The macroevolutionary dynamics of symbiotic and phenotypic diversification in lichens

Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae

Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.

Oral microbiota, co-evolution, and implications for health and disease: The case of indigenous peoples

Evidence indicates that oral microbiota plays a crucial role in human health and disease. For instance, diseases with multifactorial etiology, such as periodontitis and caries, which cause a detrimental impact on human well-being and health, can be caused by alterations in the host-microbiota interactions, where non-pathogenic bacteria give way to pathogenic orange/red-complex bacterial species (a change from a eubiotic to dysbiotic state). In this scenario, where thousands of oral microorganisms, including fungi, archaea, and phage species, and their host are co-evolving, a set of phenomena, such as the arms race and Red or Black Queen dynamics, are expected to operate. We review concepts on the subject and revisit the nature of bacterial complexes linked to oral health and diseases, as well as the problem of the bacterial resistome in the face of the use of antibiotics and what is the impact of this on the evolutionary trajectory of the members of this symbiotic ecosystem. We constructed a 16SrRNA tree to show that adaptive consortia of oral bacterial complexes do not necessarily rescue phylogenetic relationships. Finally, we remember that oral health is not exempt from health disparity trends in some populations, such as Native Americans, when compared with non-Indigenous people.

Biodiversity of Basidiomycetous Yeasts Associated with Cladonia rei Lichen in Japan, with a Description of Microsporomyces cladoniophilus sp. nov

For more than a century, lichens have been used as an example of dual-partner symbiosis. Recently, this has been challenged by the discovery of various basidiomycetous yeasts that coexist in multiple lichen species, among which Cladonia lichens from Europe and the United States were discovered to be highly specifically associated with the basidiomycetous yeast of the family Microsporomycetaceae. To verify this highly specific relationship, we investigated the diversity of basidiomycetous yeasts associated with Cladonia rei, a widely distributed lichen in Japan, by applying two approaches: yeast isolation from the lichen thalli and meta-barcoding analysis. We obtained 42 cultures of Cystobasidiomycetous yeast which were grouped into six lineages within the family Microsporomycetaceae. Unexpectedly, although the cystobasidiomycetes-specific primer was used, not only the cystobasidiomycetous yeasts but species from other classes were also detected via the meta-barcoding dataset; in particular, pucciniomycetous yeasts were found at a high frequency in some samples. Further, Halobasidium xiangyangense, which was detected in every sample with high abundance, is highly likely a generalist epiphytic fungus that has the ability to associate with C. rei. In the pucciniomycetous group, most of the detected species belong to the scale insect-associated yeast Septobasidium genus. In conclusion, even though Microsporomyces species are not the only yeast group associated with Cladonia lichen, our study demonstrated that the thalli of Cladonia rei lichen could be a suitable habit for them.

Nitrogen-based symbioses, phosphorus availability, and accounting for a modern world more productive than the Paleozoic

Evolution of high-productivity angiosperms has been regarded as a driver of Mesozoic ecosystem restructuring. However, terrestrial productivity is limited by availability of rock-derived nutrients such as phosphorus for which permanent increases in weathering would violate mass balance requirements of the long-term carbon cycle. The potential reality of productivity increases sustained since the Mesozoic is supported here with documentation of a dramatic increase in the evolution of nitrogen-fixing or nitrogen-scavenging symbioses, including more than 100 lineages of ectomycorrhizal and lichen-forming fungi and plants with specialized microbial associations. Given this evidence of broadly increased nitrogen availability, we explore via carbon cycle modeling how enhanced phosphorus availability might be sustained without violating mass balance requirements. Volcanism is the dominant carbon input, dictating peaks in weathering outputs up to twice modern values. However, times of weathering rate suppression may be more important for setting system behavior, and the late Paleozoic was the only extended period over which rates are expected to have remained lower than modern. Modeling results are consistent with terrestrial organic matter deposition that accompanied Paleozoic vascular plant evolution having suppressed weathering fluxes by providing an alternative sink of atmospheric CO₂ . Suppression would have then been progressively lifted as the crustal reservoir's holding capacity for terrestrial organic matter saturated back toward steady state with deposition of new organic matter balanced by erosion of older organic deposits. Although not an absolute increase, weathering fluxes returning to early Paleozoic conditions would represent a novel regime for the complex land biota that evolved in the interim. Volcanism-based peaks in Mesozoic weathering far surpass the modern rates that sustain a complex diversity of nitrogen-based symbioses; only in the late Paleozoic might these ecologies have been suppressed by significantly lower rates. Thus, angiosperms are posited to be another effect rather than proximal cause of Mesozoic upheaval.

Genomic diversification of the specialized parasite of the fungus-growing ant symbiosis

Fungi shape the diversity of life. Characterizing the evolution of fungi is critical to understanding symbiotic associations across kingdoms. In this study, we investigate the genomic and metabolomic diversity of the genus Escovopsis, a specialized parasite of fungus-growing ant gardens. Based on 25 high-quality draft genomes, we show that Escovopsis forms a monophyletic group arising from a mycoparasitic fungal ancestor 61.82 million years ago (Mya). Across the evolutionary history of fungus-growing ants, the dates of origin of most clades of Escovopsis correspond to the dates of origin of the fungus-growing ants whose gardens they parasitize. We reveal that genome reduction, determined by both genomic sequencing and flow cytometry, is a consistent feature across the genus Escovopsis, largely occurring in coding regions, specifically in the form of gene loss and reductions in copy numbers of genes. All functional gene categories have reduced copy numbers, but resistance and virulence genes maintain functional diversity. Biosynthetic gene clusters (BGCs) contribute to phylogenetic differences among Escovopsis spp., and sister taxa in the Hypocreaceae. The phylogenetic patterns of co-diversification among BGCs are similarly exhibited across mass spectrometry analyses of the metabolomes of Escovopsis and their sister taxa. Taken together, our results indicate that Escovopsis spp. evolved unique genomic repertoires to specialize on the fungus-growing ant-microbe symbiosis.

Toward a sociology of evolution in the Anthropocene-Shared intentionality and cooperation through understanding minds

Sociology has a long tradition of diagnosing contemporary societies, but little theoretical and empirical instruments for analyzing the long-term evolution of human coexistence. This goes hand in hand with a bias to disregard insights of evolutionary theory and research. The main argument here to develop is that a sociology of evolution should enter at the core of our discipline. This becomes even more important in the era of the Anthropocene as a new geo-chronological period of the planet's evolution that is characterized by substantial human influencing of planetary ecological mechanisms and could be found in earth sediments. If human intervention in the planet has reached such a scale that its future fate is no longer shaped mainly by natural cosmological laws, but by human intervention, then sociology has to broaden its temporal and substantive perspective; it should reflect more explicitly on the relationship between nature, culture, and technology. In what follows, we plead for giving evolutionary sociology, especially the long-term evolution of human coexistence between nature and culture, a greater place in sociology. To this end, we address three points. First, we ask why sociology is not concerned with the co-evolution of other creatures, but almost exclusively focused on the development and social change of humans over the short period of the last few centuries. Second, we argue that, with respect to the nature-culture relationship, sociology has essentially followed a questionable scientific division of labor, according to which the natural sciences deal with natural phenomena and sociology with sociocultural phenomena. Finally, we address the debate on the Anthropocene and distinguish between two ways of responding to the challenges it poses, namely with more technology or with more culture.

The Jurassic epiphytic macrolichen Daohugouthallus reveals the oldest lichen-plant interaction in a Mesozoic forest ecosystem

Lichens are well known as pioneer organisms or stress-tolerant extremophiles, potentially playing a core role in the early formation of terrestrial ecosystems. Epiphytic macrolichens are known to contribute to the water- and nutrient cycles in forest ecosystem. But due to the scarcity of fossil record, the evolutionary history of epiphytic macrolichens is poorly documented. Based on new fossil of Jurassic Daohugouthallus ciliiferus, we demonstrate the hitherto oldest known macrolichen inhabited a gymnosperm branch. We applied energy dispersive X-ray spectroscopy and geometric morphometric analysis to complementarily verify lichen affinity of D. ciliiferus and quantitatively assess the potential relationships with extant lichenized lineages, providing new approaches for study of this lichen adpression fossil. Considering the results, and the inferred age of D. ciliiferus, a new family, Daohugouthallaceae, is established. This work updates current knowledge to the early evolution of epiphytic macrolichens and reveals more complex lichen-plant interactions in a Jurassic forest ecosystem.

Mycology: Metagenomes illuminate evolutionary relationships and reframe symbiotic interactions

An intriguing new study leverages newly generated metagenomes to remap the evolution of the most species-rich clade of fungi, highlighting how some of the most intriguing and visible manifestations of symbioses - lichens - may arise.

Lichen phycobiomes as source of biodiversity for microalgae of the Stichococcus-like genera

The term phycobiome was recently introduced to designate all the microalgae (primary or non-primary) associated with lichen symbioses. Abundant non-primary symbiotic microalgae are usually obtained from lichen isolations, confirming that thalli are a source of biodiversity and new species. In this study, microalgae were isolated from thalli of Buellia zoharyi, Ramalina farinacea and Parmotrema pseudotinctorum collected in the Iberian Peninsula and the Canary Islands. Excluding Trebouxia phycobionts, 17 strains similar to Stichococcus (Prasiola clade) were obtained. Molecular identification was carried out by nuclear ITS sequencing, and a phylogenetic tree was generated from these sequences, and grouping them into 4 clades: Diplosphaera chodatti, Diplosphaera sp.1. Deuterostichocuccus sp.1. and Tritostichococcus coniocybes. It is also noteworthy that Diplosphaera sp.1 was detected and isolated from three phylogenetically distant lichenized fungi (B. zoharyi, R. farinacea and P. pseudotinctorum), which were sampled in ecologically different localities, namely Tenerife, La Gomera and Castellón. These results reinforce the idea of the constant presence of certain microalgae associated with the lichen thalli which, despite not being the main primary photobiont, probably form part of the lichen’s phycobiomes.

Trebouxia lynnae sp. nov. (Former Trebouxia sp. TR9): Biology and Biogeography of an Epitome Lichen Symbiotic Microalga

Two microalgal species, Trebouxia jamesii and Trebouxia sp. TR9, were detected as the main photobionts coexisting in the thalli of the lichen Ramalina farinacea. Trebouxia sp. TR9 emerged as a new taxon in lichen symbioses and was successfully isolated and propagated in in vitro culture and thoroughly investigated. Several years of research have confirmed the taxon Trebouxia sp. TR9 to be a model/reference organism for studying mycobiont−photobiont association patterns in lichen symbioses. Trebouxia sp. TR9 is the first symbiotic, lichen-forming microalga for which an exhaustive characterization of cellular ultrastructure, physiological traits, genetic and genomic diversity is available. The cellular ultrastructure was studied by light, electron and confocal microscopy; physiological traits were studied as responses to different abiotic stresses. The genetic diversity was previously analyzed at both the nuclear and organelle levels by using chloroplast, mitochondrial, and nuclear genome data, and a multiplicity of phylogenetic analyses were carried out to study its intraspecific diversity at a biogeographical level and its specificity association patterns with the mycobiont. Here, Trebouxia sp. TR9 is formally described by applying an integrative taxonomic approach and is presented to science as Trebouxia lynnae, in honor of Lynn Margulis, who was the primary modern proponent for the significance of symbiosis in evolution. The complete set of analyses that were carried out for its characterization is provided.

The Diversity of Lichenized Trentepohlioid Algal (Ulvophyceae) Communities is Driven by Fungal Taxonomy and Ecological Factors

Trentepohliales are a group of both free-living and lichenized algae, with most diversity occurring in tropical regions. Recent studies showed that the abundance of lichens with a trentepohlioid photobiont has been increasing in temperate habitats, probably because of global warming, which makes them an interesting study case. A detailed molecular study of the diversity of lichenized Trentepohliales, epiphytic as well as epilithic, was performed in three forests of north-western Europe. Additional samples of lichens of the Arthoniales order (associating essentially with a trentepohlioid photobiont) from other European regions and from other continents were also sequenced. A total of 195 algal sequences were obtained. Phylogenetic analyses with rbcL and ITS loci were performed and associations between phylogenetic distances of photobionts and ecological factors (substratum, climate or Wirth indices, mycobiont taxonomy, and geographic location) were tested by variation partitioning and phylogenetic signal analyses. The high number of rbcL algal haplotypes found in some lichens or on different substrata revealed that the Trentepohliales diversity in extratropical regions was underestimated. The phylogenetic patterns showed selectivity of some photobionts in their fungal partner choice and vice-versa, while others were linked with several haplotypes. Photobionts seemed to be less selective than mycobionts. The main factors influencing lichenized algal community were climate and mycobiont species. Coevolution between mycobionts and photobionts as well as switching between free living and lichenized lifestyles appeared to drive the evolution of Trentepohliales and might explain the high cryptic diversity observed, which might be changing in some regions due to climate change.

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.

A comparative genomic analysis of lichen-forming fungi reveals new insights into fungal lifestyles

Lichen-forming fungi are mutualistic symbionts of green algae or cyanobacteria. We report the comparative analysis of six genomes of lichen-forming fungi in classes Eurotiomycetes and Lecanoromycetes to identify genomic information related to their symbiotic lifestyle. The lichen-forming fungi exhibited genome reduction via the loss of dispensable genes encoding plant-cell-wall-degrading enzymes, sugar transporters, and transcription factors. The loss of these genes reflects the symbiotic biology of lichens, such as the absence of pectin in the algal cell wall and obtaining specific sugars from photosynthetic partners. The lichens also gained many lineage- and species-specific genes, including those encoding small secreted proteins. These genes are primarily induced during the early stage of lichen symbiosis, indicating their significant roles in the establishment of lichen symbiosis.Our findings provide comprehensive genomic information for six lichen-forming fungi and novel insights into lichen biology and the evolution of symbiosis.

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.

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 Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality

Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the community under higher-level selection. In certain cases, cooperation can lead to a transition in individuality, when freely reproducing, unrelated entities (genes, microbes, etc.) irreversibly integrate to form a new evolutionary unit. The textbook example is endosymbiosis, prevalent among eukaryotes but virtually lacking among prokaryotes. Concerning the ubiquity of syntrophic microbial communities, it is intriguing why evolution has not lead to more transitions in individuality in the microbial domain. We set out to distinguish syntrophy-specific aspects of major transitions, to investigate why a transition in individuality within a syntrophic pair or community is so rare. We review the field of metabolic communities to identify potential evolutionary trajectories that may lead to a transition. Community properties, like joint metabolic capacity, functional profile, guild composition, assembly and interaction patterns are important concepts that may not only persist stably but according to thought-provoking theories, may provide the heritable information at a higher level of selection. We explore these ideas, relating to concepts of multilevel selection and of informational replication, to assess their relevance in the debate whether microbial communities may inherit community-level information or not.

Chemical properties of key metabolites determine the global distribution of lichens

In lichen symbioses, fungal secondary metabolites provide UV protection on which lichen algae such as trebouxiophycean green algae-the most prominent group of photobionts in lichen symbioses-sensitively depend. These metabolites differ in their UV absorbance capability and solvability, and thus vary in their propensity of being leached from the lichen body in humid and warm environments, with still unknown implications for the global distribution of lichens. In this study covering more than 10,000 lichenised fungal species, we show that the occurrence of fungal-derived metabolites in combination with their UV absorbance capability and their probability of being leached in warm and humid environments are important eco-evolutionary drivers of global lichen distribution. Fungal-derived UV protection seems to represent an indirect environmental adaptation in which the lichen fungus invests to protect the trebouxiophycean photobiont from high UV radiation in warm and humid climates and, by doing this, secures its carbon source.

Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics

Lichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed.

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.

Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling

Lichen associations, a classic model for successful and sustainable interactions between micro-organisms, have been studied for many years. However, there are significant gaps in our understanding about how the lichen symbiosis operates at the molecular level. This review addresses opportunities for expanding current knowledge on signalling and metabolic interplays in the lichen symbiosis using the tools and approaches of systems biology, particularly network modelling. The largely unexplored nature of symbiont recognition and metabolic interdependency in lichens could benefit from applying a holistic approach to understand underlying molecular mechanisms and processes. Together with ‘omics’ approaches, the application of signalling and metabolic network modelling could provide predictive means to gain insights into lichen signalling and metabolic pathways. First, we review the major signalling and recognition modalities in the lichen symbioses studied to date, and then describe how modelling signalling networks could enhance our understanding of symbiont recognition, particularly leveraging omics techniques. Next, we highlight the current state of knowledge on lichen metabolism. We also discuss metabolic network modelling as a tool to simulate flux distribution in lichen metabolic pathways and to analyse the co-dependence between symbionts. This is especially important given the growing number of lichen genomes now available and improved computational tools for reconstructing such models. We highlight the benefits and possible bottlenecks for implementing different types of network models as applied to the study of lichens.

Consistent patterns of fungal communities within ant-plants across a large geographic range strongly suggest a multipartite mutualism

In recent decades, multipartite mutualisms involving microorganisms such as fungi have been discovered in associations traditionally thought of as bipartite. Ant-plant mutualisms were long thought to be bipartite despite fungi being noticed in an epiphytic ant-plant over 100 years ago. We sequenced fungal DNA from the three distinct domatium chambers of the epiphytic ant-plant Myrmecodia beccarii to establish if fungal communities differ by chamber type across five geographic locations spanning 675 km. The three chamber types serve different ant-associated functions including ‘waste’ chambers, where ant workers deposit waste; ‘nursery’ chambers, where the brood is kept; and ‘ventilation’ chambers, that allow air into the domatium. Overall, fungi from the order Chaetothyriales dominated the chambers in terms of the proportion of operational taxonomic units (OTUs; 13.4%) and sequence abundances of OTUs (28% of the total); however a large portion of OTUs (28%) were unidentified at the order level. Notably, the fungal community in the waste chambers differed consistently from the nursery and ventilation chambers across all five locations. We identified 13 fungal OTUs as ‘common’ in the waste chambers that were rare or in very low sequence abundance in the other two chambers. Fungal communities in the nursery and ventilation chambers overlapped more than either did with the waste chambers but were also distinct from each other. Differences in dominance of the common OTUs drove the observed patterns in the fungal communities for each of the chamber types. This suggests a multipartite mutualism involving fungi exists in this ant-plant and that the role of fungi differs among chamber types.

Sharing and double-dating in the lichen world

Historic and modern efforts to understand lichen diversity and evolution have overwhelmingly concentrated on that of the fungal partner, which represents one of the most taxonomically diverse nutritional modes among the Fungi. But what about the algal and cyanobacterial symbionts? An explosion of studies on these cryptic symbionts over the past 20+ years has facilitated a richer understanding of their diversity, patterns of association, and the symbiosis itself. In a From the Cover article in this issue of Molecular Ecology, Dal Forno et al. (2021) provide new insight into one of the most fascinating lichen symbioses. By sequencing cyanobacterial symbionts from over 650 specimens, they reveal the presence of overlooked cyanobacterial diversity, evidence for symbiont sharing among distantly related fungi, and utilize a comparative dating framework to demonstrate temporal discordance among interacting fungal and cyanobacterial lineages.

The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

Lichens Bite the Dust - A Bioweathering Scenario in the Atacama Desert

Bioweathering mediated by microorganisms plays a significant role in biogeochemical cycles on global scales over geological timescales. Single processes induced by specific taxa have been described but could rarely be demonstrated for complex communities that dominate whole landscapes. The recently discovered grit crust of the coastal Atacama Desert, which is a transitional community between a cryptogamic ground cover and a rock-bound lithic assemblage, offers the unique chance to elucidate various bioweathering processes that occur simultaneously. Here, we present a bioweathering scenario of this biocenosis including processes such as penetration of the lithomatrix, microbial responses to wet-dry cycles, alkalinolysis, enzyme activity, and mineral re-localization. Frequently occurring fog, for example, led to a volume increase of microorganisms and the lithomatrix. This, together with pH shifts and dust accumulation, consequently results in biophysical breakdown and the formation of a terrestrial protopedon, an initial stage of pedogenesis fueled by the grit crust.

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.