The complexity of symbiotic interactions influences the ecological amplitude of the host: A case study in Stereocaulon (lichenized Ascomycota)

Acquisition of green algal photobionts enables both chlorolichens and chloro-cyanolichens to activate photosynthesis at low humidity without liquid water

Cyanobacteria require liquid water for photosynthesis, whereas green algae can photosynthesise with water vapour alone. We discovered that several Lobaria spp. which normally have cyanobacteria as the sole photobiont, in some regions of the trans-Himalayas also harboured green algae. We tested whether green algal acquisition was: limited to high elevations; obtained from neighbouring chloro-Lobaria species; enabled photosynthesis at low humidity. Lobaria spp. were collected from 2000 to 4000 m elevation. Spectrophotometry quantified green algal abundance by measuring chlorophyll b (absent in cyanobacteria). Thalli cross-sections visually confirmed green algal presence. We sequenced gene regions: Lobaria (ITS-EF-1α-RPB2), green algae (18S-RBC-L) and Nostoc (16S). Phylogenetic analysis determined myco-photobiont associations. We used a custom closed-circuit gas exchange system with an infrared gas analyser to measure CO2 exchange rates for desiccated specimens at 33%, 76%, 86% and 98% humidity. Cross-sections revealed that the photobiont layers in putative cyano-Lobaria contained both cyanobacteria and green algae, indicating that they should be considered chloro-cyanolichens. Chloro-Lobaria had no visible cephalodia nor cyanobacteria in the photobiont layer. Chloro-Lobaria and chloro-cyano-Lobaria had comparable levels of chlorophyll b. Chloro-Lobaria usually contained Symbiochloris. Chloro-cyano-Lobaria mainly associated with Parachloroidium and Nostoc; infrequently with Symbiochloris, Apatococcus, Chloroidium, Pseudochlorella, Trebouxia. Sequences from two green algal genera were obtained from within some thalli. Desiccated specimens of every Lobaria species could attain net photosynthesis with light exposure and 33% humidity. CO2 exchange dynamics over a five-day period differed between species. At all elevations, chloro-cyano-Lobaria spp. had abundant green algae in the photobiont layer, but green algal strains mostly differed to those of chloro-Lobaria spp. Both chloro-Lobaria and chloro-cyano-Lobaria were capable of conducting photosynthesis without liquid water. The data strongly suggest that they attained positive net photosynthesis.

Myrmecia, Not Asterochloris, Is the Main Photobiont of Cladonia subturgida (Cladoniaceae, Lecanoromycetes)

This study explores the diversity of photobionts associated with the Mediterranean lichen-forming fungus Cladonia subturgida. For this purpose, we sequenced the whole ITS rDNA region by Sanger using a metabarcoding method for ITS2. A total of 41 specimens from Greece, Italy, France, Portugal, and Spain were studied. Additionally, two specimens from Spain were used to generate four cultures. Our molecular studies showed that the genus Myrmecia is the main photobiont of C. subturgida throughout its geographic distribution. This result contrasts with previous studies, which indicated that the main photobiont for most Cladonia species is Asterochloris. The identity of Myrmecia was also confirmed by ultrastructural studies of photobionts within the lichen thalli and cultures. Photobiont cells showed a parietal chloroplast lacking a pyrenoid, which characterizes the species in this genus. Phylogenetic analyses indicate hidden diversity within this genus. The results of amplicon sequencing showed the presence of multiple ASVs in 58.3% of the specimens studied.

Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Lichen symbiosis is centered around a relationship between a fungus and a photosynthetic microbe, usually a green alga. In addition to their main photosynthetic partner (the photobiont), lichen symbioses can contain additional algae present in low abundance. The biology of these algae and the way they interact with the rest of lichen symbionts remains largely unknown. Here we present the first genome sequence of a non-photobiont lichen-associated alga. Coccomyxa viridis was unexpectedly found in 12% of publicly available lichen metagenomes. With few exceptions, members of the Coccomyxa viridis clade occur in lichens as non-photobionts, potentially growing in thalli endophytically. The 45.7 Mbp genome of C. viridis was assembled into 18 near chromosome-level contigs, making it one of the most contiguous genomic assemblies for any lichen-associated algae. Comparing the C. viridis genome to its close relatives revealed the presence of traits associated with the lichen lifestyle. The genome of C. viridis provides a new resource for exploring the evolution of the lichen symbiosis, and how symbiotic lifestyles shaped evolution in green algae.

Fungal-Algal Association Drives Lichens' Mutualistic Symbiosis: A Case Study with Trebouxia-Related Lichens

Biotic and abiotic factors influence the formation of fungal-algal pairings in lichen symbiosis. However, the specific determinants of these associations, particularly when distantly related fungi are involved, remain poorly understood. In this study, we investigated the impact of different drivers on the association patterns between taxonomically diverse lichenized fungi and their trebouxioid symbiotic partners. We collected 200 samples from four biomes and identified 41 species of lichenized fungi, associating them with 16 species of trebouxioid green algae, of which 62% were previously unreported. The species identity of both the fungal and algal partners had the most significant effect on the outcome of the symbiosis, compared to abiotic factors like climatic variables and geographic distance. Some obviously specific associations were observed in the temperate zone; however, the nestedness value was lower in arid regions than in cold, polar, and temperate regions according to interaction network analysis. Cophylogenetic analyses revealed congruent phylogenies between trebouxioid algae and associated fungi, indicating a tendency to reject random associations. The main evolutionary mechanisms contributing to the observed phylogenetic patterns were "loss" and "failure to diverge" of the algal partners. This study broadens our knowledge of fungal-algal symbiotic patterns in view of Trebouxia-associated fungi.

Cyanobacterial Variability in Lichen Cephalodia

The ecological success of lichens is related to both myco- and photobionts which condition the physiological limits of the lichen symbioses and thus affect their ecological niches and geographic ranges. A particular type of lichen, called cephalolichen, is characterized by housing both green algal and cyanobacterial symbionts-the latter is restricted to special structures called cephalodia. In this type of lichen, questions related to specialization within species or within individuals are still unsolved as different patterns have previously been observed. In order to study the variability at the intrathalline, intraspecific, and interspecific level, cyanobionts from different cephalodia within the same thalli and from different thalli were genetically analysed in three cephalolichen species at two different forests (18 thalli, 90 cephalodia). The results showed variability in the cephalodial Nostoc OTUs in all the studied species, both at the intrathalline and intraspecific levels. The variability of Nostoc OTUs found in different cephalodia of the same thallus suggests low specialization in this relationship. Additionally, differences in OTU diversity in the three studied species and in the two forests were found. The variability observed may confer an increased ecological plasticity and an advantage to colonize or persist under additional or novel habitats or conditions.

Unrecognized diversity and distribution of soil algae from Maritime Antarctica (Fildes Peninsula, King George Island)

Introduction

Eukaryotic algae in the top few centimeters of fellfield soils of ice-free Maritime Antarctica have many important effects on their habitat, such as being significant drivers of organic matter input into the soils and reducing the impact of wind erosion by soil aggregate formation. To better understand the diversity and distribution of Antarctic terrestrial algae, we performed a pilot study on the surface soils of Meseta, an ice-free plateau mountain crest of Fildes Peninsula, King George Island, being hardly influenced by the marine realm and anthropogenic disturbances. It is openly exposed to microbial colonization from outside Antarctica and connected to the much harsher and dryer ice-free zones of the continental Antarctic. A temperate reference site under mild land use, SchF, was included to further test for the Meseta algae distribution in a contrasting environment.

Methods

We employed a paired-end metabarcoding analysis based on amplicons of the highly variable nuclear-encoded ITS2 rDNA region, complemented by a clone library approach. It targeted the four algal classes, Chlorophyceae, Trebouxiophyceae, Ulvophyceae, and Xanthophyceae, representing key groups of cold-adapted soil algae.

Results

A surprisingly high diversity of 830 algal OTUs was revealed, assigned to 58 genera in the four targeted algal classes. Members of the green algal class Trebouxiophyceae predominated in the soil algae communities. The major part of the algal biodiversity, 86.1% of all algal OTUs, could not be identified at the species level due to insufficient representation in reference sequence databases. The classes Ulvophyceae and Xanthophyceae exhibited the most unknown species diversity. About 9% of the Meseta algae species diversity was shared with that of the temperate reference site in Germany.

Discussion

In the small portion of algal OTUs for which their distribution could be assessed, the entire ITS2 sequence identity with references shows that the soil algae likely have a wide distribution beyond the Polar regions. They probably originated from soil algae propagule banks in far southern regions, transported by aeolian transport over long distances. The dynamics and severity of environmental conditions at the soil surface, determined by high wind currents, and the soil algae's high adaptability to harsh environmental conditions may account for the high similarity of soil algal communities between the northern and southern parts of the Meseta.

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.

Symbiont-specific responses to environmental cues in a threesome lichen symbiosis

Photosymbiodemes are a special case of lichen symbiosis where one lichenized fungus engages in symbiosis with two different photosynthetic partners, a cyanobacterium and a green alga, to develop two distinctly looking photomorphs. We compared gene expression of thallus sectors of the photosymbiodeme-forming lichen Peltigera britannica containing cyanobacterial photobionts with thallus sectors with both green algal and cyanobacterial photobionts and investigated differential gene expression at different temperatures representing mild and putatively stressful conditions. First, we quantified photobiont-mediated differences in fungal gene expression. Second, because of known ecological differences between photomorphs, we investigated symbiont-specific responses in gene expression to temperature increases. Photobiont-mediated differences in fungal gene expression could be identified, with upregulation of distinct biological processes in the different morphs, showing that interaction with specific symbiosis partners profoundly impacts fungal gene expression. Furthermore, high temperatures expectedly led to an upregulation of genes involved in heat shock responses in all organisms in whole transcriptome data and to an increased expression of genes involved in photosynthesis in both photobiont types at 15 and 25°C. The fungus and the cyanobacteria exhibited thermal stress responses already at 15°C, the green algae mainly at 25°C, demonstrating symbiont-specific responses to environmental cues and symbiont-specific ecological optima.

Composition, structure and robustness of Lichen guilds

Symbiosis is a major engine of evolutionary innovation underlying many extant complex organisms. Lichens are a paradigmatic example that offers a unique perspective on the role of symbiosis in ecological success and evolutionary diversification. Lichen studies have produced a wealth of information regarding the importance of symbiosis, but they frequently focus on a few species, limiting our understanding of large-scale phenomena such as guilds. Guilds are groupings of lichens that assist each other's proliferation and are intimately linked by a shared set of photobionts, constituting an extensive network of relationships. To characterize the network of lichen symbionts, we used a large data set ([Formula: see text] publications) of natural photobiont-mycobiont associations. The entire lichen network was found to be modular, but this organization does not directly match taxonomic information in the data set, prompting a reconsideration of lichen guild structure and composition. The multiscale nature of this network reveals that the major lichen guilds are better represented as clusters with several substructures rather than as monolithic communities. Heterogeneous guild structure fosters robustness, with keystone species functioning as bridges between guilds and whose extinction would endanger global stability.

A call to reconceptualize lichen symbioses

Several decades of research across disciplines have overturned historical perspectives of symbioses dominated by binary characterizations of highly specific species-species interactions. This paradigm shift has unlocked the previously underappreciated and overlooked dynamism of fungal mutualisms such as mycorrhizae. Lichens are another example of important fungal mutualisms where reconceptualization is urgently needed to realize their potential as model systems. This reconceptualization requires both an objective synthesis of new data and envisioning a revised integrative approach that unifies the spectrum of ecology and evolution. We propose a ten-theme framework that if pursued would propel lichens to the vanguard of symbiotic theory.

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.

Lichens from the littoral zone host diverse Ulvophycean photobionts

Crustose Verrucariaceae lichens form a distinctive black belt on seashores all over the world. This lifestyle is apparently enabled by a specific set of photobionts. However, their diversity is understudied. We sampled these lichens from the northern Patagonian Pacific coast of Chile. Using molecular markers, we identified both mycobionts and photobionts. The lichens, belonging to the genus Hydropunctaria and to the Wahlenbergiella group, hosted solely Ulvophycean photobionts. Pseudendoclonium submarinum (Kornmanniaceae, Ulvales) was the most common, but representatives of other closely related, yet undescribed, lineages were also found. Undulifilum symbioticum gen. et sp. nov. is described within Kornmanniaceae based on culture morphology and DNA sequence data. Furthermore, the free-living macroscopic genus Urospora (Acrosiphoniaceae, Ulotrichales) is reported as a lichen photobiont for the first time and is the first of its kind in the order. These results indicate that undescribed algal diversity is waiting to be uncovered in seashore lichens.

An Exception to the Rule? Could Photobiont Identity Be a Better Predictor of Lichen Phenotype than Mycobiont Identity?

With rare exceptions, the shape and appearance of lichen thalli are determined by the fungal partner; thus, mycobiont identity is normally used for lichen identification. However, it has repeatedly been shown in recent decades that phenotypic data often does not correspond with fungal gene evolution. Here, we report such a case in a three-species complex of red-fruited Cladonia lichens, two of which clearly differ morphologically, chemically, ecologically and in distribution range. We analysed 64 specimens of C. bellidiflora, C. polydactyla and C. umbricola, mainly collected in Europe, using five variable mycobiont-specific and two photobiont-specific molecular markers. All mycobiont markers exhibited very low variability and failed to separate the species. In comparison, photobiont identity corresponded better with lichen phenotype and separated esorediate C. bellidiflora from the two sorediate taxa. These results can be interpreted either as an unusual case of lichen photomorphs or as an example of recent speciation, in which phenotypic differentiation precedes the separation of the molecular markers. We hypothesise that association with different photobionts, which is probably related to habitat differentiation, may have triggered speciation in the mycobiont species.

Contrasting Patterns of Climatic Niche Divergence in Trebouxia-A Clade of Lichen-Forming Algae

Lichen associations are overwhelmingly supported by carbon produced by photosynthetic algal symbionts. These algae have diversified to occupy nearly all climates and continents; however, we have a limited understanding of how their climatic niches have evolved through time. Here we extend previous work and ask whether phylogenetic signal in, and the evolution of, climatic niche, varies across climatic variables, phylogenetic scales, and among algal lineages in Trebouxia—the most common genus of lichen-forming algae. Our analyses reveal heterogeneous levels of phylogenetic signal across variables, and that contrasting models of evolution underlie the evolution of climatic niche divergence. Together these analyses demonstrate the variable processes responsible for shaping climatic tolerance in Trebouxia, and provide a framework within which to better understand potential responses to climate change-associated perturbations. Such predictions reveal a disturbing trend in which the pace at which modern climate change is proceeding will vastly exceed the rate at which Trebouxia climatic niches have previously evolved.

Promiscuity in Lichens Follows Clear Rules: Partner Switching in Cladonia Is Regulated by Climatic Factors and Soil Chemistry

Climatic factors, soil chemistry and geography are considered as major factors affecting lichen distribution and diversity. To determine how these factors limit or support the associations between the symbiotic partners, we revise the lichen symbiosis as a network of relationships here. More than one thousand thalli of terricolous Cladonia lichens were collected at sites with a wide range of soil chemical properties from seven biogeographical regions of Europe. A total of 18 OTUs of the algal genus Asterochloris and 181 OTUs of Cladonia mycobiont were identified. We displayed all realized pairwise mycobiont-photobiont relationships and performed modularity analysis. It revealed four virtually separated modules of cooperating OTUs. The modules differed in mean annual temperature, isothermality, precipitation, evapotranspiration, soil pH, nitrogen, and carbon contents. Photobiont switching was strictly limited to algae from one module, i.e., algae of similar ecological preferences, and only few mycobionts were able to cooperate with photobionts from different modules. Thus, Cladonia mycobionts generally cannot widen their ecological niches through photobiont switching. The modules also differed in the functional traits of the mycobionts, e.g., sexual reproduction rate, presence of soredia, and thallus type. These traits may represent adaptations to the environmental conditions that drive the differentiation of the modules. In conclusion, the promiscuity in Cladonia mycobionts is strictly limited by climatic factors and soil chemistry.

The Role of Photobionts as Drivers of Diversification in an Island Radiation of Lichen-Forming Fungi

Speciation in oceanic islands has attracted the interest of scientists since the 19th century. One of the most striking evolutionary phenomena that can be studied in islands is adaptive radiation, that is, when a lineage gives rise to different species by means of ecological speciation. Some of the best-known examples of adaptive radiation are charismatic organisms like the Darwin finches of the Galapagos and the cichlid fishes of the great African lakes. In these and many other examples, a segregation of the trophic niche has been shown to be an important diversification driver. Radiations are known in other groups of organisms, such as lichen-forming fungi. However, very few studies have investigated their adaptive nature, and none have focused on the trophic niche. In this study, we explore the role of the trophic niche in a putative radiation of endemic species from the Macaronesian Region, the Ramalina decipiens group. The photobiont diversity was studied by Illumina MiSeq sequencing of the ITS2 region of 197 specimens spanning the phylogenetic breadth and geographic range of the group. A total of 66 amplicon sequence variants belonging to the four main clades of the algal genus Trebouxia were found. Approximately half of the examined thalli showed algal coexistence, but in most of them, a single main photobiont amounted to more than 90% of the reads. However, there were no significant differences in photobiont identity and in the abundance of ITS2 reads across the species of the group. We conclude that a segregation of the trophic niche has not occurred in the R. decipiens radiation.

Choosing the Right Life Partner: Ecological Drivers of Lichen Symbiosis

Lichens are an iconic example of symbiotic systems whose ecology is shaped by the requirements of the symbionts. Previous studies suggest that fungal (mycobionts) as well as photosynthesizing (phycobionts or cyanobionts) partners have a specific range of acceptable symbionts that can be chosen according to specific environmental conditions. This study aimed to investigate the effects of climatic conditions and mycobiont identity on phycobiont distribution within the lichen genera Stereocaulon, Cladonia, and Lepraria. The study area comprised the Canary Islands, Madeira, Sicily, and the Aeolian Islands, spanning a wide range of climatic conditions. These islands are known for their unique and diverse fauna and flora; however, lichen phycobionts have remained unstudied in most of these areas. In total, we genetically analyzed 339 lichen samples. The phycobiont pool differed significantly from that outside the studied area. Asterochloris mediterranea was identified as the most abundant phycobiont. However, its distribution was limited by climatic constraints. Other species of Asterochloris and representatives of the genera Chloroidium, Vulcanochloris, and Myrmecia were also recovered as phycobionts. The selection of symbiotic partners from the local phycobiont pool was driven by mycobiont specificity (i.e., the taxonomic range of acceptable partners) and the environmental conditions, mainly temperature. Interestingly, the dominant fungal species responded differently in their selection of algal symbionts along the environmental gradients. Cladonia rangiformis associated with its phycobiont A. mediterranea in a broader range of temperatures than Stereocaulon azoreum, which favors other Asterochloris species along most of the temperature gradient. Stereocaulon vesuvianum associated with Chloroidium spp., which also differed in their temperature optima. Finally, we described Stereocaulon canariense as a new endemic species ecologically distinct from the other Stereocaulon species on the Canary Islands.

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.

Turnover of Lecanoroid Mycobionts and Their Trebouxia Photobionts Along an Elevation Gradient in Bolivia Highlights the Role of Environment in Structuring the Lichen Symbiosis

Shifts in climate along elevation gradients structure mycobiont-photobiont associations in lichens. We obtained mycobiont (lecanoroid Lecanoraceae) and photobiont (Trebouxia alga) DNA sequences from 89 lichen thalli collected in Bolivia from a ca. 4,700 m elevation gradient encompassing diverse natural communities and environmental conditions. The molecular dataset included six mycobiont loci (ITS, nrLSU, mtSSU, RPB1, RPB2, and MCM7) and two photobiont loci (ITS, rbcL); we designed new primers to amplify Lecanoraceae RPB1 and RPB2 with a nested PCR approach. Mycobionts belonged to Lecanora s.lat., Bryonora, Myriolecis, Protoparmeliopsis, the "Lecanora" polytropa group, and the "L." saligna group. All of these clades except for Lecanora s.lat. occurred only at high elevation. No single species of Lecanoraceae was present along the entire elevation gradient, and individual clades were restricted to a subset of the gradient. Most Lecanoraceae samples represent species which have not previously been sequenced. Trebouxia clade C, which has not previously been recorded in association with species of Lecanoraceae, predominates at low- to mid-elevation sites. Photobionts from Trebouxia clade I occur at the upper extent of mid-elevation forest and at some open, high-elevation sites, while Trebouxia clades A and S dominate open habitats at high elevation. We did not find Trebouxia clade D. Several putative new species were found in Trebouxia clades A, C, and I. These included one putative species in clade A associated with Myriolecis species growing on limestone at high elevation and a novel lineage sister to the rest of clade C associated with Lecanora on bark in low-elevation grassland. Three different kinds of photobiont switching were observed, with certain mycobiont species associating with Trebouxia from different major clades, species within a major clade, or haplotypes within a species. Lecanoraceae mycobionts and Trebouxia photobionts exhibit species turnover along the elevation gradient, but with each partner having a different elevation threshold at which the community shifts completely. A phylogenetically defined sampling of a single diverse family of lichen-forming fungi may be sufficient to document regional patterns of Trebouxia diversity and distribution.

Macroclimatic conditions as main drivers for symbiotic association patterns in lecideoid lichens along the Transantarctic Mountains, Ross Sea region, Antarctica

Lecideoid lichens as dominant vegetation-forming organisms in the climatically harsh areas of the southern part of continental Antarctica show clear preferences in relation to environmental conditions (i.e. macroclimate). 306 lichen samples were included in the study, collected along the Ross Sea coast (78°S–85.5°S) at six climatically different sites. The species compositions as well as the associations of their two dominant symbiotic partners (myco- and photobiont) were set in context with environmental conditions along the latitudinal gradient. Diversity values were nonlinear with respect to latitude, with the highest alpha diversity in the milder areas of the McMurdo Dry Valleys (78°S) and the most southern areas (Durham Point, 85.5°S; Garden Spur, 84.5°S), and lowest in the especially arid and cold Darwin Area (~ 79.8°S). Furthermore, the specificity of mycobiont species towards their photobionts decreased under more severe climate conditions. The generalist lichen species Lecanora fuscobrunnea and Lecidea cancriformis were present in almost all habitats, but were dominant in climatically extreme areas. Carbonea vorticosa, Lecidella greenii and Rhizoplaca macleanii were confined to milder areas. In summary, the macroclimate is considered to be the main driver of species distribution, making certain species useful as bioindicators of climate conditions and, consequently, for assessing the consequences of climate change.

Global diversity and ecological drivers of lichenised soil fungi

Lichens play crucial roles in sustaining the functioning of terrestrial ecosystems; however, the diversity and ecological factors associated with lichenised soil fungi remain poorly understood. To address this knowledge gap, we used a global field survey including information on fungal sequences of topsoils from 235 terrestrial ecosystems. We identified 880 lichenised fungal phylotypes across nine biomes ranging from deserts to tropical forests. The diversity and proportion of lichenised soil fungi peaked in shrublands and dry grasslands. Aridity index, plant cover and soil pH were the most important factors associated with the distribution of lichenised soil fungi. Furthermore, we identified Endocarpon, Verrucaria and Rinodina as some of the most dominant lichenised genera across the globe, and they had similar environmental preferences to the lichenised fungal community. In addition, precipitation seasonality and mean diurnal temperature range were also important in predicting the proportion of these dominant genera. Using this information, we were able to create the first global maps of the richness and the proportion of dominant genera of lichenised fungi. This work provides new insight into the global distribution and ecological preferences of lichenised soil fungi, and supports their dominance in drylands across the globe.

Macroecological diversification and convergence in a clade of keystone symbionts

Lichens are classic models of symbiosis, and one of the most frequent nutritional modes among fungi. The ecologically and geographically widespread lichen-forming algal (LFA) genus Trebouxia is one of the best-studied groups of LFA and associates with over 7000 fungal species. Despite its importance, little is known about its diversification. We synthesized twenty years of publicly available data by characterizing the ecological preferences of this group and testing for time-variant shifts in climatic regimes over a distribution of trees. We found evidence for limited shifts among regimes, but that disparate lineages convergently evolved similar ecological tolerances. Early Trebouxia lineages were largely forest specialists or habitat generalists that occupied a regime whose extant members occur in moderate climates. Trebouxia then convergently diversified in non-forested habitats and expanded into regimes whose modern representatives occupy wet-warm and cool-dry climates. We rejected models in which climatic diversification slowed through time, suggesting climatic diversification is inconsistent with that expected under an adaptive radiation. In addition, we found that climatic and vegetative regime shifts broadly coincided with the evolution of biomes and associated or similar taxa. Together, our work illustrates how this keystone symbiont from an iconic symbiosis evolved to occupy diverse habitats across the globe.

Global Biodiversity Patterns of the Photobionts Associated with the Genus Cladonia (Lecanorales, Ascomycota)

The diversity of lichen photobionts is not fully known. We studied here the diversity of the photobionts associated with Cladonia, a sub-cosmopolitan genus ecologically important, whose photobionts belong to the green algae genus Asterochloris. The genetic diversity of Asterochloris was screened by using the ITS rDNA and actin type I regions in 223 specimens and 135 species of Cladonia collected all over the world. These data, added to those available in GenBank, were compiled in a dataset of altogether 545 Asterochloris sequences occurring in 172 species of Cladonia. A high diversity of Asterochloris associated with Cladonia was found. The commonest photobiont lineages associated with this genus are A. glomerata, A. italiana, and A. mediterranea. Analyses of partitioned variation were carried out in order to elucidate the relative influence on the photobiont genetic variation of the following factors: mycobiont identity, geographic distribution, climate, and mycobiont phylogeny. The mycobiont identity and climate were found to be the main drivers for the genetic variation of Asterochloris. The geographical distribution of the different Asterochloris lineages was described. Some lineages showed a clear dominance in one or several climatic regions. In addition, the specificity and the selectivity were studied for 18 species of Cladonia. Potentially specialist and generalist species of Cladonia were identified. A correlation was found between the sexual reproduction frequency of the host and the frequency of certain Asterochloris OTUs. Some Asterochloris lineages co-occur with higher frequency than randomly expected in the Cladonia species.

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.

Contribution of Cyanotoxins to the Ecotoxicological Role of Lichens

The fascinating world of lichens draws the attention of the researchers because of the numerous properties of lichens used traditionally and, in modern times, as a raw material for medicines and in the perfumery industry, for food and spices, for fodder, as dyes, and for other various purposes all over the world. However, lichens being widespread symbiotic entities between fungi and photosynthetic partners may acquire toxic features due to either the fungi, algae, or cyano-procaryotes producing toxins. By this way, several common lichens acquire toxic features. In this survey, recent data about the ecology, phytogenetics, and biology of some lichens with respect to the associated toxin-producing cyanoprokaryotes in different habitats around the world are discussed. Special attention is paid to the common toxins, called microcystin and nodularin, produced mainly by the Nostoc species. The effective application of a series of modern research methods to approach the issue of lichen toxicity as contributed by the cyanophotobiont partner is emphasized.

New lineages of photobionts in Bolivian lichens expand our knowledge on habitat preferences and distribution of Asterochloris algae

We studied the biodiversity of Asterochloris photobionts found in Bolivian lichens to better understand their global spatial distribution and adaptation strategies in the context of a worldwide phylogeny of the genus. Based on nuclear ITS rDNA, the chloroplast rbcL gene and the actin type I gene we reconstructed a phylogenetic tree that recovered nine new Asterochloris lineages, while 32 Bolivian photobiont samples were assigned to 12 previously recognized Asterochloris lineages. We also show that some previously discovered Asterochloris photobiont species and lineages may occur in a broader spectrum of climatic conditions, and mycobiont species and photobionts may show different preferences along an altitude gradient. To reveal general patterns of of mycobiont specificity towards the photobiont in Asterochloris, we tested the influence of climate, altitude, geographical distance and effects of symbiotic partner (mycobiont) at the species level of three genera of lichen forming fungi: Stereocaulon, Cladonia and Lepraria. Further, we compared the specificity of mycobionts towards Asterochloris photobionts in cosmopolitan, Neotropical, and Pantropical lichen forming fungi. Interestingly, cosmopolitan species showed the lowest specificity to their photobionts, but also the lowest haplotype diversity. Neotropical and Paleotropical mycobionts, however, were more specific.

Heavy-metal pollution induces changes in the genetic composition and anatomical properties of photobionts in pioneer lichens colonising post-industrial habitats

Certain lichens are effective colonisers of polluted sites. However, little is known about the tolerance of photobionts and the degree of mycobiont selectivity to photobionts relative to metal pollution. The present study recognises the genetic and anatomical diversity of Asterochloris photobionts in epigeic lichens, i.e. Cladonia cariosa, C. rei, and Diploschistes muscorum, in relation to a wide spectrum of soil pollution. In accordance with phylogenetic analysis, photobionts were clustered in 7 moderately- to well-supported clades, including 19 haplotypes. The mycobionts of all studied lichens demonstrated a low level of selectivity and were capable of associating with various Asterochloris lineages. This tendency was also expressed by the frequent (~25%) occurrence of multiple algal genotypes in a single thallus. This indicates that identified Asterochloris lineages are generally tolerant to heavy-metal pollution, and the low level of selectivity of mycobionts enables them to select the most suitable and/or available partner. The trend of increasing incidence of certain Asterochloris lineages and decreasing frequency of others along with increasing soil pollution was observed. This proves the superior adaptation of some photobionts to polluted sites. Such symbiotic plasticity constitute an adaptive feature necessary for the successful colonisation. High number of haplotypes at polluted sites could be the result of multiple introduction events from different areas during the initial stages of spontaneous succession. Regardless of the genetic pattern, Asterochloris cells were considerably smaller, and the density and compaction of cells in the algal layer were higher, in lichen specimens from polluted sites, indicating that photobiont characteristics may be closely dependent on heavy-metal pollution.

Extensive photobiont sharing in a rapidly radiating cyanolichen clade

Recent studies have uncovered remarkable diversity in Dictyonema s.lat. basidiolichens, here recognized as subtribe Dictyonemateae. This group includes five genera and 148 species, but hundreds more await description. The photobionts of these lichens belong to Rhizonema, a recently resurrected cyanobacterial genus known by a single species. To further investigate photobiont diversity within Dictyonemateae, we generated 765 new cyanobacterial sequences from 635 specimens collected from 18 countries. The ITS barcoding locus supported the recognition of 200 mycobiont (fungal) species among these samples, but the photobiont diversity was comparatively low. Our analyses revealed three main divisions of Rhizonema, with two repeatedly recovered as monophyletic (proposed as new species), and the third mostly paraphyletic. The paraphyletic lineage corresponds to R. interruptum and partnered with mycobionts from all five genera in Dictyonemateae. There was no evidence of photobiont-mycobiont co-speciation, but one of the monophyletic lineages of Rhizonema appears to partner predominantly with one of the two major clades of Cora (mycobiont) with samples collected largely from the northern Andes. Molecular clock estimations indicate the Rhizonema species are much older than the fungal species in the Dictyonemateae, suggesting that these basidiolichens obtained their photobionts from older ascolichen lineages and the photobiont variation in extant lineages of Dictyonemateae is the result of multiple photobiont switches. These results support the hypothesis of lichens representing "fungal farmers," in which diverse mycobiont lineages associate with a substantially lower diversity of photobionts by sharing those photobionts best suited for the lichen symbiosis among multiple and often unrelated mycobiont lineages.

Lichen-forming fungi in postindustrial habitats involve alternative photobionts

Mycobionts of many lichen genera appear to demonstrate strong selectivity in the choice of algal partner. The biological properties of a photobiont and its availability in an environment significantly determine the habitat requirements of lichens. Flexibility in photobiont choice extends the ecological amplitude of lichens; therefore, it may constitute an important adaptive strategy for colonization of extreme habitats. The photobiont inventory of the three epigeic lichens most resistant to soil pollution, i.e., Cladonia cariosa, C. rei, and the hyperaccumulator Diploschistes muscorum, was examined to verify whether and to what extent algal composition depends on the type of habitat and substrate enrichment with heavy metals. Photobionts Asterochloris and Trebouxia were identified in the studied lichen species; however, the presence of Trebouxia was directly related to anthropogenic sites with technogenic substrates, and the proportion of lichen specimens with these algae clearly depended on the level of heavy-metal soil pollution and the habitat type. The total number of algal haplotypes increased with increasing soil pollution, and the richness was associated more with soil pollution than with a given lichen species. Additionally, a large number of lichen individuals bearing multiple algal genotypes at polluted sites were recorded. Although Cladonia lichens were previously thought to be restricted to Asterochloris, they are able to start the relichenization process with Trebouxia under specific habitat conditions and to establish a stable association with these algae when colonization of disturbed sites takes place. Comparative analysis of the internal transcribed spacer (ITS) rDNA sequences revealed as many as 13 haplotypes of Trebouxia, and phylogenetic analysis grouped them into two different clades. Such a high level of genetic diversity indicates that Trebouxia is well adapted to metal pollution and could be an alternative photosynthetic partner for certain lichens, especially in polluted sites.

Trentepohlialean Algae (Trentepohliales, Ulvophyceae) Show Preference to Selected Mycobiont Lineages in Lichen Symbioses

The main aims of this work were to assess phylogenetic relationships of the trentepohlialean photobionts in tropical, mainly sterile, lichens collected in Bolivia, to examine their genetic diversity, host specificity, and the impact of habitat factors on the occurrence of Trentepohliales. Based on rbcL marker analysis, we constructed a phylogenetic tree with eight major clades of Trentepohliales, of which seven free-living species are intermingled with lichenized ones. Our analyses show that the studied photobionts are scattered across the phylogenetic tree and algae from temperate and tropical regions do not form monophyletic groups, except within one clade that seems to be restricted to the tropics. There is no significant occurrence pattern of lichenized Trentepohliaceae on a specific substratum, except Cephaleuros spp. and Phycopeltis spp., which are restricted to leaves, while some clades with lichenized algae may be specialized to tree bark and wood. Moreover, we found two patterns of associations: first, closely related algae can associate with distantly related mycobionts; second, some other trentepohlioid algae associate with selected lineages of fungi (e.g., Arthoniaceae or Graphidaceae). We also found that some lineages of photobionts are even more selective and associate exclusively with one species (e.g., Dichosporidium nigrocinctum, Diorygma antillarum) or closely related lichen-forming fungi (Herpothallon spp.). Concluding, we found that occurrence of some trentepohlialean photobionts may correlate with the particular type of the mycobiont.

Cophylogenetic patterns in algal symbionts correlate with repeated symbiont switches during diversification and geographic expansion of lichen-forming fungi in the genus Sticta (Ascomycota, Peltigeraceae)

Species in the fungal genus Sticta form symbiotic associations primarily with either green algae or cyanobacteria, but tripartite associations or photosymbiodemes involving both types of photobionts occur in some species. Sticta is known to associate with green algae in the genus Symbiochloris. However, previous studies have shown that algae from other genera, such as Heveochlorella, may also be suitable partners for Sticta. We examined the diversity of green algal partners in the genus Sticta and assessed the patterns of association between the host fungus and its algal symbiont. We used multi-locus sequence data from multiple individuals collected in Australia, Cuba, Madagascar, Mauritius, New Zealand, Reunion and South America to infer phylogenies for fungal and algal partners and performed tests of congruence to assess coevolution between the partners. In addition, event-based methods were implemented to examine which cophylogenetic processes have led to the observed association patterns in Sticta and its green algal symbionts. Our results show that in addition to Symbiochloris, Sticta associates with green algae from the genera Chloroidium, Coccomyxa, Elliptochloris and Heveochlorella, the latter being the most common algal symbiont associated with Sticta in this study. Geography plays a strong role in shaping fungal-algal association patterns in Sticta as mycobionts associate with different algal lineages in different geographic locations. While fungal and algal phylogenies were mostly congruent, event-based methods did not find any evidence for cospeciation between the partners. Instead, the association patterns observed in Sticta and associated algae, were largely explained by other cophylogenetic events such as host-switches, losses of symbiont and failure of the symbiont to diverge with its host. Our results also show that tripartite associations with green algae evolved multiple times in Sticta.

Expanding the mutualistic niche: parallel symbiont turnover along climatic gradients

Keystone mutualisms, such as corals, lichens or mycorrhizae, sustain fundamental ecosystem functions. Range dynamics of these symbioses are, however, inherently difficult to predict because host species may switch between different symbiont partners in different environments, thereby altering the range of the mutualism as a functional unit. Biogeographic models of mutualisms thus have to consider both the ecological amplitudes of various symbiont partners and the abiotic conditions that trigger symbiont replacement. To address this challenge, we here investigate 'symbiont turnover zones'--defined as demarcated regions where symbiont replacement is most likely to occur, as indicated by overlapping abundances of symbiont ecotypes. Mapping the distribution of algal symbionts from two species of lichen-forming fungi along four independent altitudinal gradients, we detected an abrupt and consistent β-diversity turnover suggesting parallel niche partitioning. Modelling contrasting environmental response functions obtained from latitudinal distributions of algal ecotypes consistently predicted a confined altitudinal turnover zone. In all gradients this symbiont turnover zone is characterized by approximately 12°C average annual temperature and approximately 5°C mean temperature of the coldest quarter, marking the transition from Mediterranean to cool temperate bioregions. Integrating the conditions of symbiont turnover into biogeographic models of mutualisms is an important step towards a comprehensive understanding of biodiversity dynamics under ongoing environmental change.

Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms

Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.

Climate Change, Bioclimatic Models and the Risk to Lichen Diversity

This paper provides an overview of bioclimatic models applied to lichen species, supporting their potential use in this context as indicators of climate change risk. First, it provides a brief summary of climate change risk, pointing to the relevance of lichens as a topic area. Second, it reviews the past use of lichen bioclimatic models, applied for a range of purposes with respect to baseline climate, and the application of data sources, statistical methods, model extents and resolution and choice of predictor variables. Third, it explores additional challenges to the use of lichen bioclimatic models, including: 1. The assumption of climatically controlled lichen distributions, 2. The projection to climate change scenarios, and 3. The issue of nonanalogue climates and model transferability. Fourth, the paper provides a reminder that bioclimatic models estimate change in the extent or range of a species suitable climate space, and that an outcome will be determined by vulnerability responses, including potential for migration, adaptation, and acclimation, within the context of landscape habitat quality. The degree of exposure to climate change, estimated using bioclimatic models, can help to inform an understanding of whether vulnerability responses are sufficient for species resilience. Fifth, the paper draws conclusions based on its overview, highlighting the relevance of bioclimatic models to conservation, support received from observational data, and pointing the way towards mechanistic approaches that align with field-scale climate change experiments.