3D biofilms: in search of the polysaccharides holding together lichen symbioses

A spectrophotometric analysis of extracted water-soluble phenolic metabolites of lichens

MAIN CONCLUSION

Rainwater most probably constitutes a relatively effective solvent for lichen substances in nature which have the potential to provide for human and environmental needs in the future. The aims were (i) to test the hypothesis on the potential solubility of lichen phenolic compounds using rainwater under conditions that partly reflect the natural environment and (ii) to propose new and effective methods for the water extraction of lichen substances. The results of spectrophotometric analyses of total phenolic metabolites in rainwater-based extracts from epigeic and epiphytic lichens, employing the Folin-Ciocalteu (F.-C.) method, are presented. The water solvent was tested at three pH levels: natural, 3, and 9. Extraction methods were undertaken from two perspectives: the partial imitation of natural environmental conditions and the potential use of extraction for economic purposes. From an ecological perspective, room-temperature water extraction ('cold' method) was used for 10-, 60-, and 120-min extraction periods. A variant of water extraction at analogous time intervals was an 'insolation' with a 100W light bulb to simulate the heat energy of the sun. For economic purposes, the water extraction method used the Soxhlet apparatus and its modified version, the 'tea-extraction' method ('hot' ones). The results showed that those extractions without an external heat source were almost ineffective, but insolation over 60- and 120-min periods proved to be more effective. Both tested 'hot' methods also proved to be effective, especially the 'tea-extraction' one. Generally, an increase in the concentration of phenolic compounds in water extracts resulted from an increasing solvent pH. The results show the probable involvement of lichen substances in biogeochemical processes in nature and their promising use for a variety of human necessities.

Synthesis of galactomannan fragments to help NMR assignment of polysaccharides extracted from lichens

The synthesis of six model trisaccharides representative of galactomannans produced by lichens was performed through stereoselective glycosylation. These standards include linear and branched galactomannans bearing either galactofuranosyl or galactopyranosyl entities. The complete assignment of 1H and 13C signals for both forms of synthetically reduced oligosaccharides was performed. The resulting NMR data were used to quickly demonstrate the structural characteristics of minor polysaccharides within different extracts of three representative lichens.

Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert

The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota, and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment-including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.

The extracellular matrix of green algae

Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.

The Tripartite Lichen Ricasolia virens: Involvement of Cyanobacteria and Bacteria in Its Morphogenesis

Ricasolia virens is an epiphytic lichen-forming fungus mainly distributed in Western Europe and Macaronesia in well-structured forests with ecological continuity that lack eutrophication. It is considered to be threatened or extinct in many territories in Europe (IUCN). Despite its biological and ecological relevance, studies on this taxon are scarce. The thalli are tripartite, and the mycobiont has a simultaneous symbiotic relationship with cyanobacteria and green microalgae, which represent interesting models to analyse the strategies and adaptations resulting from the interactions of lichen symbionts. The present study was designed to contribute to a better understanding of this taxon, which has shown a clear decline over the last century. The symbionts were identified by molecular analysis. The phycobiont is Symbiochloris reticulata, and the cyanobionts (Nostoc) are embedded in internal cephalodia. Light, transmission electron and low-temperature scanning microscopy techniques were used to investigate the thallus anatomy, ultrastructure of microalgae and ontogeny of pycnidia and cephalodia. The thalli are very similar to its closest relative, Ricasolia quercizans. The cellular ultrastructure of S. reticulata by TEM is provided. Non-photosynthetic bacteria located outside the upper cortex are introduced through migratory channels into the subcortical zone by the splitting of fungal hyphae. Cephalodia were very abundant, but never as external photosymbiodemes.

A roadmap for the creation of synthetic lichen

Lichens represent a charismatic corner of biology that has a rich history of scientific exploration, but to which modern biological techniques have been sparsely applied. This has limited our understanding of phenomena unique to lichen, such as the emergent development of physically coupled microbial consortia or distributed metabolisms. The experimental intractability of natural lichens has prevented studies of the mechanistic underpinnings of their biology. Creating synthetic lichen from experimentally tractable, free-living microbes has the potential to overcome these challenges. They could also serve as powerful new chassis for sustainable biotechnology. In this review we will first briefly introduce what lichen are, what remains mysterious about their biology, and why. We will then articulate the scientific insights that creating a synthetic lichen will generate and lay out a roadmap for how this could be achieved using synthetic biology. Finally, we will explore the translational applications of synthetic lichen and detail what is needed to advance the pursuit of their creation.

Microbiomic Analysis of Bacteria Associated with Rock Tripe Lichens in Continental and Maritime Antarctic Regions

Increased research attention is being given to bacterial diversity associated with lichens. Rock tripe lichens (Umbilicariaceae) were collected from two distinct Antarctic biological regions, the continental region near the Japanese Antarctic station (Syowa Station) and the maritime Antarctic South Orkney Islands (Signy Island), in order to compare their bacterial floras and potential metabolism. Bulk DNA extracted from the lichen samples was used to amplify the 18S rRNA gene and the V3-V4 region of the 16S rRNA gene, whose amplicons were Sanger- and MiSeq-sequenced, respectively. The fungal and algal partners represented members of the ascomycete genus Umbilicaria and the green algal genus Trebouxia, based on 18S rRNA gene sequences. The V3-V4 sequences were grouped into operational taxonomic units (OTUs), which were assigned to eight bacterial phyla, Acidobacteriota, Actinomyceota, Armatimonadota, Bacteroidota, Cyanobacteria, Deinococcota, Pseudomonadota and the candidate phylum Saccharibacteria (also known as TM7), commonly present in all samples. The OTU floras of the two biological regions were clearly distinct, with regional biomarker genera, such as Mucilaginibacter and Gluconacetobacter, respectively. The OTU-based metabolism analysis predicted higher membrane transport activities in the maritime Antarctic OTUs, probably influenced by the sampling area’s warmer maritime climatic setting.

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.

Little time left. Microrefuges may fail in mitigating the effects of climate change on epiphytic lichens

Climate change is already causing considerable reductions in biodiversity in all terrestrial ecosystems. These consequences are expected to be exacerbated in biomes that are particularly exposed to change, such as those in the Mediterranean, and in certain groups of more sensitive organisms, such as epiphytic lichens. These poikylohydric organisms find suitable light and water conditions on trunks under the tree canopy. Despite their small size, epiphytic communities contribute significantly to the functionality of forest ecosystems. In this work, we surveyed epiphytic lichen communities in a Mediterranean area (Sardinia, Italy) and hypothesized that 1) the effect of microclimate on lichens at tree scale is mediated by the functional traits of these organisms and that 2) micro-refuge trees with certain morphological characteristics can mitigate the negative effects of future climate change. Results confirm the first hypothesis, while the second is only partially supported, suggesting that the capability of specific trees to host specific conditions may not be sufficient to maintain the diversity and ecosystem functionality of lichen communities in the Mediterranean.

Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species

BACKGROUND

The genus Microbacterium belongs to the family Microbacteriaceae and phylum Actinobacteria. A detailed study on the complete genome and systematic comparative analysis of carbohydrate-active enzyme (CAZyme) among the Microbacterium species would add knowledge on metabolic and environmental adaptation. Here we present the comparative genomic analysis of CAZyme using the complete genome of Antarctic Microbacterium sp. PAMC28756 with other complete genomes of 31 Microbacterium species available.

OBJECTIVE

The genomic and CAZyme comparison of Microbacterium species and to rule out the specific features of CAZyme for the environmental and metabolic adaptation.

METHODS

Bacterial source were collected from NCBI database, CAZyme annotation of Microbacterium species was analyzed using dbCAN2 Meta server. Cluster of orthologous groups (COGs) analysis was performed using the eggNOG4.5 database. Whereas, KEGG database was used to compare and obtained the functional genome annotation information in carbohydrate metabolism and glyoxylate cycle.

RESULTS

Out of 32 complete genomes of Microbacterium species, strain No. 7 isolated from Activated Sludge showed the largest genomic size at 4.83 Mb. The genomic size of PAMC28756 isolated from Antarctic lichen species Stereocaulons was 3.54 Mb, the G + C content was 70.4% with 3,407 predicted genes, of which 3.36% were predicted CAZyme. In addition, while comparing the Glyoxylate cycle among 32 bacteria, except 10 strains, all other, including our strain have Glyoxylate pathway. PAMC28756 contained the genes that degrade cellulose, hemicellulose, amylase, pectinase, chitins and other exo-and endo glycosidases. Utilizing these polysaccharides can provides source of energy in an extreme environment. In addition, PAMC28756 assigned the (10.15%) genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation.

CONCLUSIONS

The genomic content and CAZymes distribution was varied in Microbacterium species. There was the presence of more than 10% genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. In addition, occurrence of glyoxylate cycle for alternative utilization of carbon sources suggest the adaptation of PAMC28756 in the harsh microenvironment.

The lichen market place

This article is a Commentary on Spribille et al. (2022), 234: 1566–1582.

Evolutionary biology of lichen symbioses

Lichens are the symbiotic outcomes of open, interspecies relationships, central to which are a fungus and a phototroph, typically an alga and/or cyanobacterium. The evolutionary processes that led to the global success of lichens are poorly understood. In this review, we explore the goods and services exchange between fungus and phototroph and how this propelled the success of both symbiont and symbiosis. Lichen fungal symbionts count among the only filamentous fungi that expose most of their mycelium to an aerial environment. Phototrophs export carbohydrates to the fungus, which converts them to specific polyols. Experimental evidence suggests that polyols are not only growth and respiratory substrates but also play a role in anhydrobiosis, the capacity to survive desiccation. We propose that this dual functionality is pivotal to the evolution of fungal symbionts, enabling persistence in environments otherwise hostile to fungi while simultaneously imposing costs on growth. Phototrophs, in turn, benefit from fungal protection from herbivory and light stress, while appearing to exert leverage over fungal sex and morphogenesis. Combined with the recently recognized habit of symbionts to occur in multiple symbioses, this creates the conditions for a multiplayer marketplace of rewards and penalties that could drive symbiont selection and lichen diversification.

Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature

The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.

Interactions of Fungi and Algae from the Greenland Ice Sheet

Heavily pigmented glacier ice algae Ancylonema nordenskiöldii and Ancylonema alaskanum (Zygnematophyceae, Streptophyta) reduce the bare ice albedo of the Greenland Ice Sheet, amplifying melt from the largest cryospheric contributor to eustatic sea-level rise. Little information is available about glacier ice algae interactions with other microbial communities within the surface ice environment, including fungi, which may be important for sustaining algal bloom development. To address this substantial knowledge gap and investigate the nature of algal-fungal interactions, an ex situ co-cultivation experiment with two species of fungi, recently isolated from the surface of the Greenland Ice Sheet (here proposed new species Penicillium anthracinoglaciei Perini, Frisvad and Zalar, Mycobank (MB 835602), and Articulospora sp.), and the mixed microbial community dominated by glacier ice algae was performed. The utilization of the dark pigment purpurogallin carboxylic acid-6-O-β-D-glucopyranoside (C₁₈H₁₈O₁₂) by the two fungi was also evaluated in a separate experiment. P. anthracinoglaciei was capable of utilizing and converting the pigment to purpurogallin carboxylic acid, possibly using the sugar moiety as a nutrient source. Furthermore, after 3 weeks of incubation in the presence of P. anthracinoglaciei, a significantly slower decline in the maximum quantum efficiency (F_v/F_m, inverse proxy of algal stress) in glacier ice algae, compared to other treatments, was evident, suggesting a positive relationship between these species. Articulospora sp. did uptake the glycosylated purpurogallin, but did not seem to be involved in its conversion to aglycone derivative. At the end of the incubation experiments and, in conjunction with increased algal mortality, we detected a substantially increasing presence of the zoosporic fungi Chytridiomycota suggesting an important role for them as decomposers or parasites of glacier ice algae.

Large differences in carbohydrate degradation and transport potential among lichen fungal symbionts

Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with reductions in plant cell wall-degrading enzymes, but whether this is true of lichen fungal symbionts (LFSs) is unknown. Here, we predict genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 46 genomes from the Lecanoromycetes, the largest extant clade of LFSs. All LFSs possess a robust CAZyme arsenal including enzymes acting on cellulose and hemicellulose, confirmed by experimental assays. However, the number of genes and predicted functions of CAZymes vary widely, with some fungal symbionts possessing arsenals on par with well-known saprotrophic fungi. These results suggest that stable fungal association with a phototroph does not in itself result in fungal CAZyme loss, and lends support to long-standing hypotheses that some lichens may augment fixed CO₂ with carbon from external sources.

Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. Here, Resl et al. show that, contrary to other fungal symbioses, fungal association with a phototroph in lichens does not result in loss of fungal enzymes for plant cell-wall degradation.

The effect of lichen secondary metabolites on Aspergillus fungi

A systematic review of literature data on the antifungal potential of extracted lichen compounds and individual secondary metabolites against mold species of the genus Aspergillus is provided. Crude extracts from 49 epiphytic, 16 epigeic and 22 epilithic species of lichens and 44 secondary metabolites against 10 species, Aspergillus candidus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. ochraceus, A. parasiticus, A. restrictus, A. stellatus and A. ustus, were analysed. Several measuring techniques were employed for such analyses. Lichen substances were extracted with alcoholic and other organic solvents mainly using the Soxhlet apparatus. Among the three most-studied mold species, the results showed that the crude extracts from the thalli of the lichens Cladonia foliacea, Hypotrachyna cirrhata, Leucodermia leucomelos, Platismatia glauca and Pseudevernia furfuracea against Aspergillus flavus, from C. foliacea, Nephroma arcticum and Parmelia sulcata against A. fumigatus and from Evernia prunastri, Hypogymnia physodes, Umbilicaria cylindrica and Variospora dolomiticola against A. niger have the greatest antifungal potential. The lichen secondary metabolites showed a higher inhibitory potential, e.g. protolichesterinic acid against A. flavus, lecanoric acid against A. fumigatus and orsellinic acid against A. niger; the other seven species of Aspergillus have been poorly studied and require further investigation. A comparison of the inhibitory potential of the tested mixtures of lichen substances and their secondary metabolites shows that they can compete with commonly used antifungal substances, such as ketoconazole and clotrimazole against A. flavus, A. nidulans, A. niger and A. parasiticus and fluconazole in the case of A. fumigatus.

Antarctolichenia onofrii gen. nov. sp. nov. from Antarctic Endolithic Communities Untangles the Evolution of Rock-Inhabiting and Lichenized Fungi in Arthoniomycetes

Microbial endolithic communities are the main and most widespread life forms in the coldest and hyper-arid desert of the McMurdo Dry Valleys and other ice-free areas across Victoria Land, Antarctica. There, the lichen-dominated communities are complex and self-supporting assemblages of phototrophic and heterotrophic microorganisms, including bacteria, chlorophytes, and both free-living and lichen-forming fungi living at the edge of their physiological adaptability. In particular, among the free-living fungi, microcolonial, melanized, and anamorphic species are highly recurrent, while a few species were sometimes found to be associated with algae. One of these fungi is of paramount importance for its peculiar traits, i.e., a yeast-like habitus, co-growing with algae and being difficult to propagate in pure culture. In the present study, this taxon is herein described as the new genus Antarctolichenia and its type species is A. onofrii, which represents a transitional group between the free-living and symbiotic lifestyle in Arthoniomycetes. The phylogenetic placement of Antarctolichenia was studied using three rDNA molecular markers and morphological characters were described. In this study, we also reappraise the evolution and the connections linking the lichen-forming and rock-inhabiting lifestyles in the basal lineages of Arthoniomycetes (i.e., Lichenostigmatales) and Dothideomycetes.

Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism

Lichen thalli are formed through the symbiotic association of a filamentous fungus and photosynthetic green alga and/or cyanobacterium. Recent studies have revealed lichens also host highly diverse communities of secondary fungal and bacterial symbionts, yet few studies have examined the viral component within these complex symbioses. Here, we describe viral biodiversity and functions in cyanolichens collected from across North America and Europe. As current machine-learning viral-detection tools are not trained on complex eukaryotic metagenomes, we first developed efficient methods to remove eukaryotic reads prior to viral detection and a custom pipeline to validate viral contigs predicted with three machine-learning methods. Our resulting high-quality viral data illustrate that every cyanolichen thallus contains diverse viruses that are distinct from viruses in other terrestrial ecosystems. In addition to cyanobacteria, predicted viral hosts include other lichen-associated bacterial lineages and algae, although a large fraction of viral contigs had no host prediction. Functional annotation of cyanolichen viral sequences predicts numerous viral-encoded auxiliary metabolic genes (AMGs) involved in amino acid, nucleotide, and carbohydrate metabolism, including AMGs for secondary metabolism (antibiotics and antimicrobials) and fatty acid biosynthesis. Overall, the diversity of cyanolichen AMGs suggests that viruses may alter microbial interactions within these complex symbiotic assemblages.

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.

Tremella macrobasidiata and Tremella variae have abundant and widespread yeast stages in Lecanora lichens

Dimorphism is a widespread feature of tremellalean fungi in general, but a little-studied aspect of the biology of lichen-associated Tremella. We show that Tremella macrobasidiata and Tremella variae have an abundant and widespread yeast stage in their life cycles that occurs in Lecanora lichens. Their sexual filamentous stage is restricted to a specific lichen: T. macrobasidiata only forms basidiomata on Lecanora chlarotera hymenia and T. variae only on Lecanora varia thalli. However, the yeast stage of T. macrobasidiata is less specific and can occur in L. varia lichens, whilst all life stages of T. variae may be specific to L. varia. Contrary to the hyphal stages, the yeasts are distributed across the thalli and hymenia of Lecanora lichens, and not limited to specimens with basidiomata. Tremella macrobasidiata was present in all studied L. chlarotera, and in 59% of L. varia specimens. Only in 8% of the L. varia thalli could none of the two Tremella species be detected. Our results indicate that lichen-associated Tremella may be much more abundant and widespread than previously assumed leading to skewed estimations about their distribution ranges and lichen specificity, and raise new questions about their biology, ecology and function in the symbiosis.

Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes

Basidiomycete yeasts have recently been reported as stably associated secondary fungal symbionts of many lichens, but their role in the symbiosis remains unknown. Attempts to sequence their genomes have been hampered both by the inability to culture them and their low abundance in the lichen thallus alongside two dominant eukaryotes (an ascomycete fungus and chlorophyte alga). Using the lichen Alectoria sarmentosa, we selectively dissolved the cortex layer in which secondary fungal symbionts are embedded to enrich yeast cell abundance and sequenced DNA from the resulting slurries as well as bulk lichen thallus. In addition to yielding a near-complete genome of the filamentous ascomycete using both methods, metagenomes from cortex slurries yielded a 36- to 84-fold increase in coverage and near-complete genomes for two basidiomycete species, members of the classes Cystobasidiomycetes and Tremellomycetes. The ascomycete possesses the largest gene repertoire of the three. It is enriched in proteases often associated with pathogenicity and harbors the majority of predicted secondary metabolite clusters. The basidiomycete genomes possess ∼35% fewer predicted genes than the ascomycete and have reduced secretomes even compared with close relatives, while exhibiting signs of nutrient limitation and scavenging. Furthermore, both basidiomycetes are enriched in genes coding for enzymes producing secreted acidic polysaccharides, representing a potential contribution to the shared extracellular matrix. All three fungi retain genes involved in dimorphic switching, despite the ascomycete not being known to possess a yeast stage. The basidiomycete genomes are an important new resource for exploration of lifestyle and function in fungal–fungal interactions in lichen symbioses.

Diversity of Leptogium (Collemataceae, Ascomycota) in East African Montane Ecosystems

Tropical mountains and especially their forests are hot spots of biodiversity threatened by human population pressure and climate change. The diversity of lichens in tropical Africa is especially poorly known. Here we use the mtSSU and nuITS molecular markers together with morphology and ecology to assess Leptogium (Peltigerales, Ascomycota) diversity in the tropical mountains of Taita Hills and Mt. Kasigau in Kenya and Mt. Kilimanjaro in Tanzania. The sampled habitats cover a wide range of ecosystems from savanna to alpine heath vegetation and from relatively natural forests to agricultural environments and plantation forests. We demonstrate that Leptogium diversity in Africa is much higher than previously known and provide preliminary data on over 70 putative species, including nine established species previously known from the area and over 60 phylogenetically, morphologically, and/or ecologically defined Operational Taxonomic Units (OTUs). Many traditional species concepts are shown to represent morphotypes comprised of several taxa. Many of the species were only found from specific ecosystems and/or restricted habitats and are thus threatened by ongoing habitat fragmentation and degradation of the natural environment. Our results emphasize the importance of molecular markers in species inventories of highly diverse organism groups and geographical areas.

Unraveling the sugar code: the role of microbial extracellular glycans in plant-microbe interactions

To defend against microbial invaders but also to establish symbiotic programs, plants need to detect the presence of microbes through the perception of molecular signatures characteristic of a whole class of microbes. Among these molecular signatures, extracellular glycans represent a structurally complex and diverse group of biomolecules that has a pivotal role in the molecular dialog between plants and microbes. Secreted glycans and glycoconjugates such as symbiotic lipochitooligosaccharides or immunosuppressive cyclic β-glucans act as microbial messengers that prepare the ground for host colonization. On the other hand, microbial cell surface glycans are important indicators of microbial presence. They are conserved structures normally exposed and thus accessible for plant hydrolytic enzymes and cell surface receptor proteins. While the immunogenic potential of bacterial cell surface glycoconjugates such as lipopolysaccharides and peptidoglycan has been intensively studied in the past years, perception of cell surface glycans from filamentous microbes such as fungi or oomycetes is still largely unexplored. To date, only few studies have focused on the role of fungal-derived cell surface glycans other than chitin, highlighting a knowledge gap that needs to be addressed. The objective of this review is to give an overview on the biological functions and perception of microbial extracellular glycans, primarily focusing on their recognition and their contribution to plant-microbe interactions.

Influence of secondary metabolites on surface chemistry and metal adsorption of a devitalized lichen biomonitor

Despite the broad use of lichens as biomonitors of airborne trace elements, the surface chemistry and metal adsorption parameters of these organisms are still poorly known. The current investigation is aimed at (i) quantifying the acid-base surface properties and the first-order physical-chemical parameters of Cu2+ and Zn2+ adsorption of devitalized Pseudevernia furfuracea, a lichen commonly used in biomonitoring of airborne trace elements, and (ii) comparing the results with those available for moss biomonitors. Equilibrium constants and metal-binding site concentrations were calculated with a thermodynamic model by taking into account the presence/absence of ancillary extracellular cell wall compounds, namely melanin and acetone-soluble lichen substances. An acid-base titration experiment performed in the pH range of 3-10 showed that melanised and non-melanised P. furfuracea samples have lower pHPZC (3.53-3.99) and higher metal-binding site concentrations (0.96-1.20 mmol g-1) compared to that of the mosses investigated so far at the same experimental conditions. Melanin biosynthesis increased the content of carboxyl and phosphoryl groups and reduces that of amine/polyphenols. Cu2+ and Zn2+ adsorption was unaffected by the degree of melanisation while the removal of extracellular lichen substances slightly decreased Zn2+ adsorption. Although Cu2+ and Zn2+ adsorption parameters related to P. furfuracea surfaces were 3 times lower than in the mosses, lichen samples adsorbed the same amount of Cu2+ and 30% more Zn2+. The present study contributes in understanding the role of ancillary cell wall compounds in Cu2+ and Zn2+ adsorption in a model lichen. It also provides a first comparison between the surface physico-chemical characteristics of lichens and mosses frequently used as biomonitors of trace elements.

The beauty and the yeast: can the microalgae Dunaliella form a borderline lichen with Hortaea werneckii?

Lichenized fungi usually develop complex, stratified morphologies through an intricately balanced living together with their algal partners, but several species are known to form only more or less loose associations with algae. These borderline lichens are still little explored although they could inform us about early stages of lichen evolution. We studied the association of the extremely halotolerant fungus Hortaea werneckii with the alga Dunaliella atacamensis, discovered in a cave in the Atacama Desert (Chile), and with D. salina, common inhabitant of saltern brines. D. atacamensis forms small colonies, in which cells of H. werneckii can be frequently observed, while such interaction has not been observed with D. salina. As symbiotic interactions between Dunaliella and Hortaea have not been reported, we performed a series of co-cultivation experiments to inspect whether these species could interact and develop more distinct lichen-like symbiotic structures. We set up co-cultures between axenic strains of Hortaea werneckii (isolated both from Mediterranean salterns and from the Atacama cave) and isolates of D. atacamensis (from the Atacama cave) and D. salina (isolated from Mediterranean salterns). Although we used different growth media and cultivation approaches, bright field and SEM microscopy analyses did not indicate any mutual effects in these experiments. We discuss the implications for fungal algal interactions along the transition from algal exploiters to lichen symbioses.