Symbiosis constraints: Strong mycobiont control limits nutrient response in lichens

Symbionts out of sync: Decoupled physiological responses are widespread and ecologically important in lichen associations

A core vulnerability in symbioses is the need for coordination between the symbiotic partners, which are often assumed to be closely physiologically integrated. We critically re-examine this assumed integration between symbionts in lichen symbioses, recovering a long overlooked yet fundamental physiological asymmetry in carbon balance. We examine the physiological, ecological, and transcriptional basis of this asymmetry in the lichen Evernia mesomorpha. This carbon balance asymmetry depends on hydration source and aligns with climatic range limits. Differences in gene expression across the E. mesomorpha symbiosis suggest that the physiologies of the primary lichen symbionts are decoupled. Furthermore, we use gas exchange data to show that asymmetries in carbon balance are widespread and common across evolutionarily disparate lichen associations. Using carbon balance asymmetry as an example, we provide evidence for the wide-ranging importance of physiological asymmetries in symbioses.

Do urban air pollutants induce changes in the thallus anatomy and affect the photosynthetic efficiency of the nitrophilous lichen Physcia adscendens?

Lichens are symbiotic organisms that are generally sensitive to air pollution due to their specific biological and physiological features. Physcia adscendens is a nitrophilous lichen well-known for being resistant to air pollution associated with progressive anthropopressure. The aim of this study was to investigate the effect of nitrogen oxides and suspended particulate matter (PM10 and PM2.5) on anatomical structure of the thallus and photobiont's photosynthetic efficiency in P. adscendens inhabiting sites that differ in terms of air pollution level and thereby to determine the relevance of these pollutants for shaping the structure of the thallus and the physiological condition of the photosynthetic partner. We found that P. adscendens from polluted sites had increased thickness of the algal layer and the larger size of the algae cells, but a much lower ratio of the algal layer to the whole thallus. Lichens from highly polluted sites had also higher photosynthetic efficiency, which indicates a relatively good physiological condition of the photobiont. This indicates that the photobiont of P. adscendens is well-adapted to function under air pollution stress which may contribute to its success in colonizing polluted sites. Both changes in the anatomy of the lichen thallus and the efficiency of photosynthesis may be related to the enrichment of the environment with nitrogen. The increased photosynthetic efficiency as well as investment in the size of photobiont cells and growth mycobiont hyphae confirms that P. adscendens is well-adapted to urban conditions; however, the mechanism behind those adaptations needs more focus in the context of global environmental changes.

Lichen ecophysiology in a changing climate

Lichens are one of the most iconic and ubiquitous symbioses known, widely valued as indicators of environmental quality and, more recently, climate change. Our understanding of lichen responses to climate has greatly expanded in recent decades, but some biases and constraints have shaped our present knowledge. In this review we focus on lichen ecophysiology as a key to predicting responses to present and future climates, highlighting recent advances and remaining challenges. Lichen ecophysiology is best understood through complementary whole-thallus and within-thallus scales. Water content and form (vapor or liquid) are central to whole-thallus perspectives, making vapor pressure differential (VPD) a particularly informative environmental driver. Responses to water content are further modulated by photobiont physiology and whole-thallus phenotype, providing clear links to a functional trait framework. However, this thallus-level perspective is incomplete without also considering within-thallus dynamics, such as changing proportions or even identities of symbionts in response to climate, nutrients, and other stressors. These changes provide pathways for acclimation, but their understanding is currently limited by large gaps in our understanding of carbon allocation and symbiont turnover in lichens. Lastly, the study of lichen physiology has mainly prioritized larger lichens at high latitudes, producing valuable insights but underrepresenting the range of lichenized lineages and ecologies. Key areas for future work include improving geographic and phylogenetic coverage, greater emphasis on VPD as a climatic factor, advances in the study of carbon allocation and symbiont turnover, and the incorporation of physiological theory and functional traits in our predictive models.

In vitro resynthesis of lichenization reveals the genetic background of symbiosis-specific fungal-algal interaction in Usnea hakonensis

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.

The macroevolutionary dynamics of symbiotic and phenotypic diversification in lichens

Symbioses are evolutionarily pervasive and play fundamental roles in structuring ecosystems, yet our understanding of their macroevolutionary origins, persistence, and consequences is incomplete. We traced the macroevolutionary history of symbiotic and phenotypic diversification in an iconic symbiosis, lichens. By inferring the most comprehensive time-scaled phylogeny of lichen-forming fungi (LFF) to date (over 3,300 species), we identified shifts among symbiont classes that broadly coincided with the convergent evolution of phylogenetically or functionally similar associations in diverse lineages (plants, fungi, bacteria). While a relatively recent loss of lichenization in Lecanoromycetes was previously identified, our work instead suggests lichenization was abandoned far earlier, interrupting what had previously been considered a direct switch between trebouxiophycean and trentepohlialean algal symbionts. Consequently, some of the most diverse clades of LFF are instead derived from nonlichenized ancestors and re-evolved lichenization with Trentepohliales algae, a clade that also facilitated lichenization in unrelated lineages of LFF. Furthermore, while symbiont identity and symbiotic phenotype influence the ecology and physiology of lichens, they are not correlated with rates of lineage birth and death, suggesting more complex dynamics underly lichen diversification. Finally, diversification patterns of LFF differed from those of wood-rotting and ectomycorrhizal taxa, likely reflecting contrasts in their fundamental biological properties. Together, our work provides a timeline for the ecological contributions of lichens, and reshapes our understanding of symbiotic persistence in a classic model of symbiosis.

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities

Phototrophic communities of photosynthetic algae or cyanobacteria and heterotrophic bacteria or fungi are pervasive throughout the environment¹. How interactions between members contribute to the resilience and affect the fitness of phototrophic communities is not fully understood^2,3. Here, we integrated metatranscriptomics, metabolomics and phenotyping with computational modelling to reveal condition-dependent secretion and cross-feeding of metabolites in a synthetic community. We discovered that interactions between members are highly dynamic and are driven by the availability of organic and inorganic nutrients. Environmental factors, such as ammonia concentration, influenced community stability by shifting members from collaborating to competing. Furthermore, overall fitness was dependent on genotype and streamlined genomes improved growth of the entire community. Our mechanistic framework provides insights into the physiology and metabolic response to environmental and genetic perturbation of these ubiquitous microbial associations.

Nitrogen deposition sources and patterns in the Greater Yellowstone Ecosystem determined from ion exchange resin collectors, lichens, and isotopes

Over the past century, atmospheric nitrogen deposition (N_dep) has increased across the western United States due to agricultural and urban development, resulting in degraded ecosystem quality. Regional patterns of N_dep are often estimated by coupling direct measurements from large-scale monitoring networks and atmospheric chemistry models, but such efforts can be problematic in the western US because of complex terrain and sparse sampling. This study aimed not only to understand N_dep patterns in mountainous ecosystems but also to investigate whether isotope values of lichens and throughfall deposition can be used to determine N_dep sources, and serve as an additional tool in ecosystem health assessments. We measured N_dep amounts and δ¹⁵N in montane conifer forests of the Greater Yellowstone Ecosystem using canopy throughfall and bulk monitors and lichens. In addition, we examined patterns of C:N ratios in lichens as a possible indicator of lichen physiological condition. The isotopic signature of δ¹⁵N of N_dep helps to discern emission sources, because δ¹⁵N of NO_x from combustion tends to be high (-5 to +25‰) while NH_x from agricultural sources tends to be comparatively low (-40 to -10‰). Summertime N_dep increased with elevation and ranged from 0.26 to 1.66 kg ha^-1. N_dep was higher than expected in remote areas. The δ¹⁵N values of lichens were typically -15.3 to -10‰ suggesting agriculture as a primary emission source of deposition. Lichen %N, δ¹⁵N and C:N ratios can provide important information about N_dep sources and patterns over small spatial scales in complex terrain.

The first survey of Cystobasidiomycete yeasts in the lichen genus Cladonia; with the description of Lichenozyma pisutiana gen. nov., sp. nov

The view of lichens as a symbiosis only between a mycobiont and a photobiont has been challenged by discoveries of diverse associated organisms. Specific basidiomycete yeasts in the cortex of a range of macrolichens were hypothesized to influence the lichens' phenotype. The present study explores the occurrence and diversity of cystobasidiomycete yeasts in the lichen genus Cladonia. We obtained seven cultures and 56 additional sequences using specific primers from 27 Cladonia species from all over Europe and performed phylogenetic analyses based on ITS, LSU and SSU rDNA loci. We revealed yeast diversity distinct from any previously reported. Representatives of Cyphobasidiales, Microsporomycetaceae and of an unknown group related to Symmetrospora have been found. We present evidence that the Microsporomycetaceae contains mainly lichen-associated yeasts. Lichenozyma pisutiana is circumscribed here as a new genus and species. We report the first known associations between cystobasidiomycete yeasts and Cladonia (both corticate and ecorticate), and find that the association is geographically widespread in various habitats. Our results also suggest that a great diversity of lichen associated yeasts remains to be discovered.

Symbiosis constraints: Strong mycobiont control limits nutrient response in lichens

Symbioses such as lichens are potentially threatened by drastic environmental changes. We used the lichen Peltigera aphthosa-a symbiosis between a fungus (mycobiont), a green alga (Coccomyxa sp.), and N2-fixing cyanobacteria (Nostoc sp.)-as a model organism to assess the effects of environmental perturbations in nitrogen (N) or phosphorus (P). Growth, carbon (C) and N stable isotopes, CNP concentrations, and specific markers were analyzed in whole thalli and the partners after 4 months of daily nutrient additions in the field. Thallus N was 40% higher in N-fertilized thalli, amino acid concentrations were twice as high, while fungal chitin but not ergosterol was lower. Nitrogen also resulted in a thicker algal layer and density, and a higher δ13C abundance in all three partners. Photosynthesis was not affected by either N or P. Thallus growth increased with light dose independent of fertilization regime. We conclude that faster algal growth compared to fungal lead to increased competition for light and CO 2 among the Coccomyxa cells, and for C between alga and fungus, resulting in neither photosynthesis nor thallus growth responded to N fertilization. This suggests that the symbiotic lifestyle of lichens may prevent them from utilizing nutrient abundance to increase C assimilation and growth.