Lichen-forming Fungi Research Articles

Revisiting the isolation source after half a century: Emericellopsis mirabilis on a yellow-green alga.

Fungi-algae interactions, such as lichen-forming fungi and parasitic chytrids on phytoplankton, are common in ecosystems. In contrast, interactions between filamentous fungi and soil algae that can be observed with the naked eye have been given little attention and remain unexplored. Here, we report a fungus that was associated with a visible symptom of dead algae on a soil surface in Sugadaira-kogen, Nagano, central Japan. Acremonium-like conidiophores were growing on vesicles and dead bodies of a yellow-green alga, Botrydium granulatum. The fungus was identified as Emericellopsis mirabilis based on its morphology by microscopic observation, phylogenetic analysis, and the similarity of the isolation substrate with the first description of the species. Co-culture experiments showed a filamentous cell differentiation of the alga by the fungus, but no harmful or beneficial effects on algal growth. Therefore, we speculate that E. mirabilis is a facultative parasite of B. granulatum under natural conditions.

Lichen 1. Solo fungal and algal partners

Lichens are slow-growing niche-constructing organisms that form a thallus via scripted symbiotic/mutualistic relationships between fungi, algae, and bacteria, and that are distributed across nearly all terrestrial ecosystems. Here we use quick-freeze deep-etch electron microscopy (QFDEEM) to probe the ultrastructure of a lichen-forming fungus, Cladonia grayi, and its partner alga, Asterochloris glomerata, grown separately (solo) in the laboratory. The solo fungus resembles its lichenized counterpart in: a) general cellular organization; b) the capacity to form lateral branches; c) the production of extracellular materials; and d) the generation of acellular hyphae that we call struts. It differs in carrying a fibrillar coat on its wall exterior and in often adopting two novel plasma-membrane configurations called pleated and pitted. The solo alga also resembles its lichenized counterpart in general cellular organization, but its algaenan-based wall carries a fibrillar coat not evident in the lichen, and its pyrenoid and plastoglobule endowments are less well developed. These findings are followed by four reports on the QFDEEM ultrastructure of four species of lichens, where we describe the differentiations that occur when the fungi and algae are living together in community with bacteria.

Climate-specific biosynthetic gene clusters in populations of a lichen-forming fungus.

Natural products can contribute to abiotic stress tolerance in plants and fungi. We hypothesize that biosynthetic gene clusters (BGCs), the genomic elements that underlie natural product biosynthesis, display structured differences along elevation gradients. We analysed biosynthetic gene variation in natural populations of the lichen-forming fungus Umbilicaria pustulata. We collected a total of 600 individuals from the Mediterranean and cold-temperate climates. Population genomic analyses indicate that U. pustulata contains three clusters that are highly differentiated between the Mediterranean and cold-temperate populations. One entire cluster is exclusively present in cold-temperate populations, and a second cluster is putatively dysfunctional in all cold-temperate populations. In the third cluster variation is fixed in all cold-temperate populations due to hitchhiking. In these two clusters the presence of consistent allele frequency differences among replicate populations/gradients suggests that selection rather than drift is driving the pattern. We advocate that the landscape of fungal biosynthetic genes is shaped by both positive and hitchhiking selection. We demonstrate, for the first time, the presence of climate-associated BGCs and BGC variations in lichen-forming fungi. While the associated secondary metabolites of the candidate clusters are presently unknown, our study paves the way for targeted discovery of natural products with ecological significance.

Transcriptome Analysis Identifies a Gene Cluster for the Biosynthesis of Biruloquinone, a Rare Phenanthraquinone, in a Lichen-Forming Fungus Cladonia macilenta.

Lichens are prolific producers of natural products of polyketide origin. We previously described a culture of lichen-forming fungus (LFF) Cladonia macilenta that produces biruloquinone, a purple pigment that is a phenanthraquinone rarely found in nature. However, there was no genetic information on the biosynthesis of biruloquinone. To identify a biosynthetic gene cluster for biruloquinone, we mined polyketide synthase (PKS) genes from the genome sequence of a LFF isolated from thalli of C. macilenta. The 38 PKS in C. macilenta are highly diverse, many of which form phylogenetic clades with PKS previously characterized in non-lichenized fungi. We compared transcriptional profiles of the 38 PKS genes in two chemotypic variants, one producing biruloquinone and the other producing no appreciable metabolite in vitro. We identified a PKS gene (hereafter PKS21) that was highly upregulated in the LFF that produces biruloquinone. The boundaries of a putative biruloquinone gene cluster were demarcated by co-expression patterns of six clustered genes, including the PKS21. Biruloquinone gene clusters exhibited a high degree of synteny between related species. In this study we identified a novel PKS family responsible for the biosynthesis of biruloquinone through whole-transcriptome analysis.

Correction: Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation.

Correction: Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation.

Identification of a lichen depside polyketide synthase gene by heterologous expression in Saccharomyces cerevisiae

Lichen-forming fungi produce a variety of secondary metabolites including bioactive polyketides. Advances in DNA and RNA sequencing have led to a growing database of new lichen gene clusters encoding polyketide synthases (PKS) and associated ancillary activities. Definitive assignment of a PKS gene to a metabolic product has been challenging in the lichen field due to a lack of established gene knockout or heterologous gene expression systems. Here, we report the reconstitution of a non-reducing PKS gene from the lichen Pseudevernia furfuracea and successful heterologous expression of the synthetic lichen PKS gene in engineered Saccharomyces cerevisiae. We show that P. furfuracea PFUR17_02294 produces lecanoric acid, the depside dimer of orsellinic acid, at 360 mg/L in small-scale yeast cultures. Our results unequivocally identify PFUR17_02294 as a lecanoric acid synthase and establish that a single lichen PKS synthesizes two phenolic rings and joins them by an ester linkage to form the depside product.

The Fourth Checklist of Ukrainian Lichen-Forming and Lichenicolous Fungi with Analysis of Current Additions

The “Fourth checklist of lichen-forming and lichenicolous fungi of Ukraine”, including 2150 accepted scientific names based on published records as well as analysis of current additions are provided. Current additions include 439 taxa newly recorded for Ukraine after the third checklist of lichens of Ukraine by Kondratyuk et al. (2010) and 262 nomenclatural novelties. Annotations to each taxon of 318 newly recorded to Ukraine are provided in the style of the second checklist by Kondratyuket al. (1998), i.e. data on phytogeographical regions and administrative districts (oblasts) of Ukraine as well as references to published papers are provided. Among current additions 99 taxa were annotated in the Checklist of lichenicolous fungi of Ukraine by Darmostuk and Khodosovtsev (2017) and consequent references to the latter are provided.The conclusion confirms the earlier recommendation that national checklists of lichens are to be re-published more often than once a decade.

Deep divergence between island populations in lichenized fungi

Macaronesia is characterized by a high degree of endemism and represents a noteworthy system to study the evolutionary history of populations and species. Here, we compare the population-genetic structure in three lichen-forming fungi, the widespread Lobaria pulmonaria and two Macaronesian endemics, L. immixta and L. macaronesica, based on microsatellites. We utilize population genetic approaches to explore population subdivision and evolutionary history of these taxa on the Canary Islands, Madeira, Azores, and the western Iberian Peninsula. A common feature in all species was the deep divergence between populations on the Azores, a pattern expected by the large geographic distance among islands. For both endemic species, there was a major split between archipelagos. In contrast, in the widespread L. pulmonaria, divergent individuals were distributed across multiple archipelagos, suggesting a complex evolutionary history involving repeated migration between islands and mainland.

Establishment of Agrobacterium tumefaciens-Mediated Transformation of Cladonia macilenta, a Model Lichen-Forming Fungus.

Despite the fascinating biology of lichens, such as the symbiotic association of lichen-forming fungi (mycobiont) with their photosynthetic partners and their ability to grow in harsh habitats, lack of genetic tools manipulating mycobiont has hindered studies on genetic mechanisms underpinning lichen biology. Thus, we established an Agrobacterium tumefaciens-mediated transformation (ATMT) system for genetic transformation of a mycobiont isolated from Cladonia macilenta. A set of combinations of ATMT conditions, such as input biomass of mycobiont, co-cultivation period with Agrobacterium cells, and incubation temperature, were tested to identify an optimized ATMT condition for the C. macilenta mycobiont. As a result, more than 10 days of co-cultivation period and at least 2 mg of input biomass of the mycobiont were recommended for an efficient ATMT, owing to extremely slow growth rate of mycobionts in general. Moreover, we examined T-DNA copy number variation in a total of 180 transformants and found that 88% of the transformants had a single copy T-DNA insertion. To identify precise T-DNA insertion sites that interrupt gene function in C. macilenta, we performed TAIL-PCR analyses for selected transformants. A hypothetical gene encoding ankyrin repeats at its C-terminus was interrupted by T-DNA insertion in a transformant producing dark-brown colored pigment. Although the identification of the pigment awaits further investigation, this proof-of-concept study demonstrated the feasibility of use of ATMT in construction of a random T-DNA insertion mutant library in mycobionts for studying genetic mechanisms behind the lichen symbiosis, stress tolerance, and secondary metabolite biosynthesis.

Taxonomical and chorological notes 15 (153–163)

The present part of the series provides new records of 11 taxa, among them one diatom, six lichen-forming fungi and four bryophytes. The diatom Stauroneis blazenciciae is new to Romania, and it is the second record worldwide. The six lichen species have already been reported from Hungary, however they are quite rare. Additional interesting records are presented, e.g. Calicium notarisii and Pseudothelomma ocellatum are new for the Great Hungarian Plain, Cetrelia chicitae is new for the Velence Mts and for the Transdanubian Mountain Range, Petractis clausa is new for the Gerecse Mts, and Umbilicaria polyphylla is new for the Börzsöny Mts. Parmotrema perlatum has several interesting new occurrences. Regarding the bryophyte species, Marchantia polymorpha L. subsp. montivagans is new to Hungary, Sciuro-hypnum curtum is new for the Nyírség, Brachythecium capillaceum is reported from the Great Hungarian Plain for the first time. Pseudocampylium radicale is new for the Kismohos bog, its appearance seems to be a recent event.

A cumulative checklist for the lichen-forming, lichenicolous and allied fungi of the Continental United States and Canada, version 24

A cumulative checklist for the lichen-forming, lichenicolous and allied fungi of the Continental United States and Canada, version 24

Victoria L. Sork—Recipient of the 2020 Molecular Ecology Prize

Victoria L. Sork—Recipient of the 2020 Molecular Ecology Prize

Uzupełnienia i poprawki do listy porostów i grzybów naporostowych polskich Karpat

The list includes 241 taxa of lichen-forming fungi (lichens), 108 taxa of lichenicolous fungi and two lichenicolous myxomycetes about which records from the Polish Carpathians were reported after 2003, after the publication of checklists of lichens and lichenicolous fungi for the eastern and western part of this mountain range within the borders of Poland. For each species, its distribution in physiographical units is given with reference to the original bibliographic sources. It was shown that 46 species should be excluded from the list of lichens of the Polish Carpathians, due to incorrect identification, nomenclatural changes or recent taxonomic concepts.

Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)

Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.

Нотатки щодо лишайників та ліхенофільних грибів України I.

ДАРМОСТУК В.В., ХОДОСОВЦЕВ О.Є. (2020). Нотатки щодо лишайників та ліхенофільних грибів України I. Чорноморськ. бот. ж., 16 (3): 257–274. doi: 10.32999/ksu1990553X/2020-16-3-6

Neogene speciation and Pleistocene expansion of the genus Pseudephebe (Parmeliaceae, lichenized fungi) involving multiple colonizations of Antarctica

Widespread geographic distributions in lichens have been usually explained by the high dispersal capacity of their tiny diaspores. However, recent phylogenetic surveys have challenged this assumption and provided compelling evidence for cryptic speciation and more restricted distribution ranges in diverse lineages of lichen-forming fungi. To evaluate these scenarios, we focus on the fungal genus Pseudephebe (Parmeliaceae) which includes amphitropical species, a distribution pattern whose origin has been a matter of debate since first recognized in the nineteenth century. In our study, a six-locus dataset and a broad specimen sampling covering almost all Earth’s continents is used to investigate species delimitation in Pseudephebe. Population structure, gene flow and dating analyses, as well as genealogical reconstruction methods, are employed to disentangle the most plausible transcontinental migration routes, and estimate the timing of the origin of the amphitropical distribution and the Antarctic populations. Our results demonstrate the existence of three partly admixed phylogenetic species that diverged between the Miocene and Pliocene, and whose Quaternary distribution has been strongly driven by glacial cycles. Pseudephebe minuscula is the only species showing an amphitropical distribution, with populations in Antarctica, whereas the restricted distribution of P. pubescens and an undescribed Alaskan species might reflect the survival of these species in European and North American refugia. Our microevolutionary analyses suggest a Northern Hemisphere origin for P. minuscula, which could have dispersed into the Southern Hemisphere directly and/or through “mountain-hopping” during the Pleistocene. The Antarctic populations of this species are sorted into two genetic clusters: populations of the Antarctic Peninsula were grouped together with South American ones, and the Antarctic Continental populations formed a second cluster with Bolivian and Svalbard populations. Therefore, our data strongly suggest that the current distribution of P. minuscula in Antarctica is the outcome of multiple, recent colonizations. In conclusion, our results stress the need for integrating species delimitation and population analyses to properly approach historical biogeography in lichen-forming fungi.

New insights into the systematics and phylogeny of the genus Fouragea (Arthoniales, Opegraphaceae)

The foliicolous lichen-forming fungus Opegrapha vegae was collected on the French island of Mayotte (Comoros archipelago). Phylogenetic analyses using nuLSU and RPB2 sequences place this species in the genus Fouragea (Opegraphaceae). Opegrapha alba, O. heliabravoa, O. tuxtlensis and O. vegae are newly combined in the genus Fouragea because of their foliicolous habit, their general morphology and their ascomata and ascospores types. Fouragea vegae is reported as new for the Comoros archipelago.

New and Noteworthy Lichen-Forming and Lichenicolous Fungi, 11

Fourteen species new for science are described, illustrated and compared with closely related taxa. Six species of them are from South Korea, i.e. Bryostigma huriellae S. Y. Kondr. et J.-S. Hur, Caloplaca ulleungensis S. Y. Kondr., L. Lőkös et J.-S. Hur, Enterographa dokdoensis S. Y. Kondr. et J.-S. Hur, Neobrownliella salyangensis S. Y. Kondr. et J.-S. Hur, Rufoplaca aesan- ensis S. Y. Kondr. et J.-S. Hur, Squamulea coreana S. Y. Kondr. et J.-S. Hur, and seven species are from Chile: Caloplaca nothocitrina S. Y. Kondr. et J.-S. Hur, Caloplaca nothoholocarpa S. Y. Kondr. et J.-S. Hur, Caloplaca patagoniensis S. Y. Kondr., S.-O. Oh et J.-S. Hur, Follmannia suborthoclada S. Y. Kondr. et J.-S. Hur, ‘Lecidea’buellielloides S. Y. Kondr. et J.-S. Hur, Mass- jukiella rusavskioides S. Y. Kondr. et J.-S. Hur, Rehmanniella poeltiana S. Y. Kondr. et J.-S. Hur, as well as one species, i.e. Pyrenodesmia vernadskiensis S. Y. Kondr., T. O. Kondratiuk et I. Yu. Parnikoza, similar to Antarctic endemic species Huea coralligera, is from Argentine Islands, Western Antarctic Peninsula. The member of the genus Pyrenodesmia A. Massal. is for the first time confirmed by molecular data from the Antarctic.Eighteen new combinations, i.e. Massjukiella impolita (for Caloplaca impolita Arup), Massjukiella pollinarioides (for Xanthoria pollinarioides L. Lindblom et D. M. Wright), Massjukiella stellata (for Caloplaca stellata Wetmore et Karnefelt), Massjukiella tenax (for Xanthoria tenax L. Lindblom), and Massjukiella tenuiloba (for Xanthoria tenuiloba L. Lindblom), Pyrenodesmia albopruinosa (for Biatorina albopruinosa Arnold), Pyrenodesmia ceracea (for Caloplaca ceracea J. R. Laundon), Pyrenodesmia cretensis (for Blastenia cretensis Zahlbr.), Pyrenodesmia erythrocarpa (for Patellaria erythrocarpa Pers.), Pyrenodesmia haematites (for Lecanora haematitesChaub. ex St.-Amans), Pyrenodesmia percrocata (for Blastenia percrocata Arnold), Pyrenodesmia soralifera (for Caloplaca soralifera Vondrak et Hrouzek), Pyrenodesmia transcaspica (for Lecanora transcaspica Nyl.), Pyrenodesmia viridirufa (for Lecidea viridirufa Ach.), Pyrenodesmia xerica (for Caloplaca xerica Poelt et Vezda), as well as Rehmanniella leucoxantha (for Amphilo-ma leucoxanthum Mull. Arg.), Rehmanniella syvashica (for Caloplaca syvashica Khodos., Vond- rak et Soun), and Rehmanniella subgyalectoides (for Caloplaca subgyalectoides S. Y. Kondr. et Karnefelt) are proposed.Buelliella inops and Zwackhiomyces aff. berengerianus are for the first time recorded from South America as well as from Follmannia orthoclada (as lichenicolous fungi). Caloplaca poliotera, Rinodina convexula and Rinodina kozukensis are new to the Republic of Korea, and new localities as well as illustrations for the further 13 new and rare lichen species recently described from Eastern Asia are provided too.

New and rare lichens and allied fungi from Arkhangelsk region, North-West Russia


 
 
 Thirty-one lichen-forming fungi, 12 lichenicolous fungi, and 5 non-lichenized fungi are reported as new for Arkhangelsk Region; 7 species are new for its mainland area. Micarea fallax is reported for the first time for Russia; M. laeta and M. pusilla are new for the European part of Russia. The second finding of Nicropuncta rugulosa for Russia is recorded; microconidia are first observed in this species. The records of ten species which have been included in the new edition of the Red Data Book of the Arkhangelsk Region (2020) are presented. Nephromopsis laureri from the Red Data Book of the Russian Federation (2008) and Leptogium rivulare from the IUCN Red List are reported for the first time for Arkhangelsk Region.
 
 

In vitro resynthesis of lichenization reveals the genetic background of symbiosis-specific fungal-algal interaction in Usnea hakonensis

BackgroundSymbiosis is central to ecosystems and has been an important driving force of the diversity of life. Close and long-term interactions are known to develop cooperative molecular mechanisms between the symbiotic partners and have often given them new functions as symbiotic entities. In lichen symbiosis, mutualistic relationships between lichen-forming fungi and algae and/or cyanobacteria produce unique features that make lichens adaptive to a wide range of environments. Although the morphological, physiological, and ecological uniqueness of lichens has been described for more than a century, the genetic mechanisms underlying this symbiosis are still poorly known.ResultsThis study investigated the fungal-algal interaction specific to the lichen symbiosis using Usnea hakonensis as a model system. The whole genome of U. hakonensis, the fungal partner, was sequenced by using a culture isolated from a natural lichen thallus. Isolated cultures of the fungal and the algal partners were co-cultured in vitro for 3 months, and thalli were successfully resynthesized as visible protrusions. Transcriptomes of resynthesized and natural thalli (symbiotic states) were compared to that of isolated cultures (non-symbiotic state). Sets of fungal and algal genes up-regulated in both symbiotic states were identified as symbiosis-related genes.ConclusionFrom predicted functions of these genes, we identified genetic association with two key features fundamental to the symbiotic lifestyle in lichens. The first is establishment of a fungal symbiotic interface: (a) modification of cell walls at fungal-algal contact sites; and (b) production of a hydrophobic layer that ensheaths fungal and algal cells;. The second is symbiosis-specific nutrient flow: (a) the algal supply of photosynthetic product to the fungus; and (b) the fungal supply of phosphorous and nitrogen compounds to the alga. Since both features are widespread among lichens, our result may indicate important facets of the genetic basis of the lichen symbiosis.