Oak protein profile alterations upon root colonization by an ectomycorrhizal fungus

Diversity and community structure of ectomycorrhizal mycorrhizal fungi in roots and rhizosphere soil of Abies koreana and Taxus cuspidata in Mt. Halla

In this study, the roots and rhizosphere soil of Abies koreana and Taxus cuspidata were collected from sites at two different altitudes on Mt. Halla. Ectomycorrhizal fungi (EMF) were identified by Illumina MiSeq sequencing. The proportion of EMF from the roots was 89% in A. koreana and 69% in T. cuspidata. Among EMF in rhizosphere soils, the genus Russula was the most abundant in roots of A. koreana (p < 0.05). The altitude did not affect the biodiversity of EMF communities but influenced fungal community composition. However, the host plants had the most significant effect on EMF communities. The result of the EMF community analysis showed that even if the EMF were isolated from the same altitudes, the EMF communities differed according to the host plant. The community similarity index of EMF in the roots of A. koreana was higher than that of T. cuspidata (p < 0.05). The results show that both altitude and host plants influenced the structure of EMF communities. Conifers inhabiting harsh sub-alpine environments rely strongly on symbiotic relationships with EMF. A. koreana is an endangered species with a higher host specificity of EMF and climate change vulnerability than T. cuspidata. This study provides insights into the EMF communities, which are symbionts of A. koreana, and our critical findings may be used to restore A. koreana.

The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont

Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant–microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant–microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.

Multifarious Responses of Forest Soil Microbial Community Toward Climate Change

Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO₂, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.

Changes in Soil Ectomycorrhizal Fungi Community in Oak Forests along the Urban–Rural Gradient

The ectomycorrhizal fungi communities of forests are closely correlated with forest health and ecosystem functions. To investigate the structure and composition of ectomycorrhizal fungi communities in oak forest soil and their driving factors along the urban–rural gradient, we set up a Quercus acutissima forest transect and collected samples from the center to the edge of Jinan city (urban, suburban, rural). The results showed that the ectomycorrhizal fungal community composition at the phyla level mainly included Basidiomycota and Ascomycota in three sites. At the genus level, the community compositions of ectomycorrhizal fungi, along the urban–rural gradient, exhibited significant differences. Inocybe, Russula, Scleroderma, Tomentella, Amanita and Tuber were the dominant genera in these Quercus acutissima forests. Additionally, the diversity of ectomycorrhizal fungi was the highest in rural Quercus acutissima forest, followed by urban and suburban areas. Key ectomycorrhizal fungi species, such as Tuber, Russula and Sordariales, were identified among three forests. We also found that pH, soil organic matter and ammonium nitrogen were the main driving factors of the differences in ectomycorrhizal fungi community composition and diversity along the urban–rural gradient. Overall, the differences in composition and diversity in urban–rural gradient forest were driven by the differences in soil physicochemical properties resulting from the forest location.

Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom-forming fungi

The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM habit within the hyperdiverse Russulaceae. We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 species across the order Russulales, of which 13 are newly sequenced, including a representative of a saprotrophic member of Russulaceae, Gloeopeniophorella convolvens. The genomes of ECM Russulaceae are characterized by a loss of genes for plant cell wall-degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE 'nests', or dense aggregations of TEs. Some PCWDEs have been retained or even expanded, mostly in a species-specific manner. The genome of G. convolvens possesses some characteristics of ECM genomes (e.g. loss of some PCWDEs, TE expansion, reduction in secondary metabolism clusters). Functional specialization in ECM decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ECM habit, indicating that changes in genome architecture and gene content may be necessary to prime the evolutionary switch.

Ectomycorrhizal fungi enhance the tolerance of phytotoxicity and cadmium accumulation in oak (Quercus acutissima Carruth.) seedlings: modulation of growth properties and the antioxidant defense responses

Ectomycorrhizal fungi (EMF), which form symbiotic ectomycorrhiza with tree roots, mediate heavy metal tolerance of host plants. To investigate the roles of EMF in the growth, modulation of oxidative stress, and cadmium (Cd) accumulation and translocation in Quercus acutissima seedlings, ectomycorrhizal seedlings inoculated with Suillus luteus were treated with different Cd concentrations (0.1, and 5 mg kg^-1) for 14 days. EMF accelerated seedling growth and Cd accumulation in roots under the highest Cd concentration of 5 mg kg^-1. Catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR) activities increased in the leaves of ectomycorrhizal seedlings under the highest Cd concentration. Superoxide dismutase (SOD) trended to increase under both Cd concentrations. Although reduced glutathione (GSH) increased after inoculation of EMF under both Cd concentrations, the release of malondialdehyde increased in the leaves and roots under the highest Cd concentration, indicating that the defense role of EMF in Q. acutissima depends on the Cd concentration. These results indicate that EMF mitigate Cd stress by promoting plant growth and nutrient uptake while modulating the antioxidant system to reduce oxidative stress.

Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree

Mycorrhizas are known to have a positive impact on plant growth and ability to resist major biotic and abiotic stresses. However, the metabolic alterations underlying mycorrhizal symbiosis are still understudied. By using metabolomics and transcriptomics approaches, cork oak roots colonized by the ectomycorrhizal fungus Pisolithus tinctorius were compared with non-colonized roots. Results show that compounds putatively corresponding to carbohydrates, organic acids, tannins, long-chain fatty acids and monoacylglycerols, were depleted in ectomycorrhizal cork oak colonized roots. Conversely, non-proteogenic amino acids, such as gamma-aminobutyric acid (GABA), and several putative defense-related compounds, including oxylipin-family compounds, terpenoids and B6 vitamers were induced in mycorrhizal roots. Transcriptomic analysis suggests the involvement of GABA in ectomycorrhizal symbiosis through increased synthesis and inhibition of degradation in mycorrhizal roots. Results from this global metabolomics analysis suggest decreases in root metabolites which are common components of exudates, and in compounds related to root external protective layers which could facilitate plant-fungal contact and enhance symbiosis. Root metabolic pathways involved in defense against stress were induced in ectomycorrhizal roots that could be involved in a plant mechanism to avoid uncontrolled growth of the fungal symbiont in the root apoplast. Several of the identified symbiosis-specific metabolites, such as GABA, may help to understand how ectomycorrhizal fungi such as P. tinctorius benefit their host plants.

Pb Stress and Ectomycorrhizas: Strong Protective Proteomic Responses in Poplar Roots Inoculated with Paxillus involutus Isolate and Characterized by Low Root Colonization Intensity

The commonly observed increased heavy metal tolerance of ectomycorrhized plants is usually linked with the protective role of the fungal hyphae covering colonized plant root tips. However, the molecular tolerance mechanisms in heavy metal stressed low-colonized ectormyocrrhizal plants characterized by an ectomycorrhiza-triggered increases in growth are unknown. Here, we examined Populus × canescens microcuttings inoculated with the Paxillus involutus isolate, which triggered an increase in poplar growth despite successful colonization of only 1.9% ± 0.8 of root tips. The analyzed plants, lacking a mantle—a protective fungal biofilter—were grown for 6 weeks in agar medium enriched with 0.75 mM Pb(NO₃)₂. In minimally colonized ‘bare’ roots, the proteome response to Pb was similar to that in noninoculated plants (e.g., higher abundances of PM- and V-type H⁺ ATPases and lower abundance of ribosomal proteins). However, the more intensive activation of molecular processes leading to Pb sequestration or redirection of the root metabolic flux into amino acid and Pb chelate (phenolics and citrate) biosynthesis coexisted with lower Pb uptake compared to that in controls. The molecular Pb response of inoculated roots was more intense and effective than that of noninoculated roots in poplars.

Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis

The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed.

Metabolome adjustments in ectomycorrhizal Populus × canescens associated with strong promotion of plant growth by Paxillus involutus despite a very low root colonization rate

It is believed that resource exchange, which is responsible for intensified growth of ectomycorrhizal plants, occurs in the fungus-plant interface. However, increasing evidence indicates that such intensified plant growth, especially root growth promotion, may be independent of root colonization. Nevertheless, the molecular adjustments in low-colonized plants remain poorly understood. Here, we analysed the metabolome of Populus × canescens microcuttings characterized by significantly increased growth triggered by inoculation with Paxillus involutus, which successfully colonized only 2.1 ± 0.3% of root tips. High-throughput metabolomic analyses of leaves, stems and roots of Populus × canescens microcuttings supplemented with leaf proteome data were performed to determine ectomycorrhiza-triggered changes in N-, P- and C-compounds. The molecular adjustments were relatively low in low-colonized (M) plants. Nevertheless, the levels of foliar phenolic compounds were significantly increased in M plants. Increases of total soluble carbohydrates, starch as well as P concentrations were also observed in M leaves along with the increased abundance of the majority of glycerophosphocholines detected in M roots. However, compared with the leaves of the non-inoculated controls, M leaves presented lower concentrations of both N and most photosynthesis-related proteins and all individual mono- and disaccharides. In M stems, only a few compounds with different abundances were detected, including a decrease in carbohydrates, which was also detected in M roots. Thus, these results suggest that the growth improvement of low-colonized poplar trees is independent of an increased photosynthesis rate, massively increased resource (C:N) exchange and delivery of most nutrients to leaves. The mechanism responsible for poplar growth promotion remains unknown but may be related to increased P uptake, subtle leaf pigment changes, the abundance of certain photosynthetic proteins, slight increases in stem and root amino acid levels and the increase in flavonoids (increasing the antioxidant capacity in poplar), all of which improve the fitness of low-colonized poplars.

Integrated proteomic and metabolomic analyses revealed molecular adjustments in Populus × canescens colonized with the ectomycorrhizal fungus Paxillus involutus, which limited plant host growth

Ectomycorrhizae (ECMs) are a highly context-dependent interactions that are not always beneficial for the plant host, sometimes leading to a decrease in plant growth. However, the molecular status of these plants remains unknown. We studied Populus × canescens microcuttings characterized by impaired growth in response to colonization by a Paxillus involutus strain via integrative proteomics-metabolomics analyses. The analysed strain was characterized by low compatibility and formed only mantles, not a Hartig net, in the majority of root tips. The increased abundance of photosynthetic proteins and foliar carbohydrates co-occurred with signals of intensified resource exchange via the stems of colonized plants. In the roots, intensified C metabolism resulted in the biosynthesis of secondary C compounds unavailable to the fungal partner but also C skeletons necessary to increase insufficient N uptake from the hyphae. The stress response was also detected in colonized plants but was similar to that reported previously during mutualistic ECM interactions. In colonized poplar plants, mechanisms to prevent imbalanced C/N trade-offs were activated. Root metabolism strongly depended on features of the whole plant, especially the foliar C/N budget. However, despite ECM-triggered growth impairment and the foliar nutrient status, the fungal partner was recognized to be a symbiotic partner.

Plant-Microbe Symbiosis: What Has Proteomics Taught Us?

Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.

The leaf lipid composition of ectomycorrhizal oak plants shows a drought-tolerance signature

Ectomycorrhizas have been reported to increase plant tolerance to drought. However, the mechanisms involved are not yet fully understood. Membranes are the first targets of degradation during drought, and growing evidences support a role for membrane lipids in plant tolerance and adaptation to drought. We have previously shown that improved tolerance of ectomycorrhizal oak plants to drought could be related to leaf membrane lipid metabolism, namely through an increased ability to sustain fatty acid content and composition, indicative of a higher membrane stability under stress. Here, we analysed in deeper detail the modulation of leaf lipid metabolism in oak plants mycorrhized with Pisolithus tinctorius and subjected to drought stress. Results show that mycorrhizal plants show patterns associated with water deficit tolerance, like a higher content of chloroplast lipids, whose levels are maintained upon drought stress. Likewise, mycorrhizal plants show increased levels of unsaturated fatty acids in the chloroplast phosphatidylglycerol lipid fraction. As a common response to drought, the digalactosyldiacyloglycerol/monogalactosyldiacyloglycerol ratio increased in the non-mycorrhizal plants, but not in the mycorrhizal plants, associated to smaller alterations in the expression of galactolipid metabolism genes, indicative of a higher drought tolerance. Under drought, inoculated plants showed increased expression of genes involved in neutral lipids biosynthesis, which could be related to an increased ability to tolerate drought stress. Overall, results from this study provide evidences of the involvement of lipid metabolism in the response of ectomycorrhizal plants to water deficit and point to an increased ability to maintain a stable chloroplast membrane functional integrity under stress.

Regulation of the leaf proteome by inoculation of Populus × canescens with two Paxillus involutus isolates differing in root colonization rates

During ectomycorrhizal symbioses, up to 30% of the carbon produced in leaves may be translocated to the fungal partner. Given that the leaf response to root colonization is largely unknown, we performed a leaf proteome analysis of Populus × canescens inoculated in vitro with two isolates of Paxillus involutus significantly differing in root colonization rates (65 ± 7% vs 14 ± 7%), together with plant growth and leaf biochemistry analyses to determine the response of plant leaves to ectomycorrhizal root colonization. The isolate that more efficiently colonized roots (isolate H) affected 9.1% of the leaf proteome compared with control plants. Simultaneously, ectomycorrhiza in isolate H-inoculated plants led to improved plant growth and an increased abundance of leaf proteins involved in protein turnover, stress response, carbohydrate metabolism, and photosynthesis. The protein increment was also correlated with increases in chlorophyll, foliar carbon, and carbohydrate contents. Although inoculation of P. × canescens roots with the other P. involutus isolate (isolate L, characterized by a low root colonization ratio) affected 6.8% of the leaf proteome compared with control plants, most proteins were downregulated. The proteomic signals of increased carbohydrate biosynthesis were not detected, and carbohydrate, carbon, and leaf pigment levels and plant biomass did not differ from the noninoculated plants. Our results revealed that the upregulation of the photosynthetic protein abundance and levels of leaf carbohydrate are positively related to rates of root colonization. Upregulation of photosynthetic proteins, chlorophyll, and leaf carbohydrate levels in ectomycorrhizal plants was positively related to root colonization rates and resulted in increased carbon translocation and sequestration underground.

Early stage metabolic events associated with the establishment of Vitis vinifera - Plasmopara viticola compatible interaction

Grapevine (Vitis vinifera L.) is the most widely cultivated and economically important fruit crop in the world, with 7.5 million of production area in 2017. The domesticated varieties of grapevine are highly susceptible to many fungal infections, of which downy mildew, caused by the biotrophic oomycete Plasmopara viticola (Berk. et Curt.) Berl. et de Toni is one of the most threatening. In V. vinifera, several studies have shown that a weak and transient activation of a defense mechanism occurs, but it is easily overcome by the pathogen leading to the establishment of a compatible interaction. Major transcript, protein and physiologic changes were shown to occur at later infection time-points, but comprehensive data on the first hours of interaction is scarce. In the present work, we investigated the major physiologic and metabolic changes that occur in the first 24 h of interaction between V. vinifera cultivar Trincadeira and P. viticola. Our results show that there was a negative modulation of several metabolic classes associated to pathogen defense such as flavonoids or phenylpropanoids as well as an alteration of carbohydrate content after inoculation with the pathogen. We also found an accumulation of hydrogen peroxide and increase of lipid peroxidation but to a low extent, that seems to be insufficient to restrain pathogen growth during the initial biotrophic phase of the interaction.

Emergy evaluation for decision-making in complex multifunctional farming systems

In a montado farm, commonly found in the South Portugal, human activities benefit from important fluxes of renewable resources. In this study, traditional economic and emergy evaluations are compared to determine their potential contributions to understanding this complex system and applied to a case study of a farm. This allows us to determine how each method values local natural resources and purchased factors of production and services in an empirical context. Results show that the montado farm has a renewable component evaluated at 27% of the total social costs of the system and that the work of natural resources is undervalued in economic budget accounting. Economic evaluation's relative value of purchased factors and services is three and half times higher than their emergy share. We propose that complementing economic budget accounting with emergy accounting provides a benchmark to evaluate the environmental contribution to agricultural and farming systems. In this way, factors external to markets can be evaluated for farming systems, bringing to economic analysis a full evaluation of resources, including the bio-geophysical system's contributions to wealth, enlarging total economic value of resources with a donor perspective enabling a better informed and comprehensive accounting to attain sustainable economic decisions and public policies.

Cadmium Tolerance of Perennial Ryegrass Induced by Aspergillus aculeatus

Cadmium (Cd) pollution is becoming increasingly prevalent, posing a global environmental hazard due to its negative effects on plants growth and human health. Phytoremediation is a green technology that involves uptake of Cd from the soil by a combination of plants and associated microbes. The objective of this study was to investigate the role of Aspergillus aculeatus in perennial ryegrass Cd tolerance. This fungus produced indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylate deaminase. Physiological traits including growth rate, turf quality and chlorophyll content were measured to evaluate the physiological responses of perennial ryegrass to Cd stress. These physiological traits were improved after inoculated with A. aculeatus. Inoculation of A. aculeatus actively reduced DTPA-Cd concentration in the soil and Cd translocation to plant shoots. Chlorophyll a fluorescence transient and the C/N ratio in shoots were elevated by A. aculeatus, which implied that the fungus could protect the photosystem II against Cd stress and increase the photosynthetic efficiency. These results suggested that A. aculeatus is beneficial in improving Cd tolerance of perennial ryegrass and reducing Cd-induced injuries, thus, it has promising potential for application of phytostabilization in Cd contaminated soil.

Ectomycorrhizal inoculation with Pisolithus tinctorius reduces stress induced by drought in cork oak

We investigated whether the performance of cork oak under drought could be improved by colonization with the ectomycorrhizal fungus Pisolithus tinctorius. Results show that inoculation alone had a positive effect on plant height, shoot biomass, shoot basal diameter, and root growth. Under drought, root growth of mycorrhizal plants was significantly increased showing that inoculation was effective in increasing tolerance to drought. In accordance, mycorrhizal plants subjected to drought showed less symptoms of stress when compared to non-mycorrhizal plants, such as lower concentration of soluble sugars and starch, increased ability to maintain fatty acid content and composition, and increased unsaturation level of membrane lipids. After testing some of the mechanisms suggested to contribute to the enhanced tolerance of mycorrhizal plants to drought, we could not find any by which Pisolithus tinctorius could benefit cork oak, at least under the drought conditions imposed in our experiment. Inoculation did not increase photosynthesis under drought, suggesting no effect in sustaining stomatal opening at low soil water content. Similarly, plant water status was not affected by inoculation suggesting that P. tinctorius does not contribute to an increased plant water uptake during drought. Inoculation did increase nitrogen concentration in plants but it was independent of the water status. Furthermore, no significant mycorrhizal effect on drought-induced ROS production or osmotic adjustment was detected, suggesting that these factors are not important for the improved drought tolerance triggered by P. tinctorius.