Phylogenetic placement of the lichenicolous, anamorphic genus Lichenodiplis and its connection to Muellerella-like teleomorphs

Genomic features of lichen-associated black fungi

Lichens are mutualistic associations consisting of a primary fungal host, and one to few primary phototrophic symbiont(s), usually a green alga and/or a cyanobacterium. They form complex thallus structures, which provide unique and stable habitats for many other microorganisms. Frequently isolated from lichens are the so-called black fungi, or black yeasts, which are mainly characterized by melanized cell walls and extremophilic lifestyles. It is presently unclear in which ways these fungi interact with other members of the lichen symbiosis. Genomic resources of lichen-associated black fungi are needed to better understand the physiological potential of these fungi and shed light on the complexity of the lichen consortium. Here, we present high-quality genomes of 14 black fungal lineages, isolated from lichens of the rock-dwelling genus Umbilicaria. Nine of the lineages belong to the Eurotiomycetes (Chaetothyriales), four to the Dothideomycetes, and one to the Arthoniomycetes, representing the first genome of a black fungus in this class. The PacBio-based assemblies are highly contiguous (5-42 contigs per genome, mean coverage of 79-502, N50 of 1.0-7.3 mega-base-pair (Mb), Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness generally ≥95.4%). Most contigs are flanked by a telomere sequence, suggesting we achieved near chromosome-level assemblies. Genome sizes range between 26 and 44 Mb. Transcriptome-based annotations yielded ~11,000-18,000 genes per genome. We analyzed genome content with respect to repetitive elements, biosynthetic genes, and effector genes. Each genome contained a polyketide synthase gene related to the dihydroxynaphthalene-melanin pathway. This research provides insights into genome content and metabolic potential of these relatively unknown, but frequently encountered lichen associates.

First molecular evidence of lichen-inhabiting Acrospermum and new insights into the evolution of lifestyles of Acrospermales (Dothideomycetes)

Acrospermales represent one of the least studied lineages of Dothideomycetes and are characterized by diverse ecological strategies, including saprotrophic, epiphytic, fungicolous, lichenicolous, and bryophilous lifestyles. The order is composed of two teleomorphic genera, Acrospermum and Oomyces, and five anamorphic genera of unclear relationships. The objectives of the study were to establish the phylogenetic position of Acrospermum species collected from lichens in the tropical forest of Bolivia and to infer the evolution of the lichenicolous lifestyle in Acrospermales. Our results reveal that the examined specimens from Bolivia represent a new species, A. bolivianum, which is well characterized by its phylogenetic distinctness, morphological characteristics, and host selection. The new species is the first lichenicolous member of Acrospermum and forms a well-supported clade sister to the bryophilous Acrospermum adeanum. The evolution of lifestyles, concluded by phylogenetic analyses and ancestral state reconstructions, indicated that the saprotrophic lifestyle is ancestral to Acrospermales. This corresponds to their close relationship to other saprotrophic lineages of Dothideomycetes and indicates that the wide spectrum of nutritional strategies, currently observed in Acrospermales, may be a result of more recent shifts in their ecology. Our results also suggest that the lichenicolous lifestyle in Acrospermales appeared independently at least two times. Lichenicolous species are represented in our data set by Acrospermum bolivianum and Gonatophragmium physciae, which evolved from lichenicolous and plant-parasite ancestors, respectively. The genus Oomyces, represented by O. carneoalbus, was included for the first time in the phylogenetic analysis and showed a sister relationship to the remaining taxa of Acrospermales.

The origin of human pathogenicity and biological interactions in Chaetothyriales

Fungi in the order Chaetothyriales are renowned for their ability to cause human infections. Nevertheless, they are not regarded as primary pathogens, but rather as opportunists with a natural habitat in the environment. Extremotolerance is a major trend in the order, but quite different from black yeasts in Capnodiales which focus on endurance, an important additional parameter is advancing toxin management. In the ancestral ecology of rock colonization, the association with metabolite-producing lichens is significant. Ant-association, dealing with pheromones and repellents, is another mainstay in the order. The phylogenetically derived family, Herpotrichiellaceae, shows dual ecology in monoaromatic hydrocarbon assimilation and the ability to cause disease in humans and cold-blooded vertebrates. In this study, data on ecology, phylogeny, and genomics were collected and analyzed in order to support this hypothesis on the evolutionary route of the species of Chaetothyriales. Comparing the ribosomal tree with that of enzymes involved in toluene degradation, a significant expansion of cytochromes is observed and the toluene catabolism is found to be complete in some of the Herpotrichiellaceae. This might enhance human systemic infection. However, since most species have to be traumatically inoculated in order to cause disease, their invasive potential is categorized as opportunism. Only in chromoblastomycosis, true pathogenicity might be surmised. The criterion would be the possible escape of agents of vertebrate disease from the host, enabling dispersal of adapted genotypes to subsequent generations.

Are dark septate endophytes an ancestral ecological state in the evolutionary history of the order Chaetothyriales?

Dark septate endophytes (DSE) are pigmented fungi that colonize plant roots. They represent a morpho-functional status composed of many species belonging to the phylum Ascomycota, distributed in different orders. The order Chaetothyriales has representatives with diverse lifestyles, among which the rock-inhabiting one has been proposed to be the ancestral ecological character state. However, all taxa have the phenotypic characteristic of being highly melanized. This trait has been considered relevant in most Chaetothyriales because it allows them to tolerate extreme or toxic environmental conditions. In the present study, aiming to reconstruct the evolutionary history of this order, we analyzed the contribution of the DSE habit to the diversification of the Chaetothyriales. We also report the distribution of the DSE habit among the main families and/or clades within the order. Our results suggest that DSE had a key position in the evolution of the order Chaetothyriales, both as an ancestral ecological character and as a character from which other specialized forms such as Domatium probably derived.

Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

Lichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

A re-evaluation of the Chaetothyriales using criteria of comparative biology

Chaetothyriales is an ascomycetous order within Eurotiomycetes. The order is particularly known through the black yeasts and filamentous relatives that cause opportunistic infections in humans. All species in the order are consistently melanized. Ecology and habitats of species are highly diverse, and often rather extreme in terms of exposition and toxicity. Families are defined on the basis of evolutionary history, which is reconstructed by time of divergence and concepts of comparative biology using stochastical character mapping and a multi-rate Brownian motion model to reconstruct ecological ancestral character states. Ancestry is hypothesized to be with a rock-inhabiting life style. Ecological disparity increased significantly in late Jurassic, probably due to expansion of cytochromes followed by colonization of vacant ecospaces. Dramatic diversification took place subsequently, but at a low level of innovation resulting in strong niche conservatism for extant taxa. Families are ecologically different in degrees of specialization. One of the clades has adapted ant domatia, which are rich in hydrocarbons. In derived families, similar processes have enabled survival in domesticated environments rich in creosote and toxic hydrocarbons, and this ability might also explain the pronounced infectious ability of vertebrate hosts observed in these families. Conventional systems of morphological classification poorly correspond with recent phylogenetic data. Species are hypothesized to have low competitive ability against neighboring microbes, which interferes with their laboratory isolation on routine media. The dataset is unbalanced in that a large part of the extant biodiversity has not been analyzed by molecular methods, novel taxonomic entities being introduced at a regular pace. Our study comprises all available species sequenced to date for LSU and ITS, and a nomenclatural overview is provided. A limited number of species could not be assigned to any extant family.

A new genus, Zhurbenkoa, and a novel nutritional mode revealed in the family Malmideaceae (Lecanoromycetes, Ascomycota)

Lichen-inhabiting fungi are highly specialized mycoparasites, commensals or rarely saprotrophs, that are common components of almost every ecosystem, where they develop obligate associations with lichens. Their relevance, however, contrasts with the relatively small number of these fungi described so far. Recent estimates and ongoing studies indicate that a significant fraction of their diversity remains undiscovered and may be expected in tropical regions, in particular in hyperdiverse fog-exposed montane forests. Here, we introduce the new genus Zhurbenkoa, from South America and Europe, for three lichenicolous fungi growing on thalli of the widespread lichen genus Cladonia (Lecanorales). Phylogenetic analyses based on combined sequence data of mt and nuc rDNA obtained from Andean populations (Bolivia) placed Zhurbenkoa as a member of Malmideaceae, a recently introduced family of lichen-forming fungi in the class Lecanoromycetes. Zhurbenkoa is closely related to the genera Savoronala and Sprucidea. The new genus is characterized by the development of grayish brown to almost black apothecia lacking an evident margin, an epihymenium interspersed with crystals (often seen as pruina), a strongly conglutinated hymenium made of noncapitate and sparsely branched paraphyses, a colorless exciple composed of radially arranged hyphae, a Lecanora/Micarea-like ascus type, and aseptate or 1-septate ellipsoidal colorless ascospores. Zhurbenkoa includes two Neotropical (Z. cladoniarum, Z. latispora) and one widespread (Z. epicladonia) species. The lichenicolous trophic mode is documented for the first time in the Malmideaceae, which until now included only lichen-forming associations between fungi and green algae.

ITS2 metabarcoding analysis complements lichen mycobiome diversity data

Lichen thalli harbor complex fungal communities (mycobiomes) of species with divergent trophic and ecological strategies. The complexity and diversity of lichen mycobiomes are still largely unknown, despite surveys combining culture-based methods and high-throughput sequencing (HTS). The results of such surveys are strongly influenced by the barcode locus chosen, its sensitivity in discriminating taxa, and the depth to which public sequence repositories cover the phylogenetic spectrum of fungi. Here, we use HTS of the internal transcribed spacer 2 (ITS2) to assess the taxonomic composition and diversity of a well-characterized, alpine rock lichen community that includes thalli symptomatically infected by lichenicolous fungi as well as asymptomatic thalli. Taxa belonging to the order Chaetothyriales are the major components of the observed lichen mycobiomes. We predict sequences representative of lichenicolous fungi characterized morphologically and assess their asymptomatic presence in lichen thalli. We demonstrated the limitations of metabarcoding in fungi and show how the estimation of species diversity widely differs when ITS1 or ITS2 are used as barcode, and particularly biases the detection of Basidiomycota. The complementary analysis of both ITS1 and ITS2 loci is therefore required to reliably estimate the diversity of lichen mycobiomes.

Fungal Diversity in Lichens: From Extremotolerance to Interactions with Algae

Lichen symbioses develop long-living thallus structures even in the harshest environments on Earth. These structures are also habitats for many other microscopic organisms, including other fungi, which vary in their specificity and interaction with the whole symbiotic system. This contribution reviews the recent progress regarding the understanding of the lichen-inhabiting fungi that are achieved by multiphasic approaches (culturing, microscopy, and sequencing). The lichen mycobiome comprises a more or less specific pool of species that can develop symptoms on their hosts, a generalist environmental pool, and a pool of transient species. Typically, the fungal classes Dothideomycetes, Eurotiomycetes, Leotiomycetes, Sordariomycetes, and Tremellomycetes predominate the associated fungal communities. While symptomatic lichenicolous fungi belong to lichen-forming lineages, many of the other fungi that are found have close relatives that are known from different ecological niches, including both plant and animal pathogens, and rock colonizers. A significant fraction of yet unnamed melanized (‘black’) fungi belong to the classes Chaethothyriomycetes and Dothideomycetes. These lineages tolerate the stressful conditions and harsh environments that affect their hosts, and therefore are interpreted as extremotolerant fungi. Some of these taxa can also form lichen-like associations with the algae of the lichen system when they are enforced to symbiosis by co-culturing assays.

ITS1 metabarcoding highlights low specificity of lichen mycobiomes at a local scale

As self-supporting and long-living symbiotic structures, lichens provide a habitat for many other organisms beside the traditionally considered lichen symbionts-the myco- and the photobionts. The lichen-inhabiting fungi either develop diagnostic phenotypes or occur asymptomatically. Because the degree of specificity towards the lichen host is poorly known, we studied the diversity of these fungi among neighbouring lichens on rocks in an alpine habitat. Using a sequencing metabarcoding approach, we show that lichen mycobiomes clearly reflect the overlap of multiple ecological sets of taxa, which differ in their trophic association with lichen thalli. The lack of specificity to the lichen mycobiome is further supported by the lack of community structure observed using clustering and ordination methods. The communities encountered across samples largely result from the subsampling of a shared species pool, in which we identify three major ecological components: (i) a generalist environmental pool, (ii) a lichenicolous/endolichenic pool and (iii) a pool of transient species. These taxa majorly belong to the fungal classes Dothideomycetes, Eurotiomycetes and Tremellomycetes with close relatives in adjacent ecological niches. We found no significant evidence that the phenotypically recognized lichenicolous fungi influence the occurrence of the other asymptomatic fungi in the host thalli. We claim that lichens work as suboptimal habitats or as a complex spore and mycelium bank, which modulate and allow the regeneration of local fungal communities. By performing an approach that minimizes ambiguities in the taxonomic assignments of fungi, we present how lichen mycobiomes are also suitable targets for improving bioinformatic analyses of fungal metabarcoding.

Effects of Growth Media on the Diversity of Culturable Fungi from Lichens

Microscopic and molecular studies suggest that lichen symbioses contain a plethora of associated fungi. These are potential producers of novel bioactive compounds, but strains isolated on standard media usually represent only a minor subset of these fungi. By using various in vitro growth conditions we are able to modulate and extend the fraction of culturable lichen-associated fungi. We observed that the presence of iron, glucose, magnesium and potassium in growth media is essential for the successful isolation of members from different taxonomic groups. According to sequence data, most isolates besides the lichen mycobionts belong to the classes Dothideomycetes and Eurotiomycetes. With our approach we can further explore the hidden fungal diversity in lichens to assist in the search of novel compounds.