The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis

Unravelling Novel Phytochemicals and Anticholinesterase Activity in Irish Cladonia portentosa

Acetylcholinesterase inhibitors remain the mainstay of symptomatic treatment for Alzheimer's disease. The natural world is rich in acetylcholinesterase inhibitory molecules, and research efforts to identify novel leads is ongoing. Cladonia portentosa, commonly known as reindeer lichen, is an abundant lichen species found in Irish Boglands. The methanol extract of Irish C. portentosa was identified as an acetylcholinesterase inhibitory lead using qualitative TLC-bioautography in a screening program. To identify the active components, the extract was deconvoluted using a successive extraction process with hexane, ethyl acetate and methanol to isolate the active fraction. The hexane extract demonstrated the highest inhibitory activity and was selected for further phytochemical investigations. Olivetolic acid, 4-O-methylolivetolcarboxylic acid, perlatolic acid and usnic acid were isolated and characterized using ESI-MS and two-dimensional NMR techniques. LC-MS analysis also determined the presence of the additional usnic acid derivatives, placodiolic and pseudoplacodiolic acids. Assays of the isolated components confirmed that the observed anticholinesterase activity of C. portentosa can be attributed to usnic acid (25% inhibition at 125 µM) and perlatolic acid (20% inhibition at 250 µM), which were both reported inhibitors. This is the first report of isolation of olivetolic and 4-O-methylolivetolcarboxylic acids and the identification of placodiolic and pseudoplacodiolic acids from C. portentosa.

Effect of thallus melanisation on the sensitivity of lichens to heat stress

Extreme climatic phenomena such as heat waves, heavy rainfall and prolonged droughts are one of the main problems associated with ongoing climate change. The global increase in extreme rainfalls associated with summer heatwaves are projected to increase in amplitude and frequency in the near future. However, the consequences of such extreme events on lichens are largely unknown. The aim was to determine the effect of heat stress on the physiology of lichen Cetraria aculeata in a metabolically active state and to verify whether strongly melanised thalli are more resistant than poorly melanised thalli. In the present study, melanin was extracted from C. aculeata for the first time. Our study showed that the critical temperature for metabolism is around 35 °C. Both symbiotic partners responded to heat stress, manifested by the decreased maximum quantum yield of PSII photochemistry, high level of cell membrane damage, increased membrane lipid peroxidation and decreased dehydrogenase activity. Highly melanised thalli were more sensitive to heat stress, which excludes the role of melanins as compounds protecting against heat stress. Therefore, mycobiont melanisation imposes a trade-off between protection against UV and avoidance of damage caused by high temperature. It can be concluded that heavy rainfall during high temperatures may significantly deteriorate the physiological condition of melanised thalli. However, the level of membrane lipid peroxidation in melanised thalli decreased over time after exposure, suggesting greater efficiency of antioxidant defence mechanisms. Given the ongoing climate changes, many lichen species may require a great deal of plasticity to maintain their physiological state at a level that ensures their survival.

Differential response of two acidophytic lichens to increased reactive nitrogen availability

Lichens are one of the most responsive components of the ecosystem to reactive forms of nitrogen. In this work, we selected the lichen genera Cladonia and Usnea, composed of terricolous and epiphytic lichens respectively, and described as sensitive to nitrogen, to test the effects of different doses of nitrogen on lichen physiological parameters (photobiont and mycobiont vitality, chitin quantification, nitrogen content and stable isotopes analysis). The main objectives were to check if the activation of protective mechanisms could be stimulated in case of chronic stress (low nitrogen increase for prolonged time), and, if so, if a toxicity threshold could be identified above which these mechanisms fail. The two lichen genera were generally affected by prolonged exposure to increased nitrogen availability. However, Cladonia rangiformis was able to maintain physiological functioning at the lowest nitrogen doses used, whereas thalli of Usnea become overwhelmed. Moreover, the mycobiont appeared to be more sensitive than the photobiont responding to lower nitrogen doses. Although only studies of longer duration and testing more nitrogen doses will be able to determine an accurate toxicity threshold, these results give important clues on the use of lichens as biomonitors for the establishment of environmental policies.

Interaction effect of fungicide and chitosan on non-target lichenized fungi

Excessive use of plant growth stimulants and pesticides is currently a considerable problem, especially in agriculture, horticulture, and arboriculture. Understanding the impacts of these compounds and their combinations on non-target organisms is crucial to minimize unintended consequences, while maintaining their use in plant protection. The aim of this study was to test how long-term spraying with different solutions of natural biostimulator chitosan, synthetic fungicide Switch 62.5 WG, and their combinations affects the physiology of epiphytic lichen Xanthoria parietina naturally occurring in fruit orchards and farmlands. We showed that fungicides composed of fludioxionil and cypronidil, as well as the combined use of such fungicides together with chitosan, can cause the considerable impairment of lichen physiology, and these disturbances relate to both algal and fungal partners of the symbiotic association. This negative effect was especially visible in the loss of cell membrane integrity, the high level of membrane lipid peroxidation, and changes in chlorophyll fluorescence parameters on the last day of the experiment. The combined use of these agents also leads to clear disturbances in the functioning of the mitochondrial respiratory chain, which was manifested by increased NADH dehydrogenase activity, while the use of these compounds separately led to a decrease in the activity of this enzyme. We concluded that the regular use of these agents in fruit tree cultivation may cause serious ecological consequences for epiphytic lichen communities as a result of the death of lichen thalli. This study suggests that the impact of some plant protection agents, both individually and in combinations, merits further attention in terms of their impact on non-target fungi.

Interactive effects of precipitation and above canopy nitrogen deposition on understorey vascular plants in a jack pine (Pinus banksiana) forest in northern Alberta, Canada

Elevated nitrogen (N) deposition in the bituminous sands region of northern Alberta, Canada is localized but expected to increase over time. Here we seek to determine the effects of above canopy N deposition on understorey vascular plants in a jack pine (Pinus banksiana) stand in a five-year experimental study. Aqueous N (ammonium nitrate) was applied four times annually (May through October) via helicopter above the canopy between 2011 and 2015 across a narrow but environmentally relevant N deposition gradient (0, 5, 10, 15, 20 and 25 kg N ha^-1 yr^-1). Changes in vascular plant species richness, diversity and total vascular cover were best explained by throughfall water flux, but the positive responses to precipitation decreased with increasing N application. Arctostaphylos uva-ursi and Maianthemum canadense showed positive cover increases in wet years; however, the positive cover expansion at ≥5 kg N ha^-1 yr^-1 treatments was suppressed relative to controls. Total cover expansion was muted in low precipitation years in treatments ≥10 kg N ha^-1 yr^-1. In contrast, Vaccinium vitis-idaea cover changes ≥10 kg N ha^-1 yr^-1 were consistently negative. There were no differences in soil net N mineralization rates, plant foliar N or NO₃^- leaching among treatments. We conjecture the extensive moss/lichen layer of the forest floor that accumulates most of incoming N in throughfall allows them to outcompete vascular plants for water during higher precipitation years, effectively reducing vascular cover expansion relative to controls. This work suggests the response of vascular plants in xeric jack pine ecosystems may interact with climate and these interactions should be considered in risk assessment studies.

Synthesis of lichen response to gaseous nitrogen: ammonia versus nitrogen dioxide

The dominant chemical form of nitrogen pollution in the atmosphere in the U.S. is shifting from oxidized nitrogen, primarily from combustion of fossil fuels, to reduced nitrogen from agricultural animal waste and fertilizer applications. Does it matter to lichens? In this synthesis, we characterize U.S. air concentrations of the most ubiquitous gaseous forms of reduced and oxidized nitrogen, NO2 and NH3, respectively, and their direct effects on lichens. In the U.S., the 3-year average (2017-2019) of the annual mean for each monitoring site ranges up to 56.4 μg NO2 m-3 (~30 ppb) and 6 μg NH3 m-3 (~9 ppb). The spatial coverage of current routine monitoring of NO2 and NH3 likely does not accurately represent exposures of NO2 to ecosystems in rural areas or capture spikes of NH3 concentrations proximal to intensive agriculture, which are documented to exceed 700 μg NH3 m-3 (~1000 ppb) for short durations. Both NO2 and NH3 can act as nutrients to lichens, but as exposures rise, both can cause physiological stress and mortality that then change community composition and diversity. There is a growing body of evidence that lichen community composition is altered at current levels of exposure in the U.S. with estimated no effect or lowest effect concentrations from <1-3 μg m-3 NO2 and <1 μg m-3 NH3. Better spatial characterization of both NO2 and NH3 concentrations, especially near intensive agriculture, would help to characterize the extent of the impacts across the U.S. These findings are discussed in the context of U.S. air pollution policy.

Distinguishing atmospheric nitrogen compounds (nitrate and ammonium) in lichen biomonitoring studies

Nitrogen speciation, i.e. distinguishing nitrate (NO₃^-) and ammonium (NH₄⁺), is commonly undertaken in soil studies, but has not been conducted extensively for lichens. Lichen total nitrogen contents (N wt%) reflect airborne atmospheric nitrogen loadings, originating from anthropogenic sources (e.g. vehicular and agricultural/livestock emissions). Albeit nitrogen being an essential lichen nutrient, nitrogen compound (i.e. NO₃^- and NH₄⁺) concentrations in the atmosphere can have deleterious effects on lichens. Moreover, N wt% do not provide information on individual nitrogen compounds, i.e. NO₃^- and NH₄⁺ which are major constituents of atmospheric particulate matter (e.g. PM₁₀ and PM_2.5). This study presents a novel method to separate and quantify NO₃^- and NH₄⁺ extracted from lichen material. An optimal approach was identified by testing different strengths and volumes of potassium chloride (KCl) solutions and variable extraction times, i.e. the use of 3% KCl for 6 hours can achieve a same-day extraction and subsequent ion chromatography (IC) analysis for reproducible lichen nitrate and ammonium concentration determinations. Application of the method was undertaken by comparing urban and rural Xanthoria parietina samples to investigate the relative importance of the two nitrogen compounds in contrasting environments. Findings presented showed that lichen nitrogen compound concentrations varied in rural and urban X. parietina samples, suggesting different atmospheric nitrogen loadings from potentially different sources (e.g. agricultural and traffic) and varied deposition patterns (e.g. urban layout impacts). Despite potential impacts of nitrogen compounds on lichen metabolism, the approach presented here can be used for quantification of two different nitrogen compounds in lichen biomonitoring studies that will provide specific information on spatial and temporal variability of airborne NO₃^- and NH₄⁺ concentrations that act as precursors of particulate matter, affecting air quality and subsequently human health.

Resilience of Epiphytic Lichens to Combined Effects of Increasing Nitrogen and Solar Radiation

Lichens are classified into different functional groups depending on their ecological and physiological response to a given environmental stressor. However, knowledge on lichen response to the synergistic effect of multiple environmental factors is extremely scarce, although vital to get a comprehensive understanding of the effects of global change. We exposed six lichen species belonging to different functional groups to the combined effects of two nitrogen (N) doses and direct sunlight involving both high temperatures and ultraviolet (UV) radiation for 58 days. Irrespective of their functional group, all species showed a homogenous response to N with cumulative, detrimental effects and an inability to recover following sunlight, UV exposure. Moreover, solar radiation made a tolerant species more prone to N pollution’s effects. Our results draw attention to the combined effects of global change and other environmental drivers on canopy defoliation and tree death, with consequences for the protection of ecosystems.

Intra-specific variation in lichen secondary compounds across environmental gradients on Signy Island, maritime Antarctic

Lichens produce various carbon-based secondary compounds (CBSCs) in response to abiotic conditions and herbivory. Although lichen CBSCs have received considerable attention with regard to responses to UV-B exposure, very little is known about intra-specific variation across environmental gradients and their role in protection against herbivory in the Antarctic. Here we report on the variation in CBSCs of two widely distributed and common Antarctic lichens, Usnea antarctica and Umbilicaria antarctica, between sites with different solar exposure (NW–SE) and along natural nitrogen (N) gradients which are associated with changing lichen-invertebrate associations on Signy Island (South Orkney Islands, maritime Antarctic). Fumarprotocetraric and usnic acid concentrations in Usnea showed no relationships with solar exposure, lichen-N or associated invertebrate abundance. However, fumarprotocetraric acid concentration was 13 times higher at inland sites compared to coastal sites along the N-gradients. Gyrophoric acid concentration in Umbilicaria was 33% lower in sun-facing (northerly exposed) habitats compared to more shaded (south-facing) rocks and declined with elevation. Gyrophoric acid concentration was positively correlated with the abundance and species richness of associated microarthropods, similar to the patterns found with lichen N. This initial investigation indicates that there can be large intraspecific variation in lichen CBSC concentrations across relative short distances (< 500 m) on Signy Island and raises further questions regarding current understanding of the role of CBSCs in Antarctic lichens in relation to biotic and abiotic pressures.

Ecological distribution and potential roles of Woesearchaeota in anaerobic biogeochemical cycling unveiled by genomic analysis

Woesearchaeota as a newly established member of the superphylum DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) are surprisingly abundant and diverse in a wide variety of environments, including deep oil reservoir, sulfuric springs and anoxic aquifers, indicating a high diversity of their roles in global biogeochemical cycles. However, ecological functions of them remain elusive. To fill up this gap, we analyzed and compared the global distribution patterns of Woesearchaeota using the genomes available publicly. As a result, both ecological distribution patterns and metabolic predictions support a key role of woesearchaeotal lineages in cycling of carbon, nitrogen, and sulfur. Multivariate regression analysis reveals that Woesearchaeota might function in consortium with methanogens in the cycling of carbon in anaerobic environments, particularly in soils or sediments. Moreover, comparative genomic analysis and ecological distribution suggest the potential roles of Woesearchaeota in the processes of denitrification, nitrogen fixation, and dissimilatory nitrite reduction, especially in the wastewater treatment systems; and also uncovered the potential capability of sulfate reduction, sulfide oxidation and thiosulfate oxidation in sulfuric or sulfidic-rich environments. Our findings add more information into the ecological roles of archaea in the anoxic environment.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

Alkaline air: changing perspectives on nitrogen and air pollution in an ammonia-rich world

Ammonia and ammonium have received less attention than other forms of air pollution, with limited progress in controlling emissions at UK, European and global scales. By contrast, these compounds have been of significant past interest to science and society, the recollection of which can inform future strategies. Sal ammoniac (nūshādir, nao sha) is found to have been extremely valuable in long-distance trade (ca AD 600-1150) from Egypt and China, where 6-8 kg N could purchase a human life, while air pollution associated with nūshādir collection was attributed to this nitrogen form. Ammonia was one of the keys to alchemy-seen as an early experimental mesocosm to understand the world-and later became of interest as 'alkaline air' within the eighteenth century development of pneumatic chemistry. The same economic, chemical and environmental properties are found to make ammonia and ammonium of huge relevance today. Successful control of acidifying SO₂ and NO_x emissions leaves atmospheric NH₃ in excess in many areas, contributing to particulate matter (PM_2.5) formation, while leading to a new significance of alkaline air, with adverse impacts on natural ecosystems. Investigations of epiphytic lichens and bog ecosystems show how the alkalinity effect of NH₃ may explain its having three to five times the adverse effect of ammonium and nitrate, respectively. It is concluded that future air pollution policy should no longer neglect ammonia. Progress is likely to be mobilized by emphasizing the lost economic value of global N emissions ($200 billion yr^-1), as part of developing the circular economy for sustainable nitrogen management. This article is part of a discussion meeting issue 'Air quality, past present and future'.

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata

BACKGROUND

Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution.

RESULTS

A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting.

CONCLUSIONS

The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.

The influence of growth form and substrate on lichen ecophysiological responses along an aridity gradient

In this paper, we investigated whether growth form and substrate in lichens influence their physiological responses along an aridity gradient. Thalli of the foliose lichen Parmotrema perlatum and the fruticose lichen Ramalina canariensis were transplanted in selected rural/forested sites of Southern Portugal characterized by a different aridity index. Physiological parameters including photosynthetic performances, assimilation pigments, ergosterol content and sample viability were measured prior to exposure (winter) and after 6-month exposure (summer). Photosynthetic performances were also investigated in common native foliose and fruticose epiphytic lichens and in fruticose terricolous species. Both transplanted and native lichens showed a decrease in photosynthetic performances in summer and lower performances in sites classified as drier and higher performances in humid forested sites. No relevant differences occurred between epiphytic foliose and fruticose growth forms. However, terricolous fruticose samples showed a significant difference in humid and drier sites and between winter and summer, probably due to microclimatic conditions similarly to other biological crusts.