Local Responses and Systemic Induced Resistance Mediated by Ectomycorrhizal Fungi

Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health

Plants shape and interact continuously with their rhizospheric microbiota, which play a key role in plant health and resilience. However, plant-associated microbial community can be shaped by several factors including plant phenotype and cropping system. Thus, understanding the interplay between microbiome assembly during the onset of plant-pathogen interactions and long-lasting resistance traits in ligneous plants remains a major challenge. To date, such attempts were mainly investigated in herbaceous plants, due to their phenotypic characteristics and their short life cycle. However, only few studies have focused on the microbial structure, dynamic and their drivers in perennial ligneous plants. Ligneous plants coevolved in interaction with specific fungal and bacterial communities that differ from those of annual plants. The specificities of such ligneous plants in shaping their own functional microbial communities could be dependent on their high heterozygosis, physiological and molecular status associated to seasonality and their aging processes, root system and above-ground architectures, long-lasting climatic variations, and specific cultural practices. This article provides an overview of the specific characteristics of perennial ligneous plants that are likely to modulate symbiotic interactions in the rhizosphere, thus affecting the plant's fitness and systemic immunity. Plant and microbial traits contributing to the establishment of plant-microbiome interactions and the adaptation of this holobiont are also discussed.

Phosphatases: Decoding the Role of Mycorrhizal Fungi in Plant Disease Resistance

Mycorrhizal fungi, a category of fungi that form symbiotic relationships with plant roots, can participate in the induction of plant disease resistance by secreting phosphatase enzymes. While extensive research exists on the mechanisms by which mycorrhizal fungi induce resistance, the specific contributions of phosphatases to these processes require further elucidation. This article reviews the spectrum of mycorrhizal fungi-induced resistance mechanisms and synthesizes a current understanding of how phosphatases mediate these effects, such as the induction of defense structures in plants, the negative regulation of plant immune responses, and the limitation of pathogen invasion and spread. It explores the role of phosphatases in the resistance induced by mycorrhizal fungi and provides prospective future research directions in this field.

Symphony of survival: Insights into cross-talk mechanisms in plants, bacteria, and fungi for strengthening plant immune responses

Plants coexist with a diverse array of microorganisms, predominantly bacteria and fungi, in both natural and agricultural environments. While some microorganisms positively influence plant development and yield, others can cause harm to the host, leading to significant adverse impacts on the environment and the economy. Plant growth-promoting microorganisms (PGPM), including plant growth-promoting bacteria, arbuscular mycorrhizal fungus (AMF), and rhizobia, have been found to increase plant biomass production by synthesizing hormones, fixing nitrogen, and solubilizing phosphate and potassium. Numerous studies have contributed to unraveling the complex process of plant-microbe interactions in recent decades. In light of the increasing global challenges such as population growth, climate change, and resource scarcity, it has become imperative to explore the potential of plant-bacteria-fungi crosstalk in promoting sustainability. This review aims to bridge existing knowledge gaps, providing a roadmap for future research in this dynamic field by synthesizing current knowledge and identifying emerging trends.

Exploring the Influence of Date Palm Cultivars on Soil Microbiota

Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses.

Colonization by orchid mycorrhizal fungi primes induced systemic resistance against necrotrophic pathogen

Orchids and arbuscular mycorrhiza (AM) plants evolved independently and have different structures and fungal partners, but they both facilitate nutrient uptake. Orchid mycorrhiza (OM) supports orchid seed germination, but unlike AM, its role in disease resistance of mature plants is largely unknown. Here, we examined whether OM induces systemic disease resistance against a necrotrophic pathogen in a similar fashion to AM. We investigated the priming effect of mycorrhizal fungi inoculation on resistance of a terrestrial orchid, Bletilla striata, to soft rot caused by Dickeya fangzhongdai. We found that root colonization by a compatible OM fungus primed B. striata seedlings and induced systemic resistance against the infection. Transcriptome analysis showed that priming was mediated by the downregulation of jasmonate and ethylene pathways and that these pathways are upregulated once infection occurs. Comparison with the reported transcriptome of AM fungus-colonized rice leaves revealed similar mechanisms in B. striata and in rice. These findings highlight a novel aspect of commonality between OM and AM plants in terms of induced systemic resistance.

Different ectomycorrhizal fungal species impact poplar growth but not phosphorus utilization under low P supply

Tree growth is often limited by phosphorus (P) availability. The trade-off between P homeostasis and growth is unknown. Ectomycorrhizal fungi (EMF) facilitate P availability but this trait varies among different fungal species and isolates. Here, we tested the hypotheses that (i) colonization with EMF boosts plant growth under P-limited conditions and that (ii) the poplars show P homeostasis because increased P uptake is used for growth and not for P accumulation in the tissues. We used two P treatments (high phosphate [HP]: 64 μM Pi, low phosphate [LP]: 0.64 μM Pi in the nutrient solution) and four fungal treatments (Paxillus involutus MAJ, Paxillus involutus NAU, Laccaria bicolor dikaryon LBD, Laccaria bicolor monokaryon LBM) in addition to non-inoculated poplar plants (NI) to measure growth, biomass, gas exchange and P contents. High phosphate (HP) stimulated growth compared with LP conditions. Poplars colonized with MAJ, NAU and NI showed higher growth and biomass production than those with LBD or LBM. Photosynthesis rates of poplars with lower biomass production were similar to or higher than those of plants with higher growth rates. The tissue concentrations of P were higher under HP than LP conditions and rarely affected by ectomycorrhizal colonization. Under LP, the plants produced 44% greater biomass per unit of P than under HP. At a given P supply, the tissue concentration was stable irrespective of the growth rate indicating P homeostasis. Laccaria bicolor caused growth inhibition, irrespective of P availability. These results suggest that in young poplars distinct species-specific ectomycorrhizal traits overshadowed potential growth benefits.

Mycorrhiza-induced resistance in citrus against Tetranychus urticae is plant species dependent and inversely correlated to basal immunity

BACKGROUND

Mycorrhizal plants show enhanced resistance to biotic stresses, but few studies have addressed mycorrhiza-induced resistance (MIR) against biotic challenges in woody plants, particularly citrus. Here we present a comparative study of two citrus species, Citrus aurantium, which is resistant to Tetranychus urticae, and Citrus reshni, which is highly susceptible to T. urticae. Although both mycorrhizal species are protected in locally infested leaves, they show very distinct responses to MIR.

RESULTS

Previous studies have indicated that C. aurantium is insensitive to MIR in systemic tissues and MIR-triggered antixenosis. Conversely, C. reshni is highly responsive to MIR which triggers local, systemic and indirect defense, and antixenosis against the pest. Transcriptional, hormonal and inhibition assays in C. reshni indicated the regulation of jasmonic acid (JA)- and abscisic acid-dependent responses in MIR. The phytohormone jasmonic acid isoleucine (JA-Ile) and the JA biosynthesis gene LOX2 are primed at early timepoints. Evidence indicates a metabolic flux from phenylpropanoids to specific flavones that are primed at 24 h post infestation (hpi). MIR also triggers the priming of naringenin in mycorrhizal C. reshni, which shows a strong correlation with several flavones and JA-Ile that over-accumulate in mycorrhizal plants. Treatment with an inhibitor of phenylpropanoid biosynthesis C4H enzyme impaired resistance and reduced the symbiosis, demonstrating that phenylpropanoids and derivatives mediate MIR in C. reshni.

CONCLUSION

MIR's effectiveness is inversely correlated to basal immunity in different citrus species, and provides multifaceted protection against T. urticae in susceptible C. reshni, activating rapid local and systemic defenses that are mainly regulated by the accumulation of specific flavones and priming of JA-dependent responses. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Maintenance of host specialisation gradients in ectomycorrhizal symbionts

Many fungi that form ectomycorrhizas exhibit a degree of host specialisation, and individual trees are frequently colonised by communities of mycorrhizal fungi comprising species that fall on a gradient of specialisation along genetic, functional and taxonomic axes of variation. By contrast, arbuscular mycorrhizal fungi exhibit little specialisation. Here, we propose that host tree root morphology is a key factor that gives host plants fine-scale control over colonisation and therefore opportunities for driving specialisation and speciation of ectomycorrhizal fungi. A gradient in host specialisation is likely driven by four proximate mechanistic 'filters' comprising partner availability, signalling recognition, competition for colonisation, and symbiotic function (trade, rewards and sanctions), and the spatially restricted colonisation seen in heterorhizic roots enables these mechanisms, especially symbiotic function, to be more effective in driving the evolution of specialisation. We encourage manipulation experiments that integrate molecular genetics and isotope tracers to test these mechanisms, alongside mathematical simulations of eco-evolutionary dynamics in mycorrhizal symbioses.

Modified source-sink dynamics govern resource exchange in ectomycorrhizal symbiosis

Ectomycorrhizal symbiosis between roots and fungi is founded on the movement of carbon from plants to fungi, and of soil resources from fungi to plants. Framing this movement as a trade can facilitate an understanding of how this mutualism has developed over evolutionary time, but fails to explain experimental observations of carbon and nutrient movement. Here, I propose that source-sink dynamics are an essential basic model to explain the movement of plant and fungal resources, which may be modified by plant immune response, variability in fungal molecular repertoires, and competition in the soil. Source-sink dynamics provide testable hypotheses to illuminate mechanisms of ectomycorrhizal resource movement and its consequences for mutualism stability and forest function under climate change.

Fungal metabolism and free amino acid content may predict nitrogen transfer to the host plant in the ectomycorrhizal relationship between Pisolithus spp. and Eucalyptus grandis

Ectomycorrhizal (ECM) fungi are crucial for tree nitrogen (N) nutrition; however, mechanisms governing N transfer from fungal tissues to the host plant are not well understood. ECM fungal isolates, even from the same species, vary considerably in their ability to support tree N nutrition, resulting in a range of often unpredictable symbiotic outcomes. In this study, we used isotopic labelling to quantify the transfer of N to the plant host by isolates from the ECM genus Pisolithus, known to have significant variability in colonisation and transfer of nutrients to a host. We considered the metabolic fate of N acquired by the fungi and found that the percentage of plant N acquired through symbiosis significantly correlated to the concentration of free amino acids in ECM extra-radical mycelium. Transcriptomic analyses complemented these findings with isolates having high amino acid content and N transfer showing increased expression of genes related to amino acid transport and catabolic pathways. These results suggest that fungal N metabolism impacts N transfer to the host plant in this interaction and that relative N transfer may be possible to predict through basic biochemical analyses.

Soil microbial community response to ectomycorrhizal dominance in diverse neotropical montane forests

Ectomycorrhizal (EM) associations can promote the dominance of tree species in otherwise diverse tropical forests. These EM associations between trees and their fungal mutualists have important consequences for soil organic matter cycling, yet the influence of these EM-associated effects on surrounding microbial communities is not well known, particularly in neotropical forests. We examined fungal and prokaryotic community composition in surface soil samples from mixed arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) stands as well as stands dominated by EM-associated Oreomunnea mexicana (Juglandaceae) in four watersheds differing in soil fertility in the Fortuna Forest Reserve, Panama. We hypothesized that EM-dominated stands would support distinct microbial community assemblages relative to the mixed AM-EM stands due to differences in carbon and nitrogen cycling associated with the dominance of EM trees. We expected that this microbiome selection in EM-dominated stands would lead to lower overall microbial community diversity and turnover, with tighter correspondence between general fungal and prokaryotic communities. We measured fungal and prokaryotic community composition via high-throughput Illumina sequencing of the ITS2 (fungi) and 16S rRNA (prokaryotic) gene regions. We analyzed differences in alpha and beta diversity between forest stands associated with different mycorrhizal types, as well as the relative abundance of fungal functional groups and various microbial taxa. We found that fungal and prokaryotic community composition differed based on stand mycorrhizal type. There was lower prokaryotic diversity and lower relative abundance of fungal saprotrophs and pathogens in EM-dominated than AM-EM mixed stands. However, contrary to our prediction, there was lower homogeneity for fungal communities in EM-dominated stands compared to mixed AM-EM stands. Overall, we demonstrate that EM-dominated tropical forest stands have distinct soil microbiomes relative to surrounding diverse forests, suggesting that EM fungi may filter microbial functional groups in ways that could potentially influence plant performance or ecosystem function.

Ectomycorrhizal symbiosis prepares its host locally and systemically for abiotic cue signaling

Tree growth and survival are dependent on their ability to perceive signals, integrate them, and trigger timely and fitted molecular and growth responses. While ectomycorrhizal symbiosis is a predominant tree-microbe interaction in forest ecosystems, little is known about how and to what extent it helps trees cope with environmental changes. We hypothesized that the presence of Laccaria bicolor influences abiotic cue perception by Populus trichocarpa and the ensuing signaling cascade. We submitted ectomycorrhizal or non-ectomycorrhizal P. trichocarpa cuttings to short-term cessation of watering or ozone fumigation to focus on signaling networks before the onset of any physiological damage. Poplar gene expression, metabolite levels, and hormone levels were measured in several organs (roots, leaves, mycorrhizas) and integrated into networks. We discriminated the signal responses modified or maintained by ectomycorrhization. Ectomycorrhizas buffered hormonal changes in response to short-term environmental variations systemically prepared the root system for further fungal colonization and alleviated part of the root abscisic acid (ABA) signaling. The presence of ectomycorrhizas in the roots also modified the leaf multi-omics landscape and ozone responses, most likely through rewiring of the molecular drivers of photosynthesis and the calcium signaling pathway. In conclusion, P. trichocarpa-L. bicolor symbiosis results in a systemic remodeling of the host's signaling networks in response to abiotic changes. In addition, ectomycorrhizal, hormonal, metabolic, and transcriptomic blueprints are maintained in response to abiotic cues, suggesting that ectomycorrhizas are less responsive than non-mycorrhizal roots to abiotic challenges.

Local Competition and Enhanced Defense: How Metarhizium brunneum Inhibits Verticillium longisporum in Oilseed Rape Plants

Metarhizium brunneum is a soil-borne fungal entomopathogen that can be associated with plant roots. Previous studies have demonstrated that root colonization by beneficial fungi can directly affect soil-borne pathogens through competition and antibiosis and can activate a systemic response in plants, resulting in a primed state for a faster and/or stronger response to stressors. However, the mechanisms by which Metarhizium inoculation ameliorates symptoms caused by plant pathogens are not well known. This study evaluated the ability of M. brunneum to protect oilseed rape (Brassica napus L.) plants against the soil-borne pathogen Verticillium longisporum and investigated whether the observed effects are a result of direct interaction and/or plant-mediated effects. In vitro and greenhouse experiments were conducted to measure fungal colonization of the rhizosphere and plant tissues, and targeted gene expression analysis was used to evaluate the plant response. The results show that M. brunneum delayed pathogen colonization of plant root tissues, resulting in decreased disease symptoms. Direct competition and antibiosis were found to be part of the mechanisms, as M. brunneum growth was stimulated by the pathogen and inhibited the in vitro growth of V. longisporum. Additionally, M. brunneum changed the plant response to the pathogen by locally activating key defense hormones in the salicylic acid (SA) and abscisic acid (ABA) pathways. Using a split-root setup, it was demonstrated that there is a plant-mediated effect, as improved plant growth and decreased disease symptoms were observed when M. brunneum was in the systemic compartment. Moreover, a stronger systemic induction of the gene PR1 suggested a priming effect, involving the SA pathway. Overall, this study sheds light on the mechanisms underlying the protective effects of M. brunneum against soil-borne pathogens in oilseed rape plants, highlighting the potential of this fungal entomopathogen as a biocontrol agent in sustainable agriculture.

Synergistic effects of methyl jasmonate treatment and propagation method on Norway spruce resistance against a bark-feeding insect

Utilizing plants with enhanced resistance traits is gaining interest in plant protection. Two strategies are especially promising for increasing resistance against a forest insect pest, the pine weevil (Hylobius abietis): exogenous application of the plant defense hormone methyl jasmonate (MeJA), and production of plants through the clonal propagation method somatic embryogenesis (SE). Here, we quantified and compared the separate and combined effects of SE and MeJA on Norway spruce resistance to pine weevil damage. Plants produced via SE (emblings) and nursery seedlings (containerized and bare-root), were treated (or not) with MeJA and exposed to pine weevils in the field (followed for 3 years) and in the lab (with a non-choice experiment). Firstly, we found that SE and MeJA independently decreased pine weevil damage to Norway spruce plants in the field by 32-33% and 53-59%, respectively, compared to untreated containerized and bare-root seedlings. Secondly, SE and MeJA together reduced damage to an even greater extent, with treated emblings receiving 86-87% less damage when compared to either untreated containerized or bare-root seedlings in the field, and by 48% in the lab. Moreover, MeJA-treated emblings experienced 98% lower mortality than untreated containerized seedlings, and this high level of survival was similar to that experienced by treated bare-root seedlings. These positive effects on survival remained for MeJA-treated emblings across the 3-year experimental period. We conclude that SE and MeJA have the potential to work synergistically to improve plants' ability to resist damage, and can thus confer a strong plant protection advantage. The mechanisms underlying these responses merit further examination.

DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus

Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.

Beech Leaf Disease Severity Affects Ectomycorrhizal Colonization and Fungal Taxa Composition

Beech leaf disease (BLD) is an emerging forest infestation affecting beech trees (Fagus spp.) in the midwestern and northeastern United States and southeastern Canada. BLD is attributed to the newly recognized nematode Litylenchus crenatae subsp. mccannii. First described in Lake County, Ohio, BLD leads to the disfigurement of leaves, canopy loss, and eventual tree mortality. Canopy loss limits photosynthetic capacity, likely impacting tree allocation to belowground carbon storage. Ectomycorrhizal fungi are root symbionts, which rely on the photosynthesis of autotrophs for nutrition and growth. Because BLD limits tree photosynthetic capacity, ECM fungi may receive less carbohydrates when associating with severely affected trees compared with trees without BLD symptoms. We sampled root fragments from cultivated F. grandifolia sourced from two provenances (Michigan and Maine) at two timepoints (fall 2020 and spring 2021) to test whether BLD symptom severity alters colonization by ectomycorrhizal fungi and fungal community composition. The studied trees are part of a long-term beech bark disease resistance plantation at the Holden Arboretum. We sampled from replicates across three levels of BLD symptom severity and compared fungal colonization via visual scoring of ectomycorrhizal root tip abundance. Effects of BLD on fungal communities were determined through high-throughput sequencing. We found that ectomycorrhizal root tip abundance was significantly reduced on the roots of individuals of the poor canopy condition resulting from BLD, but only in the fall 2020 collection. We found significantly more ectomycorrhizal root tips from root fragments collected in fall 2020 than in spring 2021, suggesting a seasonal effect. Community composition of ectomycorrhizal fungi was not impacted by tree condition but did vary between provenances. We found significant species level responses of ectomycorrhizal fungi between levels of both provenance and tree condition. Of the taxa analyzed, two zOTUs had significantly lower abundance in high-symptomatology trees compared with low-symptomatology trees. These results provide the first indication of a belowground effect of BLD on ectomycorrhizal fungi and contribute further evidence to the role of these root symbionts in studies of tree disease and forest pathology.

A Look at Plant-Growth-Promoting Bacteria

Bacteria have been used to increase crop yields. For their application on crops, bacteria are provided in inoculant formulations that are continuously changing, with liquid- and solid-based products. Bacteria for inoculants are mainly selected from natural isolates. In nature, microorganisms that favor plants exhibit various strategies to succeed and prevail in the rhizosphere, such as biological nitrogen fixation, phosphorus solubilization, and siderophore production. On the other hand, plants have strategies to maintain beneficial microorganisms, such as the exudation of chemoattractanst for specific microorganisms and signaling pathways that regulate plant-bacteria interactions. Transcriptomic approaches are helpful in attempting to elucidate plant-microorganism interactions. Here, we present a review of these issues.

Fast and easy bioassay for the necrotizing fungus Botrytis cinerea on poplar leaves

BACKGROUND

Necrotizing pathogens pose an immense economic and ecological threat to trees and forests, but the molecular analysis of these pathogens is still in its infancy because of lacking model systems. To close this gap, we developed a reliable bioassay for the widespread necrotic pathogen Botrytis cinerea on poplars (Populus sp.), which are established model organisms to study tree molecular biology.

RESULTS

Botrytis cinerea was isolated from Populus x canescens leaves. We developed an infection system using fungal agar plugs, which are easy to handle. The method does not require costly machinery and results in very high infection success and significant fungal proliferation within four days. We successfully tested the fungal plug infection on 18 poplar species from five different sections. Emerging necroses were phenotypically and anatomically examined in Populus x canescens leaves. We adapted methods for image analyses of necrotic areas. We calibrated B. cinerea DNA against Ct-values obtained by quantitative real-time polymerase chain reaction and measured the amounts of fungal DNA in infected leaves. Increases in necrotic area and fungal DNA were strictly correlated within the first four days after inoculation. Methyl jasmonate pretreatment of poplar leaves decreased the spreading of the infection.

CONCLUSIONS

We provide a simple and rapid protocol to study the effects of a necrotizing pathogen on poplar leaves. The bioassay and fungal DNA quantification for Botrytis cinerea set the stage for in-depth molecular studies of immunity and resistance to a generalist necrotic pathogen in trees.

Applying molecular and genetic methods to trees and their fungal communities

Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.

Research progress and hotspot analysis of rhizosphere microorganisms based on bibliometrics from 2012 to 2021

Rhizosphere microorganisms are important organisms for plant growth promotion and bio-control. To understand the research hot topics and frontier trends of rhizosphere microorganisms comprehensively and systematically, we collected 6,056 publications on rhizosphere microorganisms from Web of Science and performed a bibliometric analysis by CiteSpace 6.1.3 and R 5.3.1. The results showed that the total number of references issued in this field has been on the rise in the past decades. China, India, and Pakistan are the top three countries in terms of the number of articles issued, while Germany, the United States, and Spain were the countries with the highest number of co-published papers with other countries. The core research content in this field were the bio-control, bacterial community, ACC deaminase, phytoremediation, induced systematic resistance, and plant growth promotion. Seeding growth, Bacillus velezensis, plant-growth, and biological-control were currently and may be the highlights in the field of rhizosphere microorganisms research for a long time in the future. The above study results quantitatively, objectively, and scientifically described the research status and research focus of rhizosphere microorganisms from 2012 to 2021 from the perspective of referred papers, with a view to promoting in-depth research in this field and providing reference information for scholars in related fields to refine research trends and scientific issues.

Unearthing the alteration in plant volatiles induced by mycorrhizal fungi: A shield against plant pathogens

Plants produce a large range of structurally varied low molecular weight secondary metabolites, which evaporate, known as volatile organic compounds (VOCs). Several of them are emitted in response to biotic stress as a defensive measure against pathogen attacks. Arbuscular Mycorrhizal Fungi (AMFs) can change the VOC pattern in parts of the plant and may promote plant defense via direct or indirect mechanisms. Mycorrhization of plants positively affects plant immunization along with growth and yield. The presence of AMF may raise the concentration of phenolic compounds and the activity of critical defense-related enzymes. AMF-induced changes in plant chemistry and associated volatile emissions lead to stronger immunity against pathogenic microorganisms. Despite substantial research into the origins of diversity in VOC-mediated plant communication, very little is known about the mechanism of influence of several AMFs on plant VOC emissions and modulation of plant immunization. Moreover, the molecular mechanism for VOC sensing in plants and mycorrhizal association is still unclear. In the present review, we have presented an up-to-date understanding of the cross-talk of AMF and VOC patterns in plants and the subsequent modulation of resistance against microbial pathogens.

Parametarhizium hingganense, a Novel Ectomycorrhizal Fungal Species, Promotes the Growth of Mung Beans and Enhances Resistance to Disease Induced by Rhizoctonia solani

The mutualistic interactions between mycorrhizae and plants first occurred along with the terrestrialization of plants. The majority of vascular plants are in symbiosis with mycorrhizal fungi. Due to their importance to the economy and ecology, arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi emerge as the most popular ones. However, the mechanism underlying the beneficial function of ECM fungi is not as clear as AM fungi. Here, the interaction between Parametarhizium hingganense, a novel fungal species isolated from forest litter, and mung bean (Vigna radiata) was studied. P. hingganense demonstrated P solubilization ability in vitro. Treatment of P. hingganense on the seeds resulted in promoted growth with enhanced P content. The hyphae of green fluorescence protein (GFP)-tagged P. hingganense were found to surround the roots and develop between cells, suggesting the establishment of an ectomycorrhizal symbiosis. Upon symbiosis with P. hingganense, the levels of jasmonic acid (JA) and gibberellin (GA₁) and total phenolic and flavonoid content elevated. Meanwhile, damping off caused by Rhizoctonia solani in mycorrhizal plants was alleviated. Taken together, the above findings suggested that symbiosis with P. hingganense conferred growth promotion and priming of defense responses to host plants which should be associated with facilitated P uptake and increased JA and GA₁ levels.

Mechanisms of stress tolerance and their effects on the ecology and evolution of mycorrhizal fungi

Stress is ubiquitous and disrupts homeostasis, leading to damage, decreased fitness, and even death. Like other organisms, mycorrhizal fungi evolved mechanisms for stress tolerance that allow them to persist or even thrive under environmental stress. Such mechanisms can also protect their obligate plant partners, contributing to their health and survival under hostile conditions. Here we review the effects of stress and mechanisms of stress response in mycorrhizal fungi. We cover molecular and cellular aspects of stress and how stress impacts individual fitness, physiology, growth, reproduction, and interactions with plant partners, along with how some fungi evolved to tolerate hostile environmental conditions. We also address how stress and stress tolerance can lead to adaptation and have cascading effects on population- and community-level diversity. We argue that mycorrhizal fungal stress tolerance can strongly shape not only fungal and plant physiology, but also their ecology and evolution. We conclude by pointing out knowledge gaps and important future research directions required for both fully understanding stress tolerance in the mycorrhizal context and addressing ongoing environmental change.

The bacterial and fungal microbiomes of ectomycorrhizal roots from stone oaks and Yunnan pines in the subtropical forests of the Ailao Mountains of Yunnan

Ectomycorrhizal (ECM) symbioses play an important role in tree biology and forest ecology. However, little is known on the composition of bacterial and fungal communities associated to ECM roots. In the present study, we surveyed the bacterial and fungal microbiome of ECM roots from stone oaks (Lithocarpus spp.) and Yunnan pines (Pinus yunnanensis) in the subtropical forests of the Ailao Mountains (Yunnan, China). The bacterial community was dominated by species pertaining to Rhizobiales and Acidobacteriales, whereas the fungal community was mainly composed of species belonging to the Russulales and Thelephorales. While the bacterial microbiome hosted by ECM roots from stone oaks and Yunnan pines was very similar, the mycobiome of these host trees was strikingly distinct. The microbial networks for bacterial and fungal communities showed a higher complexity in Lithocarpus ECM roots compared to Pinus ECM roots, but their modularity was higher in Pinus ECM roots. Seasonality also significantly influenced the fungal diversity and their co-occurrence network complexity. Our findings thus suggest that the community structure of fungi establishing and colonizing ECM roots can be influenced by the local soil/host tree environment and seasonality. These results expand our knowledge of the ECM root microbiome and its diversity in subtropical forest ecosystems.

Systemic effects of Tuber melanosporum inoculation in two Corylus avellana genotypes

Roots of the European hazelnut (Corylus avellana L.), i.e., one of the most economically important nut species, form symbiosis with ectomycorrhizal (ECM) fungi, including truffles. Although physical interactions only occur in roots, the presence of mycorrhizal fungi can lead to metabolic changes at a systemic level, i.e., in leaves. However, how root colonization by ECM fungi modifies these processes in the host plant has so far not been widely studied. This work aimed to investigate the response in two C. avellana genotypes, focusing on leaves from plants inoculated with the black truffle Tuber melanosporum Vittad. Transcriptomic profiles of leaves of colonized plants were compared with those of non-colonized plants, as well as sugar and polyphenolic content. Results suggested that T. melanosporum has the potential to support plants in stressed conditions, leading to the systemic regulation of several genes involved in signaling and defense responses. Although further confirmation is needed, our results open new perspectives for future research aimed to highlight novel aspects in ECM symbiosis.

Improvement of Sphaeropsis Shoot Blight Disease Resistance by Applying the Ectomycorrhizal Fungus Hymenochaete sp. Rl and Mycorrhizal Helper Bacterium Bacillus pumilus HR10 to Pinus thunbergii

Ectomycorrhizal fungi (EMFs) form symbioses with plant roots to promote nutrient uptake by plants but it is controversial as to whether they induce disease resistance in plants. Here, we inoculated pine seedlings with Sphaeropsis sapinea, which was presymbiotic with the EMF Hymenochaete sp. Rl, and the mycorrhizal helper bacterium (MHB) Bacillus pumilus HR10, which promotes the formation of Pinus thunbergia-Hymenochaete sp. Rl mycorrhizae. The results showed that inoculation with Hymenochaete sp. Rl, B. pumilus HR10, and the consortium significantly reduced pine shoot blight disease caused by S. sapinea. After inoculation with pathogenic fungi, callose deposition was significantly increased in needles of pine seedlings inoculated with Hymenochaete sp. Rl, B. pumilus HR10, and the consortium, together with an increase in enzymatic and nonenzymatic systemic antioxidant activity as well as early priming for upregulated expression of PR3 and PR5 genes. Our findings suggest that ectomycorrhizal colonization enhances the resistance of pine seedlings to Sphaeropsis shoot blight by triggering a systemic defense response and that interactions between EMFs and MHBs are essential for mycorrhizal-induced disease resistance.

Split down the middle: studying arbuscular mycorrhizal and ectomycorrhizal symbioses using split-root assays

Most land plants symbiotically interact with soil-borne fungi to ensure nutrient acquisition and tolerance to various environmental stressors. Among these symbioses, arbuscular mycorrhizal and ectomycorrhizal associations can be found in a large proportion of plants, including many crops. Split-root assays are widely used in plant research to study local and systemic signaling responses triggered by local treatments, including nutrient availability, interaction with soil microbes, or abiotic stresses. However, split-root approaches have only been occasionally used to tackle these questions with regard to mycorrhizal symbioses. This review compiles and discusses split-root assays developed to study arbuscular mycorrhizal and ectomycorrhizal symbioses, with a particular emphasis on colonization by multiple beneficial symbionts, systemic resistance induced by mycorrhizal fungi, water and nutrient transport from fungi to colonized plants, and host photosynthate allocation from the host to fungal symbionts. In addition, we highlight how the use of split-root assays could result in a better understanding of mycorrhizal symbioses, particularly for a broader range of essential nutrients, and for multipartite interactions.

Does resource exchange in ectomycorrhizal symbiosis vary with competitive context and nitrogen addition?

Ectomycorrhizal symbiosis is essential for the nutrition of most temperate forest trees and helps regulate the movement of carbon (C) and nitrogen (N) through forested ecosystems. The factors governing the exchange of plant C for fungal N, however, remain obscure. Because competition and soil resources may influence ectomycorrhizal resource movement, we performed a 10-month split-root microcosm study using Pinus muricata seedlings with Thelephora terrestris, Suillus pungens, or no ectomycorrhizal fungus, under two N concentrations in artificial soil. Fungi competed directly with roots and indirectly with each other. We used stable isotope enrichment to track plant photosynthate and fungal N. For T. terrestris, plants received N commensurate with the C given to their fungal partners. Thelephora terrestris was a superior mutualist under high-N conditions. For S. pungens, plant C and fungal N exchange were not coupled. However, in low-N conditions, plants preferentially allocated C to S. pungens rather than T. terrestris. Our results suggest that ectomycorrhizal resource transfer depends on competitive and nutritional context. Plants can exchange C for fungal N, but coupling of these resources can depend on the fungal species and soil N. Understanding the diversity of fungal strategies, and how they change with environmental context, reveals mechanisms driving this important symbiosis.

Mycorrhiza-Tree-Herbivore Interactions: Alterations in Poplar Metabolome and Volatilome

Plants are continuously interacting with other organisms to optimize their performance in a changing environment. Mycorrhization is known to affect the plant growth and nutrient status, but it also can lead to adjusted plant defense and alter interactions with other trophic levels. Here, we studied the effect of Laccaria bicolor-mycorrhization on the poplar (Populus x canescens) metabolome and volatilome on trees with and without a poplar leaf beetle (Chrysomela populi) infestation. We analyzed the leaf and root metabolomes employing liquid chromatography–mass spectrometry, and the leaf volatilome employing headspace sorptive extraction combined with gas-chromatography–mass spectrometry. Mycorrhization caused distinct metabolic adjustments in roots, young/infested leaves and old/not directly infested leaves. Mycorrhization adjusted the lipid composition, the abundance of peptides and, especially upon herbivory, the level of various phenolic compounds. The greatest change in leaf volatile organic compound (VOC) emissions occurred four to eight days following the beetle infestation. Together, these results prove that mycorrhization affects the whole plant metabolome and may influence poplar aboveground interactions. The herbivores and the mycorrhizal fungi interact with each other indirectly through a common host plant, a result that emphasizes the importance of community approach in chemical ecology.

Responses to larval herbivory in the phenylpropanoid pathway of Ulmus minor are boosted by prior insect egg deposition

Elms, which have received insect eggs as a 'warning' of larval herbivory, enhance their anti-herbivore defences by accumulating salicylic acid and amplifying phenylpropanoid-related transcriptional and metabolic responses to hatching larvae. Plant responses to insect eggs can result in intensified defences against hatching larvae. In annual plants, this egg-mediated effect is known to be associated with changes in leaf phenylpropanoid levels. However, little is known about how trees-long-living, perennial plants-improve their egg-mediated, anti-herbivore defences. The role of phytohormones and the phenylpropanoid pathway in egg-primed anti-herbivore defences of a tree species has until now been left unexplored. Using targeted and untargeted metabolome analyses we studied how the phenylpropanoid pathway of Ulmus minor responds to egg-laying by the elm leaf beetle and subsequent larval feeding. We found that when compared to untreated leaves, kaempferol and quercetin concentrations increased in feeding-damaged leaves with prior egg deposition, but not in feeding-damaged leaves without eggs. PCR analyses revealed that prior insect egg deposition intensified feeding-induced expression of phenylalanine ammonia lyase (PAL), encoding the gateway enzyme of the phenylpropanoid pathway. Salicylic acid (SA) concentrations were higher in egg-treated, feeding-damaged leaves than in egg-free, feeding-damaged leaves, but SA levels did not increase in response to egg deposition alone-in contrast to observations made of Arabidopsis thaliana. Our results indicate that prior egg deposition induces a SA-mediated response in elms to feeding damage. Furthermore, egg deposition boosts phenylpropanoid biosynthesis in subsequently feeding-damaged leaves by enhanced PAL expression, which results in the accumulation of phenylpropanoid derivatives. As such, the elm tree shows similar, yet distinct, responses to insect eggs and larval feeding as the annual model plant A. thaliana.

Ectomycorrhizal Fungal Strains Facilitate Cd2+ Enrichment in a Woody Hyperaccumulator under Co-Existing Stress of Cadmium and Salt

Cadmium (Cd²⁺) pollution occurring in salt-affected soils has become an increasing environmental concern in the world. Fast-growing poplars have been widely utilized for phytoremediation of soil contaminating heavy metals (HMs). However, the woody Cd²⁺-hyperaccumulator, Populus × canescens, is relatively salt-sensitive and therefore cannot be directly used to remediate HMs from salt-affected soils. The aim of the present study was to testify whether colonization of P. × canescens with ectomycorrhizal (EM) fungi, a strategy known to enhance salt tolerance, provides an opportunity for affordable remediation of Cd²⁺-polluted saline soils. Ectomycorrhization with Paxillus involutus strains facilitated Cd²⁺ enrichment in P. × canescens upon CdCl₂ exposures (50 μM, 30 min to 24 h). The fungus-stimulated Cd²⁺ in roots was significantly restricted by inhibitors of plasmalemma H⁺-ATPases and Ca²⁺-permeable channels (CaPCs), but stimulated by an activator of plasmalemma H⁺-ATPases. NaCl (100 mM) lowered the transient and steady-state Cd²⁺ influx in roots and fungal mycelia. Noteworthy, P. involutus colonization partly reverted the salt suppression of Cd²⁺ uptake in poplar roots. EM fungus colonization upregulated transcription of plasmalemma H⁺-ATPases (PcHA4, 8, 11) and annexins (PcANN1, 2, 4), which might mediate Cd²⁺ conductance through CaPCs. EM roots retained relatively highly expressed PcHAs and PcANNs, thus facilitating Cd²⁺ enrichment under co-occurring stress of cadmium and salinity. We conclude that ectomycorrhization of woody hyperaccumulator species such as poplar could improve phytoremediation of Cd²⁺ in salt-affected areas.

Plant Tolerance to Drought Stress in the Presence of Supporting Bacteria and Fungi: An Efficient Strategy in Horticulture

Increasing temperature leads to intensive water evaporation, contributing to global warming and consequently leading to drought stress. These events are likely to trigger modifications in plant physiology and microbial functioning due to the altered availability of nutrients. Plants exposed to drought have developed different strategies to cope with stress by morphological, physiological, anatomical, and biochemical responses. First, visible changes influence plant biomass and consequently limit the yield of crops. The presented review was undertaken to discuss the impact of climate change with respect to drought stress and its impact on the performance of plants inoculated with plant growth-promoting microorganisms (PGPM). The main challenge for optimal performance of horticultural plants is the application of selected, beneficial microorganisms which actively support plants during drought stress. The most frequently described biochemical mechanisms for plant protection against drought by microorganisms are the production of phytohormones, antioxidants and xeroprotectants, and the induction of plant resistance. Rhizospheric or plant surface-colonizing (rhizoplane) and interior (endophytic) bacteria and fungi appear to be a suitable alternative for drought-stress management. Application of various biopreparations containing PGPM seems to provide hope for a relatively cheap, easy to apply and efficient way of alleviating drought stress in plants, with implications in productivity and food condition.

Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.