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The analysis of the interaction between main bionts (mycobiont and photobiont) in the lichen symbiosis delivers substantial information about their preferences in the selection of symbiotic partners, and their ecological preferences. The selectivity in the Parmelia genus has been defined as strong so far. However, data on this lichen genus, which includes several widely distributed species, are biogeographically limited. Therefore, using specialization indicators and extended sampling, in this study, we estimated the interactions between the main bionts of selected Parmelia spp., using two levels of estimation (species/OTU and haplotype). A comparison of mycobiont-photobiont interactions at different levels showed that considering only mycobiont species and Trebouxia OTUs, greater specialization is found, while Parmelia species studied in this work present a more generalistic strategy in photobiont choice when haplotypes are considered. Despite the uneven sampling of Parmelia species, the interpretation of specialization within species and individuals of the genus leads to a more precise and accurate interpretation of their adaptation strategies. Furthermore, the data from P . sulcata indicate the existence of a different pool of compatible haplotypes in some geographical regions compared to neighboring areas. This observation suggests the potential influence of climatic factors.

Patterns of specificity among symbiotic partners are key to a comprehensive understanding of the evolution of symbiotic systems. Specificity of mutualistic partners, within a widespread monophyletic group for which all species are sampled has rarely been explored. Here, we assess the level of specificity between the cosmopolitan lichen-forming fungus (mycobiont) from the genus Peltigera, section Polydactylon, and its cyanobacterial partner Nostoc (cyanobiont). The mycobiont and cyanobiont phylogenies are inferred from five nuclear loci and the rbcLX region, respectively. These sequences were obtained from 206 lichen thalli, representing ca. 40 closely related Peltigera species sampled worldwide, doubling the number of known species in this group. We found a broad spectrum of specificity for both partners ranging from strict specialists to generalists. Overall, mycobionts are more specialized than cyanobionts by associating mostly with one or a few Nostoc phylogroups, whereas most cyanobionts associate frequently with several Peltigera species. Specialist mycobionts are older than generalists, supporting the hypothesis that specialization of mycobionts to one or few cyanobionts, is favored through time in geographic areas where species have been established for long periods of time. The relatively recent colonization of a new geographic area (Central and South America) by members of section Polydactylon is associated with a switch to a generalist pattern of association and an increased diversification rate by the fungal partner, suggesting that switches to generalism are rare events that are advantageous in new environments. We detected higher genetic diversity in generalist mycobionts. We also found that Peltigera species specialized on a single Nostoc phylogroup have narrower geographical distributions compared with generalist species.

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.

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

Background Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. Results The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders— Sphingomonadales , Rhodospirillales , Myxococcales , Chthoniobacterales , and Sphingobacteriales— harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols. Conclusions Functions that facilitate the persistence of Lobaria pulmonaria under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like Chthoniobacterales ( Verrucomicrobia ) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.

Nostoc cyanobacteria are among the few organisms capable of fixing both carbon and nitrogen. These metabolic features are essential for the cyanolichen symbiosis, where Nostoc supplies both carbon (as glucose) and nitrogen (as ammonium) to a cyanolichen-forming fungal partner. This nutrient flow was established by seminal biochemical studies published in the 20th century. Since then, cyanolichen metabolism has received little attention, and the molecular mechanisms that underlie the physiology of lichenized Nostoc remain mostly unknown. Here, we aimed to elucidate the genomic and transcriptional changes that enable Nostoc’s metabolic role in cyanolichens. We used comparative genomics across 243 genomes of Nostoc s. lat. coupled with metatranscriptomic experiments using Peltigera cyanolichens. We found that genes for photoautotrophic carbon fixation are upregulated in lichenized Nostoc. This likely results in a higher rate of carbon fixation that allows Nostoc to provide carbon to the fungal partner while meeting its own metabolic needs. We also found that the transfer of ammonium from Nostoc to the lichen-forming fungus is facilitated by two molecular mechanisms: (i) transcriptional downregulation of glutamine synthetase, the key enzyme responsible for ammonium assimilation in Nostoc; and (ii) frequent losses of a putative high-affinity ammonium permease, which likely reduces Nostoc’s capacity to recapture leaked ammonium. Finally, we found that the development of motile hormogonia is downregulated in lichenized Nostoc, which resembles the repression of motility in Nostoc symbionts after they colonize symbiotic cavities of their plant hosts. Our results pave the way for a revival of cyanolichen ecophysiology in the omics era.

Lichens are generally considered as mutualisms between fungi and green algae or cyanobacteria. These partnerships allow light-exposed and long-living joint structures. The unique organization of lichens provides still unexplored environments for microbial communities. To study lichen-associated bacterial communities, we analyze samples, by a polyphasic approach, from three lichen species ( Cladonia arbuscula , Lecanora polytropa and Umbilicaria cylindrica ) from alpine environments. Our results indicate that bacteria can form highly structured, biofilm-like assemblages on fungal surfaces and reach considerable abundances of up to 10 8 cells per gram fresh weight. Fluorescence in situ hybridization reveals the predominance of Alphaproteobacteria . Microbial fingerprints performed by PCR-single-strand conformation polymorphism analysis using universal and group-specific primers show distinct patterns for each lichen species. Characterization of cultivable strains and presence of functional genes in the total fraction suggest the involvement of associated bacteria in nutrient cycling. Ubiquitous nifH genes, which encode the nitrogenase reductase, show a high diversity and are assigned to Alphaproteobacteria and Firmicutes , for example, Paenibacillus . Cultivable strains mainly belonging to the genera Acinetobacter , Bacillus , Burkholderia , Methylobacterium and Paenibacillus show lytic (chitinolytic, glucanolytic, and proteolytic) activities, hormone production (indole-3-acetic acid) as well as phosphate mobilization and antagonistic activity toward other microorganisms. The traditional concept of lichens has to be expanded to consider multiple bacterial partners.

Persistent fungal pathogens remain a threat to global food security as these pathogens continue to infect crops despite different mitigating strategies. Traditionally, synthetic fungicides are used to combat these threats, but their environmental and health impacts have spurred interest in a more sustainable, eco-friendly approach. Endolichenic fungi (ELF) are a relatively underexplored group of microorganisms found thriving inside the lichen thalli. They are seen as promising alternatives for developing sustainable plant disease management strategies. Hence, in this study, a total of forty ELF isolates from two fruticose lichen hosts—Ramalina and Usnea, were tested and compared for their antagonistic activities against three economically important filamentous fungal pathogens—Colletotrichum gloeosporioides, Cladosporium cladosporioides, and Fusarium oxysporum. The results of the dual culture assay showed that all ELF isolates successfully reduced the growth of the three filamentous fungal pathogens with varying degrees, and with direct contact inhibition as the predominant trait among the endolichenic fungi. Comparing the antagonistic activities between the different endolichenic fungi from the two lichen hosts, ELF isolates from Ramalina generally demonstrated a higher percentage inhibition of growth of the test fungi as compared to ELF isolates from Usnea. This study underscores the importance of endolichenic fungi as an efficient biocontrol agent.

Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss. We developed an approach to determine the phylogenetic structure of the partners that interact with a focal species while accounting for their availability. When applied in four empirical network datasets, we found that a large proportion of species interact with phylogenetically random partners.

The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: The AMT family as defined here exhibits vertical gene transfer (i.e., standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers (HGTs). These ancient HGT events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This recircumscription of the ammonium transporters/ammonia permeases family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to functionally different groups, with AMTs and ammonia permeases forming two distinct and possibly monophyletic groups.