhiza (isotype, GZU): (A) upper surface of mature and juvenile specimens (GZU); (B) lower surface. Bars: A&B=1 cm.

opencc-zeroFeb 2022View details →

Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens

The Colorado River and its tributaries on the Colorado Plateau are home to unique desert river ecosystems and changing environmental conditions. Within this region, the Glen Canyon National Recreation Area (GCNRA) is comprised of rugged, high desert terrain and is managed by the United States National Parks Service as both a recreational and conservation area. Despite the ecological and economic importance of GCNRA, significant components of the ecological communities therein remain poorly characterized, including lichens. Accurately characterizing lichen-forming fungal diversity is challenging due to poorly known taxonomic groups, underexplored regions/habitats, and varying interpretations of morphological differences, including the recognition of environmentally modified forms. To better understand lichen diversity in GCNRA, we used an integrative taxonomic approach, incorporating both traditional morphology-based identification and information from the standard fungal DNA barcoding marker, the ITS, to compile a thorough inventory of lichen-forming fungi in Fifty-Mile Canyon. Vouchered lichen specimens were collected in 2019, and from these the ITS marker was sequenced. Candidate species-level lineages were delimited from family-level multiple sequence alignments using the Assemble Species by Automatic Partitioning web server. Specimens comprising DNA-based candidate species were then evaluated using traditional taxonomically diagnostic characters to link these, where possible, to currently described species. For Fifty-Mile Canyon, we document 100 putative species in 15 families, each represented by vouchered specimens, ITS sequence data, and photographic documentation. For comparison, a survey of historic records from GCNRA revealed a total of 124 documented lichen-forming fungal species throughout the NRA and adjacent land. Approximately 50% of the species documented in Fifty-Mile Canyon had not previously been found in GCNRA, and similar proportions of species diversity have been documented in GCNRA but not observed in our survey. We report three species new to North America – Calogaya ferrugineoides (H. Magn.) Arup, Froden & Sochting, Endocarpon deserticola T. Zhang, X. L. Wei & J. C. Wei and Xanthocarpia ferrari (Bagl.) Frödén, Arup & Søchting – verified using ITS sequencing data. In addition, Circinaria squamulosa sp. nov. is formally described here, currently known only from sandstone slabs in Fifty-Mile Canyon. However, the taxonomic identity of many of the candidate species from Fifty-Mile Canyon remained ambiguous at the species level, and some collections likely represent undescribed species-level lineages. Our results revealed unexpected, high species-level diversity of lichen-forming fungi at local scales and that overall lichen diversity across the entire GCNRA is likely vastly undercounted. These data – including DNA barcodes for the vast majority of lichen-forming fungi occurring in this canyon – provide an important resource that can be integrated into subsequent lichen biodiversity research in the southwestern United States and other semi-arid climates.

opencc-zeroMar 2022View details →

Multiple drivers of large‐scale lichen decline in boreal forest canopies

Thin, hair-like lichens (Alectoria, Bryoria, Usnea) form conspicuous epiphyte communities across the boreal biome. These poikilohydric organisms provide important ecosystem functions and are useful indicators of global change. We analyse how environmental drivers influence changes in occurrence and length of these lichens on Norway spruce (Picea abies) over 10 years in managed forests in Sweden using data from >6000 trees. Alectoria and Usnea showed strong declines in southern-central regions, whereas Bryoria declined in northern regions. Overall, relative loss rates across the country ranged from 1.7% per year in Alectoria to 0.5% in Bryoria. These losses contrasted with increased length of Bryoria and Usnea in some regions. Occurrence trajectories (extinction, colonization, presence, absence) on remeasured trees correlated best with temperature, rain, nitrogen deposition, and stand age in multinomial logistic regression models. Our analysis strongly suggests that industrial forestry, in combination with nitrogen, is the main driver of lichen declines. Logging of forests with long continuity of tree cover, short rotation cycles, substrate limitation and low light in dense forests are harmful for lichens. Nitrogen deposition has decreased but is apparently still sufficiently high to prevent recovery. Warming correlated with occurrence trajectories of Alectoria and Bryoria, likely by altering hydration regimes and increasing respiration during autumn/winter. The large-scale lichen decline on an important host has cascading effects on biodiversity and function of boreal forest canopies. Forest management must apply a broad spectrum of methods, including uneven-aged continuous cover forestry and retention of large patches, to secure the ecosystem functions of these important canopy components under future climates. Our findings highlight interactions among drivers of lichen decline (forestry, nitrogen, climate), functional traits (dispersal, lichen colour, sensitivity to nitrogen, water storage), and population processes (extinction/colonization).