Fungal Diversity in Lichens: From Extremotolerance to Interactions with Algae

Study on endolichenic fungal assemblage in Parmotrema and Heterodermia lichens of Shivamoga, Karnataka

BACKGROUND

Lichen is a symbiotic association of algae and fungi, recognized as a self-sustaining ecosystem that constitutes an indeterminant number of bacteria, actinomycetes, fungi, and protozoa. We evaluated the endolichenic fungal assemblage given the dearth of knowledge on endolichenic fungi (ELFs), particularly from part of the Central Western Ghats, Karnataka, and conducted a phylogenetic analysis of xylariaceous fungi, the most diversified group of fungi using ITS and ITS+Tub2 gene set.

RESULTS

Out of 17 lichen thalli collected from 5 ecoregions, 42 morphospecies recovered, belong to the class Sordariomycetes, Eurotiomycetes, Dothideomycetes, Leotiomycetes, Saccharomycetes. About 19 and 13 ELF genera have been reported from Parmotrema and Heterodermia thallus. Among the ecoregions EC2 showing highest species diversity (Parmotrema (1-D) = 0.9382, (H) = 2.865, Fisher-α = 8.429, Heterodermia (1-D) = 0.8038, H = 1.894, F-α = 4.57) followed the EC3 and EC1. Xylariales are the predominant colonizer reported from at least one thallus from four ecoregions. The morphotypes ELFX04, ELFX05, ELFX08 and ELFX13 show the highest BLAST similarity (> 99%) with Xylaria psidii, X. feejeensis, X. berteri and Hypoxylon fragiforme respectively. Species delimitation and phylogenetic position reveal the closest relation of Xylariaceous ELFs with plant endophytes.

CONCLUSIONS

The observation highlights that the deciduous forest harness a high number of endolichenic fungi, a dominant portion of these fungi are non-sporulating and still exist as cryptic. Overall, 8 ELF species recognized based on phylogenetic analysis, including the two newly reported fungi ELFX03 and ELFX06 which are suspected to be new species based on the present evidence. The study proved, that the lichen being rich source to establish fungal diversity and finding new species. Successful amplification of most phylogenetic markers like RPB2, building of comprehensive taxonomic databases and application of multi-omics data are further needed to understand the complex nature of lichen-fungal symbiosis.

A direct PCR approach with low-biomass insert opens new horizons for molecular sciences on cryptogam communities

Molecular sequence data have transformed research on cryptogams (e.g., lichens, microalgae, fungi, and symbionts thereof) but methods are still strongly hampered by the small size and intermingled growth of the target organisms, poor cultivability and detrimental effects of their secondary metabolites. Here, we aim to showcase examples on which a modified direct PCR approach for diverse aspects of molecular work on environmental samples concerning biocrusts, biofilms, and cryptogams gives new options for the research community. Unlike traditional approaches, this methodology only requires biomass equivalent to colonies and fragments of 0.2 mm in diameter, which can be picked directly from the environmental sample, and includes a quick DNA lysis followed by a standardized PCR cycle that allows co-cycling of various organisms/target regions in the same run. We demonstrate that this modified method can (i) amplify the most widely used taxonomic gene regions and those used for applied and environmental sciences from single colonies and filaments of free-living cyanobacteria, bryophytes, fungi, and lichens, including their mycobionts, chlorobionts, and cyanobionts from both isolates and in situ material during co-cycling; (ii) act as a tool to confirm that the dominant lichen photobiont was isolated from the original sample; and (iii) optionally remove inhibitory secondary lichen substances. Our results represent examples which highlight the method's potential for future applications covering mycology, phycology, biocrusts, and lichenology, in particular.IMPORTANCECyanobacteria, green algae, lichens, and other cryptogams play crucial roles in complex microbial systems such as biological soil crusts of arid biomes or biofilms in caves. Molecular investigations on environmental samples or isolates of these microorganisms are often hampered by their dense aggregation, small size, or metabolism products which complicate DNA extraction and subsequent PCRs. Our work presents various examples of how a direct DNA extraction and PCR method relying on low biomass inserts can overcome these common problems and discusses additional applications of the workflow including adaptations.

Alleviating the adverse effects of Cd-Pb contamination through the application of silicon fertilizer: Enhancing soil microbial diversity and mitigating heavy metal contamination

The use of silicon fertilizer (SF) as a means of remediating cadmium (Cd) and lead (Pb) pollution has proven to be beneficial. However, the mechanism via which SF enhances soil quality and crop productivity under Cd- and Pb-contaminated soil (S) remains unclear. This study investigated the impacts of chemical fertilizer, mineral SF (MSF), and organic SF (OSF) on microbial community structure, activity of nutrient acquisition enzymes, and growth of tobacco in the presence of S condition. SF significantly reduced the contents of Cd and Pb in soil under S condition by 6.92-42.43% and increased plant height and leaf area by 15.27-81.77%. Moreover, the use of SF was observed to increase the efficiency of soil carbon and phosphorus cycling under S condition by 6.88-23.08%. Concurrently, SF was found to play a crucial role in facilitating the establishment of a complex, efficient, and interdependent molecular ecological network among soil microorganisms. In this context, Actinobacteriota, Bacteroidota, Ascomycota, and Basidiomycota were observed to be integral components of this network. SF was found to have a substantial positive impact on the metabolic functions and organismal systems of soil microorganisms. Moreover, the combined utilization of the Mantel test and partial least squares path model provided empirical evidence supporting the assertion that the administration of SF had a positive impact on both soil nutrient acquisition enzyme activity and tobacco growth, which was attributed to the enhancement of soil microbial diversity resulting from the application of SF. Furthermore, compared with MSF, OSF has advantages in reducing soil Pb and Cd content, promoting tobacco agronomic traits, increasing the number of key microbial communities, and maintaining the structural stability of microbial networks. The aforementioned findings, therefore, suggest that the OSF played a pivotal role in alleviating the adverse impacts of S, thereby demonstrating its efficacy in this particular process.

Recolonization dynamics of marble monuments after cleaning treatments: A nine-year follow-up study

The prevention and control of biological patinas on outdoor stone monuments represent a demanding challenge for the conservation of cultural heritage also due to some microorganisms, particularly resistant to treatments, such as black meristematic fungi, an eco-physiological group well known for its tolerance to extreme conditions. Even if several methods and eco-friendly products have been proposed as new alternatives, traditional biocides are still far from being completely replaced. Recolonization is a natural process that occurs sooner or later after cleaning. The time that elapses until its occurrence can vary considerably depending on environmental conditions and the used products; unfortunately, the papers describing the effect of treatments over time are rare. This work aims to shed light on the recolonization process of marble surfaces in the ancient monumental cemetery of Bonaria (Cagliari) after nine years from treatments, evaluating the long-term efficiency of two different cleaning methods, namely dimethyl sulfoxide-based gel (DMSO-based gel) and Biotin T (a didecyldimethylammonium chloride-based product-). In this context, the microflora present before treatments and in the following years was assessed by culture-based methods and identified by molecular techniques, with attention on black meristematic fungi, which were used as reference for the most resistant lithobiontic organisms. Different environmental parameters, such as temperature, exposition, dominant winds, and rainfall, were considered, and infrared thermography, portable light microscopy, and image analysis were used. This research evidenced the influence of water availability and lightning in recolonization processes, the transition from the pioneer fungal community versus more resistant black fungal species after Biotin T treatment, and the long-lasting efficiency of the DMSO-based gel. These findings prove that this low-impact method deserves more attention in the conservation of outdoor marble monuments, emphasizing the importance of long-term studies.

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.

Lichen-associated microbial members are prevalent in the snow microbiome of a sub-arctic alpine tundra

Snow is the largest component of the cryosphere, with its cover and distribution rapidly decreasing over the last decade due to climate warming. It is imperative to characterize the snow (nival) microbial communities to better understand the role of microorganisms inhabiting these rapidly changing environments. Here, we investigated the core nival microbiome, the cultivable microbial members, and the microbial functional diversity of the remote Uapishka mountain range, a massif of alpine sub-arctic tundra and boreal forest. Snow samples were taken over a two-month interval along an altitude gradient with varying degree of anthropogenic traffic and vegetation cover. The core snow alpine tundra/boreal microbiome, which was present across all samples, constituted of Acetobacterales, Rhizobiales and Acidobacteriales bacterial orders, and of Mycosphaerellales and Lecanorales fungal orders, with the dominant fungal taxa being associated with lichens. The snow samples had low active functional diversity, with Richness values ranging from 0 to 19.5. The culture-based viable microbial enumeration ranged from 0 to 8.05 × 103 CFUs/mL. We isolated and whole-genome sequenced five microorganisms which included three fungi, one alga, and one potentially novel bacterium of the Lichenihabitans genus; all of which appear to be part of lichen-associated taxonomic clades.

Regulation of symbiotic interactions and primitive lichen differentiation by UMP1 MAP kinase in Umbilicaria muhlenbergii

Lichens are of great ecological importance but mechanisms regulating lichen symbiosis are not clear. Umbilicaria muhlenbergii is a lichen-forming fungus amenable to molecular manipulations and dimorphic. Here, we established conditions conducive to symbiotic interactions and lichen differentiation and showed the importance of UMP1 MAP kinase in lichen development. In the initial biofilm-like symbiotic complexes, algal cells were interwoven with pseudohyphae covered with extracellular matrix. After longer incubation, fungal-algal complexes further differentiated into primitive lichen thalli with a melanized cortex-like and pseudoparenchyma-like tissues containing photoactive algal cells. Mutants deleted of UMP1 were blocked in pseudohyphal growth and development of biofilm-like complexes and primitive lichens. Invasion of dividing mother cells that contributes to algal layer organization in lichens was not observed in the ump1 mutant. Overall, these results showed regulatory roles of UMP1 in symbiotic interactions and lichen development and suitability of U. muhlenbergii as a model for studying lichen symbiosis.

Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata

Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus), which together generate a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here, we provide a comparative view of the biosynthetic gene clusters of three lichen mycobionts derived from Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. In addition, we present a high-quality PacBio metagenome of Parmelia sulcata, from which we extracted the mycobiont bin containing 214 biosynthetic gene clusters. Most biosynthetic gene clusters in these genomes were associated with T1PKSs, followed by NRPSs and terpenes. This study focused on biosynthetic gene clusters related to polyketide synthesis. Based on ketosynthase homology, we identified nine highly syntenic clusters present in all three species. Among the four clusters belonging to nonreducing PKSs, two are putatively linked to lichen substances derived from orsellinic acid (orcinol depsides and depsidones, e.g., lecanoric acid, physodic acid, lobaric acid), one to compounds derived from methylated forms of orsellinic acid (beta orcinol depsides, e.g., atranorin), and one to melanins. Five clusters with orthologs in all three species are linked to reducing PKSs. Our study contributes to sorting and dereplicating the vast PKS diversity found in lichenized fungi. High-quality sequences of biosynthetic gene clusters of these three common species provide a foundation for further exploration into biotechnological applications and the molecular evolution of lichen substances.

Nine new species of black lichenicolous fungi from the genus Cladophialophora (Chaetothyriales) from two different climatic zones of China

Lichenicolous fungi are parasites of lichens. Many of these fungi are referred to as "black fungi". A diversity of these black fungi include species that are pathogenic to humans and plants. A majority of black fungi reside in the phylum Ascomycota within the sub-classes Chaetothyriomycetidae and Dothideomycetidae. To explore the diversity of lichenicolous "black fungi" associated with lichens in China, we conducted several field surveys in the Inner Mongolia Autonomous Region and Yunnan Province between 2019 and 2020. We recovered 1,587 fungal isolates from the lichens collected during these surveys. During the preliminary identification of these isolates using the complete internal transcribed spacer (ITS), partial large subunit of nuclear ribosomal RNA gene (LSU), and small subunit of nuclear ribosomal RNA gene (SSU), we identified 15 fungal isolates from the genus Cladophialophora. However, these isolates had low sequence similarities with all known species from the genus. Therefore, we amplified additional gene regions, such as, translation elongation factor (TEF) and partial β-tubulin gene (TUB), and constructed a multi-gene phylogeny using maximum likelihood, maximum parsimony, and Bayesian inference. In our datasets, we included type sequences where available for all Cladophialophora species. Phylogenetic analyses revealed that none of the 15 isolates belonged to any of the previously described species in the genus. Therefore, using both morphological and molecular data, we classified these 15 isolates as nine new species within the genus Cladophialophora: C. flavoparmeliae, C. guttulate, C. heterodermiae, C. holosericea, C. lichenis, C. moniliformis, C. mongoliae, C. olivacea, and C. yunnanensis. The outcome from this study shows that lichens are an important refugia for black lichenicolous fungi, such as those from Chaetothyriales.

Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert

Introduction

Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert.

Methods

This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total Bacteria, Cyanobacteria, Archaea, and Fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, and electrical conductivity.

Results

Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. Apart from richness within Archaea (p = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition (p ≥ 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations.

Discussion

Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world.

Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways

Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem

Freshwater network ecosystems consist of interconnected lotic and lentic environments within the same catchment area. Using Plitvice Lakes as an example, we studied the changes in environmental conditions and microbial communities (bacteria and fungi) that occur with downstream flow. Water samples from tributaries, interlake streams, connections of the cascading lakes, and the Korana River, the main outflow of the system, were characterized using amplicon sequencing of bacterial 16S rRNA and fungal ITS2 genes. Our results show that different environmental conditions and bacterial and fungal communities prevail among the three stream types within the freshwater network ecosystem during multiple sampling seasons. Microbial community differences were also confirmed along the longitudinal gradient between the most distant sampling sites. The higher impact of "mass effect" was evident during spring and winter, while "species sorting" and "environmental selection" was more pronounced during summer. Prokaryotic community assembly was majorly influenced by deterministic processes, while fungal community assembly was highly dominated by stochastic processes, more precisely by the undominated fraction, which is not dominated by any process. Despite the differences between stream types, the microbial community of Plitvice Lakes is shown to be very stable by the core microbiome that makes up the majority of stream communities. Our results suggest microbial community succession along the river-lake continuum of microbial communities in small freshwater network ecosystems with developed tufa barriers. IMPORTANCE Plitvice Lakes represent a rare freshwater ecosystem consisting of a complex network of lakes and waterfalls connecting them, as well as rivers and streams supplying water to the lake basin. The unique geomorphological, hydrological, biogeochemical, and biological phenomenon of Plitvice Lakes lies in the biodynamic process of forming tufa barriers. In addition to microbial communities, abiotic water factors also have a major influence on the formation of tufa. Therefore, it is important to understand how changes in environmental conditions and microbial community assembly affect the functioning of the ecosystem of a freshwater network with developed tufa barriers.

Fungal Diversity Associated with Thirty-Eight Lichen Species Revealed a New Genus of Endolichenic Fungi, Intumescentia gen. nov. (Teratosphaeriaceae)

Fungi from the Teratosphaeriaceae (Mycosphaerellales; Dothideomycetes; Ascomycota) have a wide range of lifestyles. Among these are a few species that are endolichenic fungi. However, the known diversity of endolichenic fungi from Teratosphaeriaceae is far less understood compared to other lineages of Ascomycota. We conducted five surveys from 2020 to 2021 in Yunnan Province of China, to explore the biodiversity of endolichenic fungi. During these surveys, we collected multiple samples of 38 lichen species. We recovered a total of 205 fungal isolates representing 127 species from the medullary tissues of these lichens. Most of these isolates were from Ascomycota (118 species), and the remaining were from Basidiomycota (8 species) and Mucoromycota (1 species). These endolichenic fungi represented a wide variety of guilds, including saprophytes, plant pathogens, human pathogens, as well as entomopathogenic, endolichenic, and symbiotic fungi. Morphological and molecular data indicated that 16 of the 206 fungal isolates belonged to the family Teratosphaeriaceae. Among these were six isolates that had a low sequence similarity with any of the previously described species of Teratosphaeriaceae. For these six isolates, we amplified additional gene regions and conducted phylogenetic analyses. In both single gene and multi-gene phylogenetic analyses using ITS, LSU, SSU, RPB2, TEF1, ACT, and CAL data, these six isolates emerged as a monophyletic lineage within the family Teratosphaeriaceae and sister to a clade that included fungi from the genera Acidiella and Xenopenidiella. The analyses also indicated that these six isolates represented four species. Therefore, we established a new genus, Intumescentia gen. nov., to describe these species as Intumescentia ceratinae, I. tinctorum, I. pseudolivetorum, and I. vitii. These four species are the first endolichenic fungi representing Teratosphaeriaceae from China.

Culturable Diversity of Lichen-Associated Yeasts through Enrichment Strategies

Lichens are symbiotic partnerships between a filamentous fungus and a photosymbiotic “alga”. Studies show that lichens harbor endothallic fungi, but that some taxa have been difficult to isolate from the main filamentous thallus-forming fungus and other faster growing lichenicolous/endothallic fungi. Therefore, we aimed to develop and evaluate liquid yeast-enrichment strategies to (1) isolate lichen-associated yeasts in pure culture, and (2) determine the taxonomic placement and breadth of the diversity of culturable yeasts. Eighty-two lichen samples were collected and washed with distilled water, and healthy thalli were ground up and added to seven different yeast-enrichment broths. Yeast colonies were isolated in pure culture and identified using molecular techniques. Initial isolates were identified using BLASTn analysis, and a taxonomic refinement was completed using PhyML analysis. In total, 215 isolates were obtained. The most prevalently isolated ascomycetous yeasts were within the Dothideomycetes (Aureobasidium, Plowrightia, and Dothiora), while the most frequently isolated basidiomycetous yeasts belonged to the genera Curvibasidium, Sporobolomyces, and Tremella. The generic placements could not be determined for 17 isolates, and in total 25 novel species were recovered. The results of this research indicate that (1) lichen-associated yeasts are diverse, (2) employing liquid enrichment strategies is effective for isolating many of these, and (3) lichen thalli represent a valuable untapped reservoir of diverse and novel yeast species.

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.

Lichen and Lichenicolous Fungal Communities Tested as Suitable Systems for the Application of Cross-Taxon Analysis

Lichens are outstanding examples of fungal symbioses that form long-lived structures, the lichen thalli, in which a multiplicity of other microorganisms are hosted. Among these, microfungi seem to establish diverse trophic relationships with their lichen hosts. The most specialised of these fungi are the parasitic lichenicolous fungi, of which the diversity has hardly been explained as a proxy for the diversity of lichen species. Here, we used an exemplar dataset of a well-studied alpine lichen community composed of 63 lichen and 41 lichenicolous fungal species and tested it to verify the strength of the co-occurrences of the two species groups with predictive co-correspondence analyses. The results showed that the distribution of lichen abundances affects the abundance and variation of lichenicolous fungi and supports our hypothesis to use lichens as surrogates for lichenicolous fungi in surrogacy analysis.

Penicillium chrysogenum as a fungal factory for feruloyl esterases

Plant biomass is a promising substrate for biorefinery, as well as a source of bioactive compounds, platform chemicals, and precursors with multiple industrial applications. These applications depend on the hydrolysis of its recalcitrant structure. However, the effective biological degradation of plant cell walls requires several enzymatic groups acting synergistically, and novel enzymes are needed in order to achieve profitable industrial hydrolysis processes. In the present work, a feruloyl esterase (FAE) activity screening of Penicillium spp. strains revealed a promising candidate (Penicillium rubens Wisconsin 54-1255; previously Penicillium chrysogenum), where two FAE-ORFs were identified and subsequently overexpressed. Enzyme extracts were analyzed, confirming the presence of FAE activity in the respective gene products (PrFaeA and PrFaeB). PrFaeB-enriched enzyme extracts were used to determine the FAE activity optima (pH 5.0 and 50-55 °C) and perform proteome analysis by means of MALDI-TOF/TOF mass spectrometry. The studies were completed with the determination of other lignocellulolytic activities, an untargeted metabolite analysis, and upscaled FAE production in stirred tank reactors. The findings described in this work present P. rubens as a promising lignocellulolytic enzyme producer. KEY POINTS: • Two Penicillium rubens ORFs were first confirmed to have feruloyl esterase activity. • Overexpression of the ORFs produced a novel P. rubens strain with improved activity. • The first in-depth proteomic study of a P. rubens lignocellulolytic extract is shown.

Microbial community associated with the crustose lichen Rhizocarpon geographicum L. (DC.) living on oceanic seashore: A large source of diversity revealed by using multiple isolation methods

Recently, the study of the interactions within a microcosm between hosts and their associated microbial communities drew an unprecedented interest arising from the holobiont concept. Lichens, a symbiotic association between a fungus and an alga, are redefined as complex ecosystems considering the tremendous array of associated microorganisms that satisfy this concept. The present study focuses on the diversity of the microbiota associated with the seashore located lichen Rhizocarpon geographicum, recovered by different culture-dependent methods. Samples harvested from two sites allowed the isolation and the molecular identification of 68 fungal isolates distributed in 43 phylogenetic groups, 15 bacterial isolates distributed in five taxonomic groups and three microalgae belonging to two species. Moreover, for 12 fungal isolates belonging to 10 different taxa, the genus was not described in GenBank. These fungal species have never been sequenced or described and therefore non-studied. All these findings highlight the novel and high diversity of the microflora associated with R. geographicum. While many species disappear every day, this work suggests that coastal and wild environments still contain an unrevealed variety to offer and that lichens constitute a great reservoir of new microbial taxa which can be recovered by multiplying the culture-dependent techniques.

Fruticose Lichen Communities at the Edge: Distribution and Diversity in a Desert Sky Island on the Colorado Plateau

Subalpine habitats in sky islands in the Southwestern USA are currently facing large-scale transformations. Lichens have widely been used as bioindicators of environmental change. On the Colorado Plateau, fruticose lichens occur in patchy, disconnected populations, including unique lichen-draped conifer sites in subalpine forests in the La Sal Mountains in southeastern Utah. Here, we document the distribution and fungal diversity within these lichen communities. We find that lichen-draped conifer sites in the La Sal Mountains are restricted to only three known, small areas in Picea englemannii forests above 3000 m above sea level, two of which have recently been impacted by wildfire. We document 30 different species of lichen-forming fungi in these communities, several which represent the first reports from the Colorado Plateau. We also characterize mycobiont haplotype diversity for the fruticose lichens Evernia divaricata, Ramalina sinensis, and multiple Usnea species. We also report a range of diverse fungi associated with these lichens, including genetic clusters representing 22 orders spanning seven classes of Ascomycetes and fewer clusters representing Basidiomycetes. Our results provide a baseline for ongoing monitoring and help to raise awareness of unique lichen communities and other biodiversity in the region.

A review of the potential of lichen substances as antifungal agents: the effects of extracts and lichen secondary metabolites on Fusarium fungi

The present meta-analysis provides literature data on the effect of lichen extracts and single secondary metabolites used against Fusarium spp. moulds. Lichen extracts were obtained from 51 corticolous, 17 terricolous and 18 saxicolous lichen species and 37 secondary compounds were tested against eight fungal species, i.e., Fusarium acuminatum, F. avenaceum, F. culmorum, F. fujikuroi, F. oxysporum, F. roseum, F. solani and F. udum. The researchers used several test methods, mostly to determine MIC and IZ. Extracts were obtained using several solvents, mainly organic ones with use of the Soxhlet apparatus. The most frequently tested species was F. oxysporum, against which lichen substances from Alectoria sarmentosa, Cladonia mitis, C. rangiferina, Flavoparmelia caperata, Hypotrachyna cirrhata, Leucodermia leucomelos, Parmotrema austrosinense, P. reticulatum, Physcia aipolia, Pseudevernia furfuracea, Roccella montagnei and Umbilicaria nylanderiana and secondary metabolites such as 2-hydroxy-4-methoxy-3,6-dimethylbenzoic acid, atranorin, lecanoric and (+)-usnic acids showed the highest antifungal potential. These agencies could compete with the potential of fungicides, such as flucytosine and fluconazole. Other species have been poorly investigated. Statistical analysis of literature data showed that the fungistatic potential of lichen extracts is significantly different from individual secondary metabolites. Similarly, the potential of secondary metabolites often differs significantly from that of non-lichen substances. This meta-analysis indicates the potential of lichen substances as future anti-fusarial agents.

Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom

Fungi are well-known decomposers of organic matter that thrive in virtually any environment on earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts, but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals, but beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.

Lichen cell factories: methods for the isolation of photobiont and mycobiont partners for defined pure and co-cultivation

Background

Due to their huge biodiversity and the capability to produce a wide range of secondary metabolites, lichens have a great potential in biotechnological applications. They have, however, hardly been used as cell factories to date, as it is considered to be difficult and laborious to cultivate lichen partners in pure or co-culture in the laboratory. The various methods used to isolate lichen fungi, based on either the ascospores, the conidia, or the thallus, have so far not been compared or critically examined. Therefore, here we systematically investigate and compare the known methods and two new methods to identify the most suitable technology for isolation of fungi from lichens.

Results

Within this study six lichen fungi species were isolated and propagated as pure cultures. All of them formed colonies within one month. In case of lichens with ascocarps the spore discharge was the most suitable method. Spores were already discharged within 2 days and germinated within only four days and the contamination rate was low. Otherwise, the soredia and thallus method without homogenization, as described in this work, are also well suited to obtain pure fungal cultures. For the isolation of algae, we were also successful with the thallus method without homogenization.

Conclusion

With the methods described here and the proposed strategic approach, we believe that a large proportion of the lichen fungi can be cultivated within a reasonable time and effort. Based on this, methods of controlled cultivation and co-cultivation must now be developed in order to use the potential of lichens with regard to their secondary metabolites, but also for other applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01804-6.

Phylogeny and Ecology of Trebouxia Photobionts From Bolivian Lichens

In the past few years, new phylogenetic lineages in Trebouxia were detected as a result of molecular approaches. These studies included symbiont selectivity in lichen communities, transects along altitudinal gradients at local and global scales and the photobiont diversity in local populations of lichen-forming fungal species. In most of these studies, phylogenetic and haplotype analyses based on the internal transcribed spacer (ITS) locus have continuously allowed the recognition of new monophyletic lineages, which suggests that still numerous undiscovered Trebouxia lineages can be hidden in lichens from unexplored areas, especially in the tropics. Here, we estimated the biodiversity of photobionts in Bolivian Andean vegetation and assessed their specificity. About 403 lichen samples representing 42 genera, e.g., Haematomma, Heterodermia, Hypotrachyna, Lecanora, Lepra, Leucodermia, Parmotrema, Pertusaria, Polyblastidium, and Usnea, containing Trebouxia photobionts, were analyzed. ITS ribosomal DNA (rDNA) and rbcL markers were used. We obtained Trebouxia sequences from Bolivian samples belonging to already described clades A, C, I, and S. Thirty-nine Trebouxia lineages were distinguished within these clades, while 16 were new. To reveal the structure of the community of Bolivian photobionts and their relationships with mycobionts, the comparative effects of climate, altitude, geographical distances, substrate, and habitat type, as well as functional traits of lichens such as growth forms, propagation mode and secondary metabolites, were analyzed. Furthermore, new Bolivian records were included in analysis on a global scale. In our study, the mycobiont genus or even species are the most important factors correlated with photobiont identity. Moreover, we revealed that the community of Bolivian photobionts is shaped by altitude.

Predicting global numbers of teleomorphic ascomycetes

Sexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.

Metagenomes of Lichens Solorina crocea and Peltigera canina

Lichen genomes are usually considered genomes of separately cultured mycobiont and photobiont. Analysis of lichen metagenomes can give important information on specific lichen-associated microorganisms that can affect lichen metabolism. Here, we report a metagenome of peltigeralean lichens, containing cyanobacterial (Peltigera canina) and cyanobacterial/green algal (Solorina crocea) partners.

Biodiversity Patterns and Ecological Preferences of the Photobionts Associated With the Lichen-Forming Genus Parmelia

The worldwide, ecologically relevant lichen-forming genus Parmelia currently includes 41 accepted species, of which the Parmelia sulcata group (PSULgp) and the Parmelia saxatilis group (PSAXgp) have received considerable attention over recent decades; however, phycobiont diversity is poorly known in Parmelia s. lat. Here, we studied the diversity of Trebouxia microalgae associated with 159 thalli collected from 30 locations, including nine Parmelia spp.: P. barrenoae, P. encryptata, P. ernstiae, P. mayi, P. omphalodes, P. saxatilis, P. serrana, P. submontana, and P. sulcata. The mycobionts were studied by carrying out phylogenetic analyses of the nrITS. Microalgae genetic diversity was examined by using both nrITS and LSU rDNA markers. To evaluate putative species boundaries, three DNA species delimitation analyses were performed on Trebouxia and Parmelia. All analyses clustered the mycobionts into two main groups: PSULgp and PSAXgp. Species delimitation identified 13 fungal and 15 algal species-level lineages. To identify patterns in specificity and selectivity, the diversity and abundance of the phycobionts were identified for each Parmelia species. High specificity of each Parmelia group for a given Trebouxia clade was observed; PSULgp associated only with clade I and PSAXgp with clade S. However, the degree of specificity is different within each group, since the PSAXgp mycobionts were less specific and associated with 12 Trebouxia spp., meanwhile those of PSULgp interacted only with three Trebouxia spp. Variation-partitioning analyses were conducted to detect the relative contributions of climate, geography, and symbiotic partner to phycobiont and mycobiont distribution patterns. Both analyses explained unexpectedly high portions of variability (99 and 98%) and revealed strong correlations between the fungal and algal diversity. Network analysis discriminated seven ecological clusters. Even though climatic conditions explained the largest proportion of the variation among these clusters, they seemed to show indifference relative to climatic parameters. However, the cluster formed by P. saxatilis A/P. saxatilis B/Trebouxia sp. 2/Trebouxia sp. S02/Trebouxia sp. 3A was identified to prefer cold-temperate as well as humid summer environments.

Fungal diversity in the coastal waters of King George Island (maritime Antarctica)

Fungi have been reported as common inhabitants of the maritime waters in Antarctica by studies based on culture-dependent methods. More recently, results obtained using DNA sequencing technologies, revealed that fungal diversity worldwide has been underestimated by culture methods. The present study provides the first characterization of fungal communities in the coastal waters of King George Island (maritime Antarctica) using both culture-dependent and high-throughput sequencing (HTS) methods. HTS demostrated a higher level of fungal diversity than the obtained by culture methods. A high prevalence of basidiomycetous yeasts and ascomycetous filamentous fungi was confirmed by both methods, however, Chythriomycota, Rozellomycota, lichenized fungi and Malassezia spp. were detected only by HTS. Correspondingly, members of some genera, such as Metschnikowia, were only found by culture-dependent methods. Our results confirm that culturing and HTS, should be seen as complementary approaches that enable one to obtain a more comprehensive picture of the composition of microbial communities.

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.

Enhanced culturing techniques for the mycobiont isolated from the lichen Xanthoria parietina

Lichens and their isolated symbionts are potentially valuable resources for biotechnological approaches. Especially mycobiont cultures that produce secondary lichen products are receiving increasing attention, but lichen mycobionts are notoriously slow-growing organisms. Sufficient biomass production often represents a limiting factor for scientific and biotechnological investigations, requiring improvement of existing culturing techniques as well as methods for non-invasive assessment of growth. Here, the effects of pH and the supplement of growth media with either D-glucose or three different sugar alcohols that commonly occur in lichens, D-arabitol, D-mannitol and ribitol, on the growth of the axenically cultured mycobiont isolated from the lichen Xanthoria parietina were tested. Either D-glucose or different sugar alcohols were offered to the fungus at different concentrations, and cumulative growth and growth rates were assessed using two-dimensional image analysis over a period of 8 weeks. The mycobiont grew at a pH range from 4.0 to 7.0, whereas no growth was observed at higher pH values. Varying the carbon source in Lilly-Barnett medium (LBM) by replacing 1% D-glucose used in the originally described LBM by either 1%, 2% or 3% of D-mannitol, or 3% of D-glucose increased fungal biomass production by up to 26%, with an exponential growth phase between 2 and 6 weeks after inoculation. In summary, we present protocols for enhanced culture conditions and non-invasive assessment of growth of axenically cultured lichen mycobionts using image analysis, which may be useful for scientific and biotechnological approaches requiring cultured lichen mycobionts.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11557-021-01707-7.

Thallus Growth Stage and Geographic Origin Shape Microalgal Diversity in Ramalina farinacea Lichen Holobionts

Lichen symbioses are microecosystems hosting many other living organisms besides the two major lichen symbionts (i.e., lichenized fungi [the mycobiont] and green microalgae or cyanobacteria [the photobiont]). Recent investigations evidenced that other fungi, non-photosynthetic bacteria, and microalgae co-inhabit within the lichen thalli, but their diversity and their roles are still underinvestigated. Here we present an ad hoc stratified sampling design and in-depth Illumina paired-end metabarcoding approach to explore microalgal diversity in lichen thalli of the model species Ramalina farinacea from different ecologies. Lichen thalli were surveyed according to three different sizes, and different thallus parts were considered for molecular, bioinformatics, and community diversity analyses. The results revealed that microalgal diversity strongly depends on the growth stage of the thalli, the geographic area, and the habitat type. The results also show that microalgal diversity does not vary along the thallus branches (lacinias)-that is, it does not correlate with the apical growth and founder effects-and that there is no balanced co-presence of two main photobionts as previously established in R. farinacea. The sampling design performed here minimizes bias in the assessment of photobiont diversity in lichens and is proposed to be reliable and applicable to further study microalgal diversity in lichen symbioses.

The Lichens' Microbiota, Still a Mystery?

Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont's contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

Phytohormone release by three isolated lichen mycobionts and the effects of indole-3-acetic acid on their compatible photobionts

Evidence is emerging that phytohormones represent key inter-kingdom signalling compounds supporting chemical communication between plants, fungi and bacteria. The roles of phytohormones for the lichen symbiosis are poorly understood, particularly in the process of lichenization, i.e. the key events which lead free-living microalgae and fungi to recognize each other, make physical contact and start developing a lichen thallus. Here, we studied cellular and extracellularly released phytohormones in three lichen mycobionts, Cladonia grayi, Xanthoria parietina and Tephromela atra, grown on solid medium, and the effects of indole-3-acetic acid (IAA) on their respective photobionts, Asterochloris glomerata, Trebouxia decolorans, Trebouxia sp. Using ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) we found that mycobionts produced IAA, salicylic acid (SA) and jasmonic acid (JA). IAA represented the most abundant phytohormone produced and released by all mycobionts, whereas SA was released by X. parietina and T. atra, and JA was released by C. grayi only. With a half-life of 5.2 days, IAA degraded exponentially in solid BBM in dim light. When IAA was exogenously offered to the mycobionts' compatible photobionts at "physiological" concentrations (as released by their respective mycobionts and accumulated in the medium over seven days), the photobionts' water contents increased up to 4.4%. Treatment with IAA had no effects on the maximum quantum yield of photosystem II, dry mass, and the contents of photosynthetic pigments and α-tocopherol of the photobionts. The data presented may be useful for designing studies aimed at elucidating the roles of phytohormones in lichens.

Diversity and Distribution Patterns of Endolichenic Fungi in Jeju Island, South Korea

Lichens are symbiotic organisms containing diverse microorganisms. Endolichenic fungi (ELF) are one of the inhabitants living in lichen thalli, and have potential ecological and industrial applications due to their various secondary metabolites. As the function of endophytic fungi on the plant ecology and ecosystem sustainability, ELF may have an influence on the lichen diversity and the ecosystem, functioning similarly to the influence of endophytic fungi on plant ecology and ecosystem sustainability, which suggests the importance of understanding the diversity and community pattern of ELF. In this study, we investigated the diversity and the factors influencing the community structure of ELF in Jeju Island, South Korea by analyzing 619 fungal isolates from 79 lichen samples in Jeju Island. A total of 112 ELF species was identified and the most common species belonged to Xylariales in Sordariomycetes. The richness and community structure of ELF were significantly influenced by the host taxonomy, together with the photobiont types and environmental factors. Our results suggest that various lichen species in more diverse environments need to be analyzed to expand our knowledge of the diversity and ecology of ELF.

Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): An impetus for developing an integrated taxonomy

Lichens provide valuable systems for studying symbiotic interactions. In lichens, these interactions are frequently described in terms of availability, selectivity and specificity of the mycobionts and photobionts towards one another. The lichen-forming, green algal genus Trebouxia Puymaly is among the most widespread photobiont, associating with a broad range of lichen-forming fungi. To date, 29 species have been described, but studies consistently indicate that the vast majority of species-level lineages still lack formal description, and new, previously unrecognized lineages are frequently reported. To reappraise the diversity and the evolutionary relationships of species-level lineages in Trebouxia, we assembled DNA sequence data from over 1600 specimens, compiled from a range of sequences from previously published studies, axenic algal cultures, and lichens collected from poorly sampled regions. From these samples, we selected representatives of the currently known genetic diversity in the lichenized Trebouxia and inferred a phylogeny from multi-locus sequence data (ITS, rbcL, cox2). We demonstrate that the current formally described species woefully underrepresent overall species-level diversity in this important lichen-forming algal genus. We anticipate that an integrative taxonomic approach, incorporating morphological and physiological data from axenic cultures with genetic data, will be required to establish a robust, comprehensive taxonomy for Trebouxia. The data presented here provide an important impetus and reference dataset for more reliably characterizing diversity in lichenized algae and in using lichens to investigate the evolution of symbioses and holobionts.

What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

Biodiversity and ecology of microorganisms in high pressure membrane filtration systems

High-pressure membrane filtration (reverse osmosis and nanofiltration) is used to purify different water sources, including wastewater, surface water, groundwater and seawater. A major concern in membrane filtration is the accumulation and growth of micro-organisms and their secreted polymeric substances, leading to reduced membrane performance and membrane biofouling. The fundamental understanding of membrane biofouling is limited despite years of research, as the means of microbial interactions and response to the conditions on the membrane surface are complicated. Here, we discuss studies that investigated the microbial diversity of fouled high-pressure membranes. High-throughput amplicon sequencing of the 16S rRNA gene have shown that Burkholderiales, Pseudomonadales, Rhizobiales, Sphingomonadales and Xanthomonadales frequently obtain a high relative abundance on fouled membranes. The bacterial communities present in the diverse feed water types and in pre-treatment compartments are different from the communities on the membrane, because high-pressure membrane filtration provides a selective environment for certain bacterial groups. The biofilms that form within the pre-treatment compartments do not commonly serve as an inoculum for the subsequent high-pressure membranes. Besides bacteria also fungi are detected in the water treatment compartments. In contrast to bacteria, the fungal community does not change much throughout membrane cleaning. The stable fungal diversity indicates that they are more significant in membrane biofouling than previously thought. By reviewing the biodiversity and ecology of microbes in the whole high pressure membrane filtration water chain, we have been able to identify potentials to improve biofouling control. These include modulation of hydrodynamic conditions, nutrient limitation and the combination of cleaning agents to target the entire membrane microbiome.

Trace elements baseline levels in Usnea antarctica from Clearwater Mesa, James Ross Island, Antarctica

Clearwater Mesa is a pristine area located SE of Croft Bay in James Ross Island, at the northeast of the Antarctic Peninsula. The closest anthropic construction is the summer Mendel station located 25 km to the NE. Clearwater is a remote basalt volcanic mesa, (64° 01' S, 57° 42' W) located at ~ 250 m a.s.l., with around 50 small shallow lakes, a well-developed lichens flora and scarce fauna. The mesa offers a good opportunity to use lichens, like Usnea antarctica, as a biomonitor species. The aim of this study was to determine the baseline levels of trace elements in Usnea antarctica and their relationships with geographical parameters and climatological aspects, to use them as reference levels in futures studies. Usnea antarctica was collected in 23 sites in two transects: perpendicular and parallel to the shore. We found high contents of the elements associated with long-distance transport like Sm, La, Sc, Fe, Co, Hg, and Ca. The elements linked to the marine biogenic cycle as Sr, Rb, Cs, K, Na, Sb, As, Se, and Br were less significant. The distance to the sea was the factor that related the element contents. Hg, Se, As, and Br content in Usnea antarctica increased from the inland towards the sea coast.

Determination of the effect of RBBR on laccase activity and gene expression level of fungi in lichen structure

This study provides information about the differential transcription regulation of laccase genes in response to RBBR dye. To this purpose, we determined the laccase gene expression, laccase activity, and protein profile of lichen-forming fungi supported to RBBR dye. For those obtained from optimal laccase genes expression profiles, we modified different RNA extraction protocols to obtain high quality and quantity RNA to be used in downstream applications in lichen-forming fungus. We also determined the expression of ten laccase genes in response to RBBR dye by qRT-PCR and validated protein profile. As a result of our study, a high laccase activity of 522 U mL^-1 was obtained after submerged fermentation for 17 days. The maximal laccase activity to RBBR dye was obtained at 408 h. The expression profiles of laccase gene expression on ten laccase genes showed up- or down-regulation in course of eight fermentation times. The most up-regulated gene during the process was lac8. However, poxa1b gene expression was lowest in lichen-forming fungi biomass supplemented with RBBR dye. This study has revealed the influence of RBBR dye on laccase activity levels and the determination of gene expression levels in lichen-forming fungi.