Laser microdissection unravels cell-type-specific transcription in arbuscular mycorrhizal roots, including CAAT-box transcription factor gene expression correlating with fungal contact and spread

Nuclear factors NF-YC3 and NF-YBs positively regulate arbuscular mycorrhizal symbiosis in tomato

The involvement of nuclear factor Y (NF-Y) in transcriptional reprogramming during arbuscular mycorrhizal symbiosis has been demonstrated in several plant species. However, a comprehensive picture is lacking. We showed that the spatial expression of NF-YC3 was observed in cortical cells containing arbuscules via the cis-regulatory element GCC boxes. Moreover, the NF-YC3 promoter was transactivated by the combination of CYCLOPS and autoactive calcium and calmodulin-dependent kinase (CCaMK) via GCC boxes. Knockdown of NF-YC3 significantly reduced the abundance of all intraradical fungal structures and affected arbuscule size. BCP1, SbtM1, and WRI5a, whose expression associated with NF-YC3 levels, might be downstream of NF-YC3. NF-YC3 interacted with NF-YB3a, NF-YB5c, or NF-YB3b, in yeast (Saccharomyces cerevisiae) and in planta, and interacted with NF-YA3a in yeast. Spatial expression of 3 NF-YBs was observed in all cell layers of roots under both mock and mycorrhizal conditions. Simultaneous knockdown of 3 NF-YBs, but not individually, reduced the fungal colonization level, suggesting that there might be functional redundancy of NF-YBs to regulate AM symbiosis. Collectively, our data suggest that NF-YC3 and NF-YBs positively regulate AM symbiosis in tomato, and arbuscule-related NF-YC3 may be an important downstream gene of the common symbiosis signaling pathway.

Differential root and cell regulation of maize aquaporins by the arbuscular mycorrhizal symbiosis highlights its role in plant water relations

This study aims to elucidate if the regulation of plant aquaporins by the arbuscular mycorrhizal (AM) symbiosis occurs only in roots or cells colonized by the fungus or at whole root system. Maize plants were cultivated in a split-root system, with half of the root system inoculated with the AM fungus and the other half uninoculated. Plant growth and hydraulic parameters were measured and aquaporin gene expression was determined in each root fraction and in microdissected cells. Under well-watered conditions, the non-colonized root fractions of AM plants grew more than the colonized root fraction. Total osmotic and hydrostatic root hydraulic conductivities (Lo and Lpr) were higher in AM plants than in non-mycorrhizal plants. The expression of most maize aquaporin genes analysed was different in the mycorrhizal root fraction than in the non-mycorrhizal root fraction of AM plants. At the cellular level, differential aquaporin expression in AM-colonized cells and in uncolonized cells was also observed. Results indicate the existence of both, local and systemic regulation of plant aquaporins by the AM symbiosis and suggest that such regulation is related to the availability of water taken up by fungal hyphae in each root fraction and to the plant need of water mobilization.

Growth, profitability, nutritional, and anti-nutritional properties of seven Manihot esculenta Crantz (cassava) varieties as affected by arbuscular mycorrhizal fungi

Despite a range of methods used to promote modern agriculture with several outcomes, food quality and availability problems remain. This work aims to evaluate the effect of AM fungi inoculation on the growth, yield, nutritional, and antinutritional properties of 7 varieties of cassava. Growth characteristics, yields, rentability, nutritional, and antinutritional of tubers of each treatment were determined at harvest. All the cassava varieties used form a symbiosis with AM fungi at various frequencies, with the I090590 variety being the best (61.66 %). The best amount of chlorophyll, carotenoid, and height of plants were recorded at 9 months old. The 96/1414, TME/693 and MD varieties respectively show the best amount of chlorophyll, size, and carotenoids at 9 months old. Following AM fungi inoculation, an increase in the content of chlorophyll, size, and carotenoids was recorded for all the varieties with the best rate attributed respectively to 92/0326, MD, and 92/0326. Tuber yields vary significantly depending on the cassava varieties, with the best (56.16 t/ha) recorded for the I090590 variety. Following inoculation with AM fungi, a significant increase in yields was recorded, with the best ratio (2.7) obtained with the AE variety. The I090590 variety shows the best yield and by then the most profitable. Inoculation with AM fungi leads to a significant increase in the sugar, protein, fibre, and phosphorus content of all cassava varieties, with the best ratios obtained in 96/1414, 01/1797, and I090590 varieties respectively. Similarly, the inoculation of cassava varieties with AM fungi leads to a significant reduction in the content of cyanides, oxalates, and phytates. The best ratio of reduction for cyanide was 1.91 for the MD variety. AM fungi inoculation is an important way to ensure safe, exponential production and high economic profitability of foodstuffs.

Breaking barriers: improving time and space resolution of arbuscular mycorrhizal symbiosis with single-cell sequencing approaches

The cell and molecular bases of arbuscular mycorrhizal (AM) symbiosis, a crucial plant-fungal interaction for nutrient acquisition, have been extensively investigated by coupling traditional RNA sequencing techniques of roots sampled in bulk, with methods to capture subsets of cells such as laser microdissection. These approaches have revealed central regulators of this complex relationship, yet the requisite level of detail to effectively untangle the intricacies of temporal and spatial development remains elusive.The recent adoption of single-cell RNA sequencing (scRNA-seq) techniques in plant research is revolutionizing our ability to dissect the intricate transcriptional profiles of plant-microbe interactions, offering unparalleled insights into the diversity and dynamics of individual cells during symbiosis. The isolation of plant cells is particularly challenging due to the presence of cell walls, leading plant researchers to widely adopt nuclei isolation methods. Despite the increased resolution that single-cell analyses offer, it also comes at the cost of spatial perspective, hence, it is necessary the integration of these approaches with spatial transcriptomics to obtain a comprehensive overview.To date, few single-cell studies on plant-microbe interactions have been published, most of which provide high-resolution cell atlases that will become crucial for fully deciphering symbiotic interactions and addressing future questions. In AM symbiosis research, key processes such as the mutual recognition of partners during arbuscule development within cortical cells, or arbuscule senescence and degeneration, remain poorly understood, and these advancements are expected to shed light on these processes and contribute to a deeper understanding of this plant-fungal interaction.

The role of strigolactones in resistance to environmental stress in plants

Abiotic stress impairs plant growth and development, thereby causing low yield and inferior quality of crops. Increasing studies reported that strigolactones (SL) are plant hormones that enhance plant stress resistance by regulating plant physiological processes and gene expressions. In this review, we introduce the response and regulatory role of SL in salt, drought, light, heat, cold and cadmium stresses in plants. This review also discusses how SL alleviate the damage of abiotic stress in plants, furthermore, introducing the mechanisms of SL enhancing plant stress resistance at the genetic level. Under abiotic stress, the exogenous SL analog GR24 can induce the biosynthesis of SL in plants, and endogenous SL can alleviate the damage caused by abiotic stress. SL enhanced the stress resistance of plants by protecting photosynthesis, enhancing the antioxidant capacity of plants and promoting the symbiosis between plants and arbuscular mycorrhiza (AM). SL interact with abscisic acid (ABA), salicylic acid (SA), auxin, cytokinin (CK), jasmonic acid (JA), hydrogen peroxide (H2O2) and other signal molecules to jointly regulate plant stress resistance. Lastly, both the importance of SL and their challenges for future work are outlined in order to further elucidate the specific mechanisms underlying the roles of SL in plant responses to abiotic stress.

Phosphatidyl Ethanolamine Binding Protein FLOWERING LOCUS T-like 12 (OsFTL12) Regulates the Rice Heading Date under Different Day-Length Conditions

Plant FLOWERING LOCUS T-Like (FTL) genes often redundantly duplicate on chromosomes and functionally diverge to modulate reproductive traits. Rice harbors thirteen FTL genes, the functions of which are still not clear, except for the Hd3a and RFT genes. Here, we identified the molecular detail of OsFTL12 in rice reproductive stage. OsFTL12 encoding protein contained PEBP domain and localized into the nucleus, which transcripts specifically expressed in the shoot and leaf blade with high abundance. Further GUS-staining results show the OsFTL12 promoter activity highly expressed in the leaf and stem. OsFTL12 knock-out concurrently exhibited early flowering phenotype under the short- and long-day conditions as compared with wild-type and over-expression plants, which independently regulates flowering without an involved Hd1/Hd3a and Ehd1/RFT pathway. Further, an AT-hook protein OsATH1 was identified to act as upstream regulator of OsFTL12, as the knock-out OsATH1 elevated the OsFTL12 expression by modifying Histone H3 acetylation abundance. According to the dissection of OsFTL12 molecular functions, our study expanded the roles intellectual function of OsFTL12 in the mediating of a rice heading date.

How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis

The evolution of plants to efficiently transport water and assimilates over long distances is a major evolutionary success that facilitated their growth and colonization of land. Vascular tissues, namely xylem and phloem, are characterized by high specialization, cell heterogeneity, and diverse cell components. During differentiation and maturation, these tissues undergo an irreversible sequence of events, leading to complete protoplast degradation in xylem or partial degradation in phloem, enabling their undisturbed conductive function. Due to the unique nature of vascular tissue, and the poorly understood processes involved in xylem and phloem development, studying the molecular basis of tissue differentiation is challenging. In this review, we focus on methods crucial for gene expression research in conductive tissues, emphasizing the importance of initial anatomical analysis and appropriate material selection. We trace the expansion of molecular techniques in vascular gene expression studies and discuss the application of single-cell RNA sequencing, a high-throughput technique that has revolutionized transcriptomic analysis. We explore how single-cell RNA sequencing will enhance our knowledge of gene expression in conductive tissues.

Fixation and Laser Capture Microdissection of Plant Tissue for RNA Extraction and RNASeq Library Preparation

To study the transcriptome of individual plant cells at specific points in time, we developed protocols for fixation, embedding, and sectioning of plant tissue followed by laser capture microdissection (LCM) and processing for RNA recovery. LCM allows the isolation of individual cell types from heterogeneous tissue sections and is particularly suited to plant processing because it does not require the breakdown of cell walls. This approach allows accurate separation of a small volume of cells that can be used to study gene expression profiles in different tissues or cell layers. The technique requires neither separation of cells by enzymatic digestion of any kind nor cell-specific reporter genes, and it allows storage of fixed and embedded tissue for months before capture. The methods for fixation, embedding, sectioning, and capturing of plant cells that we describe yield high-quality RNA suitable for making libraries for RNASeq. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Tissue Preparation for Laser Capture Microdissection Basic Protocol 2: Tissue Sectioning Basic Protocol 3: Laser Capture Microdissection of Embedded Tissue Basic Protocol 4: RNA Extraction from Laser Capture Microdissection Samples.

Long-lasting impact of chitooligosaccharide application on strigolactone biosynthesis and fungal accommodation promotes arbuscular mycorrhiza in Medicago truncatula

The establishment of arbuscular mycorrhiza (AM) between plants and Glomeromycotina fungi is preceded by the exchange of chemical signals: fungal released Myc-factors, including chitooligosaccharides (CO) and lipo-chitooligosaccharides (LCO), activate plant symbiotic responses, while root-exuded strigolactones stimulate hyphal branching and boost CO release. Furthermore, fungal signaling reinforcement through CO application was shown to promote AM development in Medicago truncatula, but the cellular and molecular bases of this effect remained unclear. Here, we focused on long-term M. truncatula responses to CO treatment, demonstrating its impact on the transcriptome of both mycorrhizal and nonmycorrhizal roots over several weeks and providing an insight into the mechanistic bases of the CO-dependent promotion of AM colonization. CO treatment caused the long-lasting regulation of strigolactone biosynthesis and fungal accommodation-related genes. This was mirrored by an increase in root didehydro-orobanchol content, and the promotion of accommodation responses to AM fungi in root epidermal cells. Lastly, an advanced downregulation of AM symbiosis marker genes was observed at the latest time point in CO-treated plants, in line with an increased number of senescent arbuscules. Overall, CO treatment triggered molecular, metabolic, and cellular responses underpinning a protracted acceleration of AM development.

Reconditioning of plant metabolism by arbuscular mycorrhizal networks in cadmium contaminated soils: Recent perspectives

Cadmium (Cd) is one of the most perilous nonessential heavy metal for plants, owing to its high water solubility and obstruction with various physiological and biochemical processes. It enters food chain via plant uptake from contaminated soil, posing a grave menace to ecosystem and mankind. Green remediation comprises approaches intended at prudent use of natural resources for increasing profits to humans and environment. Arbuscular mycorrhizal (AM) fungi are considered a promising green technological tool for remedial of Cd-polluted soils. They are naturally associated with root system of plants in Cd-contaminated soils, evidencing their tolerance to Cd. AM can decrease Cd uptake by plants broadly through two strategies: (1) extracellular mechanisms involving Cd chelation by root exudates, binding to fungal cell wall/structures or to the glycoprotein glomalin; (2) intracellular means involving transfer via hyphal network, detoxification and vacuolar sequestration mediated by complexation of Cd with glutathione (GSH), phytochelatins (PCs), metallothioneins (MTs) and polyphosphate granules. Additionally, mycorrhizal symbiosis facilitates reconditioning of plants' metabolism primarily through dilution effect, increased water and mineral uptake. Recently, AM-induced remodelling of root cell wall synthesis has been reported to improve plant vigor and survival under Cd stressed environments. The present article highlights Cd impacts on AM growth, its diversity in Cd contaminated soils, and variations among diverse AM fungal species for imparting plant Cd tolerance. The most recent perspectives on AM-mediated Cd tolerance mechanisms in plants, including cellular and molecular studies have also been reviewed for successful utilization of these beneficial microbes in sustainable agriculture.

NF-YB family transcription factors in Arabidopsis: Structure, phylogeny, and expression analysis in biotic and abiotic stresses

Nuclear factor-Y (NF-Y) transcription factors (TFs) are conserved heterotrimeric complexes present and widespread across eukaryotes. Three main subunits make up the structural and functional aspect of the NF-Y TFs: NF-YA, NF-YB and NF-YC, which bind to the conserved CCAAT- box of the promoter region of specific genes, while also interacting with each other, thereby forming myriad combinations. The NF-YBs are expressed differentially in various tissues and plant development stages, likely impacting many of the cellular processes constitutively and under stress conditions. In this study, ten members of NF-YB family from Arabidopsis thaliana were identified and expression profiles were mined from microarray data under different biotic and abiotic conditions, revealing key insights into the involvement of this class of proteins in the cellular and biological processes in Arabidopsis. Analysis of cis-acting regulatory elements (CAREs) indicated the presence of abiotic and biotic stress-related transcription factor binding sites (TFBs), shedding light on the multifaceted roles of these TFs. Microarray data analysis inferred distinct patterns of expression in various tissues under differing treatments such as drought, cold and heat stress as well as bacterial, fungal, and viral stress, indicating their likelihood of having an expansive range of regulatory functions under native and stressed conditions; while quantitative real-time PCR (qRT-PCR) based expression analysis revealed that these TFs get real-time-modulated in a stress dependent manner. This study, overall, provides an understanding of the AtNF-YB family of TFs in their regulation and participation in various morphogenetic and defense- related pathways and can provide insights for development of transgenic plants for trait dependent studies.

Signaling and Detoxification Strategies in Plant-Microbes Symbiosis under Heavy Metal Stress: A Mechanistic Understanding

Plants typically interact with a variety of microorganisms, including bacteria, mycorrhizal fungi, and other organisms, in their above- and below-ground parts. In the biosphere, the interactions of plants with diverse microbes enable them to acquire a wide range of symbiotic advantages, resulting in enhanced plant growth and development and stress tolerance to toxic metals (TMs). Recent studies have shown that certain microorganisms can reduce the accumulation of TMs in plants through various mechanisms and can reduce the bioavailability of TMs in soil. However, relevant progress is lacking in summarization. This review mechanistically summarizes the common mediating pathways, detoxification strategies, and homeostatic mechanisms based on the research progress of the joint prevention and control of TMs by arbuscular mycorrhizal fungi (AMF)-plant and Rhizobium-plant interactions. Given the importance of tripartite mutualism in the plant-microbe system, it is necessary to further explore key signaling molecules to understand the role of plant-microbe mutualism in improving plant tolerance under heavy metal stress in the contaminated soil environments. It is hoped that our findings will be useful in studying plant stress tolerance under a broad range of environmental conditions and will help in developing new technologies for ensuring crop health and performance in future.

MtNF-YC6 and MtNF-YC11 are involved in regulating the transcriptional program of arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal fungi are obligate symbionts that transfer mineral nutrients to host plants through arbuscules, a fungal structure specialized for exchange for photosynthetic products. MtNF-YC6 and MtNF-YC11, which encode the C subunits of nuclear factor Y (NF-Y) family in Medicago truncatula are induced specifically by arbuscular mycorrhizal symbiosis (AMS). A previous study showed that MtNF-YC6 and MtNF-YC11 are activated in cortical cells of mycorrhizal roots, but the gene functions were unknown. Herein, we identified both MtNF-YB17 and MtNF-YB12 as the interacting partners of MtNF-YC6 and MtNF-YC11 in yeast and plants. MtNF-YB17 was highly induced by AMS and activated in cortical cells only in mycorrhizal roots but MtNF-YB12 was not affected. The formation of B/C heterodimers led the protein complexes to transfer from the cytoplasm to the nucleus. Silencing MtNF-YC6 and C11 by RNA interference (RNAi) resulted in decreased colonization efficiency and arbuscule richness. Coincidently, genes associated with arbuscule development and degeneration in RNAi roots were also downregulated. In silico analysis showed CCAAT-binding motifs in the promoter regions of downregulated genes, further supporting the involvement of NF-Y complexes in transcriptional regulation of symbiosis. Taken together, this study identifies MtNF-YC6- or MtNF-YC11-containing protein complexes as novel transcriptional regulators of symbiotic program and provides a list of potential downstream target genes. These data will help to further dissect the AMS regulatory network.

The Roles of Phosphorus and Nitrogen Nutrient Transporters in the Arbuscular Mycorrhizal Symbiosis

More than 80% of land plant species can form symbioses with arbuscular mycorrhizal (AM) fungi, and nutrient transfer to plants is largely mediated through this partnership. Over the last few years, great progress has been made in deciphering the molecular mechanisms underlying the AM-mediated modulation of nutrient uptake progress, and a growing number of fungal and plant genes responsible for the uptake of nutrients from soil or transfer across the fungal-root interface have been identified. In this review, we outline the current concepts of nutrient exchanges within this symbiosis (mechanisms and regulation) and focus on P and N transfer from the fungal partner to the host plant, with a highlight on a possible interplay between P and N nutrient exchanges. Transporters belonging to the plant or AM fungi can synergistically process the transmembrane transport of soil nutrients to the symbiotic interface for further plant acquisition. Although much progress has been made to elucidate the complex mechanism for the integrated roles of nutrient transfers in AM symbiosis, questions still remain to be answered; for example, P and N transporters are less studied in different species of AM fungi; the involvement of AM fungi in plant N uptake is not as clearly defined as that of P; coordinated utilization of N and P is unknown; transporters of cultivated plants inoculated with AM fungi and transcriptomic and metabolomic networks at both the soil-fungi interface and fungi-plant interface have been insufficiently studied. These findings open new perspectives for fundamental research and application of AM fungi in agriculture.

A CCaMK/Cyclops response element in the promoter of Lotus japonicus calcium-binding protein 1 (CBP1) mediates transcriptional activation in root symbioses

Early gene expression in arbuscular mycorrhiza (AM) and the nitrogen-fixing root nodule symbiosis (RNS) is governed by a shared regulatory complex. Yet many symbiosis-induced genes are specifically activated in only one of the two symbioses. The Lotus japonicus T-DNA insertion line T90, carrying a promoterless uidA (GUS) gene in the promoter of Calcium Binding Protein 1 (CBP1) is exceptional as it exhibits GUS activity in both root endosymbioses. To identify the responsible cis- and trans-acting factors, we subjected deletion/modification series of CBP1 promoter : reporter fusions to transactivation and spatio-temporal expression analysis and screened ethyl methanesulphonate (EMS)-mutagenized T90 populations for aberrant GUS expression. We identified one cis-regulatory element required for GUS expression in the epidermis and a second element, necessary and sufficient for transactivation by the calcium and calmodulin-dependent protein kinase (CCaMK) in combination with the transcription factor Cyclops and conferring gene expression during both AM and RNS. Lack of GUS expression in T90 white mutants could be traced to DNA hypermethylation detected in and around this element. We concluded that the CCaMK/Cyclops complex can contribute to at least three distinct gene expression patterns on its direct target promoters NIN (RNS), RAM1 (AM), and CBP1 (AM and RNS), calling for yet-to-be identified specificity-conferring factors.

Mycorrhizal symbiosis reprograms ion fluxes and fatty acid metabolism in wild jujube during salt stress

Chinese jujube (Ziziphus jujuba) is an important fruit tree in China, and soil salinity is the main constraint affecting jujube production. It is unclear how arbuscular mycorrhizal (AM) symbiosis supports jujube adaptation to salt stress. Herein, we performed comparative physiological, ion flux, fatty acid (FA) metabolomic, and transcriptomic analyses to examine the mechanism of AM jujube responding to salt stress. AM seedlings showed better performance during salt stress. AM symbiosis altered phytohormonal levels: indole-3-acetic acid and abscisic acid contents were significantly increased in AM roots and reduced by salt stress. Mycorrhizal colonization enhanced root H+ efflux and K+ influx, while inducing expression of plasma membrane-type ATPase 7 (ZjAHA7) and high-affinity K+ transporter 2 (ZjHAK2) in roots. High K+/Na+ homeostasis was maintained throughout salt exposure. FA content was elevated in AM leaves as well as roots, especially for palmitic acid, oleic acid, trans oleic acid, and linoleic acid, and similar effects were also observed in AM poplar (Populus. alba × Populus. glandulosa cv. 84K) and Medicago truncatula, indicating AM symbiosis elevating FA levels could be a conserved physiological effect. Gene co-expression network analyses uncovered a core gene set including 267 genes in roots associated with AM symbiosis and conserved transcriptional responses, for example, FA metabolism, phytohormone signal transduction, SNARE interaction in vesicular transport, and biotin metabolism. In contrast to widely up-regulated genes related to FA metabolism in AM roots, limited genes were affected in leaves. We propose a model of AM symbiosis-linked reprogramming of FA metabolism and provide a comprehensive insight into AM symbiosis with a woody species adaptation to salt stress.

The potential role of Mucoromycotina 'fine root endophytes' in plant nitrogen nutrition

Mycorrhizal associations between fungi and plant roots have globally significant impacts on nutrient cycling. Mucoromycotina 'fine root endophytes' (MFRE) are a distinct and recently characterised group of mycorrhiza-forming fungi that associate with the roots of a range of host plant species. Given their previous misidentification and assignment as arbuscular mycorrhizal fungi (AMF) of the Glomeromycotina, it is now important to untangle the specific form and function of MFRE symbioses. In particular, relatively little is known about the nature of MFRE colonisation and its role in N uptake and transfer to host plants. Even less is known about the mechanisms by which MFRE access and assimilate N, and how this N is processed and subsequently exchanged with host plants for photosynthates. Here, we summarise and contrast the structures formed by MFRE and arbuscular mycorrhizal fungi in host plants as well as compare the N source preference of each mycorrhizal fungal group with what is currently known for MFRE N uptake. We compare the mechanisms of N assimilation and transfer to host plants utilised by the main groups of mycorrhizal fungi and hypothesise potential mechanisms for MFRE N assimilation and transfer, outlining directions for future research.

Plant-Mycorrhizal Fungi Interactions in Phytoremediation of Geogenic Contaminated Soils

Soil contamination by geogenic contaminants (GCs) represents an imperative environmental problem. Various soil remediation methods have been successfully employed to ameliorate the health risks associated with GCs. Phytoremediation is considered as an eco-friendly and economical approach to revegetate GC-contaminated soils. However, it is a very slow process, as plants take a considerable amount of time to gain biomass. Also, the process is limited only to the depth and surface area of the root. Inoculation of arbuscular mycorrhizal fungi (AMF) with remediating plants has been found to accelerate the phytoremediation process by enhancing plant biomass and their metal accumulation potential while improving the soil physicochemical and biological characteristics. Progress in the field application is hindered by a lack of understanding of complex interactions between host plant and AMF that contribute to metal detoxification/(im)mobilization/accumulation/translocation. Thus, this review is an attempt to reveal the underlying mechanisms of plant-AMF interactions in phytoremediation.

Rhizophagus intraradices improves arsenic tolerance in Sophora viciifolia Hance

Purpose

Arbuscular mycorrhizal fungi (AMF) are capable of protecting host plants against heavy metal toxicity, whereas rare knowledge has been acquired on the underlying effects of AMF on woody leguminous species under arsenic (As) stress. This study was aimed that whether AMF inoculation improves the As tolerance in Sophora viciifolia (a king of leguminous shrub).

Methods

S. viciifolia seedlings were inoculated with AMF Rhizophagus intraradices, and then the seedlings were grown at three levels (0, 50, and 100 mg As kg−1 soil) of As-polluted soil by performing the potted experiments. The plant growth, photosynthetic parameter, oxidative damage, antioxidant enzyme activities and gene expression of phytochelatin synthase in R. intraradices- and non-inoculated S. davidii seedlings under the different levels of As stress were analyzed.

Result

Compared with non-inoculated S. viciifolia at the identical As level, R. intraradices-inoculated S. viciifolia were higher in the shoot and root dry weight, plant height, root length, photosynthetic rate, stomatal conductance, transpiration rate, maximal photochemical efficiency of PSII photochemistry, actual quantum yield, and photochemical quenching values, while the intercellular CO2 concentration and non-photochemical quenching values were lower. As-induced oxidative stress generating malondialdehyde, hydrogen peroxide and superoxide in the S. viciifolia leaves and roots reduced significantly by R. intraradices inoculation, whereas the activities of antioxidative enzymes (e.g., superoxide dismutase, peroxidase, and catalase) in S. viciifolia leaves and roots were increased by R. intraradices inoculation. Notably, R. intraradices inoculation up-regulated the gene expression of S. viciifolia phytochelatins in the leaves and roots.

Conclusion

These results demonstrated that R. intraradices inoculation enhanced the As tolerance in S. viciifolia seedlings by improving the plant growth, gas exchange, chlorophyll fluorescence, reactive oxygen species, antioxidant enzymes and gene expression of S. viciifolia phytochelatins. The present study verified a multifarious positive role of AMF for woody leguminous species under As stress.

Root cortex development is fine-tuned by the interplay of MIGs, SCL3 and DELLAs during arbuscular mycorrhizal symbiosis

Root development is a crucial process that determines the ability of plants to acquire nutrients, adapt to the substrate and withstand changing environmental conditions. Root plasticity is controlled by a plethora of transcriptional regulators that allow, in contrast to tissue development in animals, post-embryonic changes that give rise to new tissue and specialized cells. One of these changes is the accommodation in the cortex of hyperbranched hyphae of symbiotic arbuscular mycorrhizal (AM) fungi, called arbuscules. Arbuscule-containing cells undergo massive reprogramming to coordinate developmental changes with transport processes. Here we describe a novel negative regulator of arbuscule development, MIG3. MIG3 induces and interacts with SCL3, both of which modulate the activity of the central regulator DELLA, restraining cortical cell growth. As in a tug-of-war, MIG3-SCL3 antagonizes the function of the complex MIG1-DELLA, which promotes the cell expansion required for arbuscule development, adjusting cell size during the dynamic processes of the arbuscule life cycle. Our results in the legume plant Medicago truncatula advance the knowledge of root development in dicot plants, showing the existence of additional regulatory elements not present in Arabidopsis that fine-tune the activity of conserved central modules.

Plant-Fungal Interactions: Laser Microdissection as a Tool to Study Cell Specificity

In the past 20 years, laser microdissection (LMD) technology has been widely applied to plant tissues, allowing to obtain new information on the role of different cell-type populations during plant development and interactions, including plant-pathogen interactions. The application of a LMD approach allowed verifying the response of plant and pathogen during the progression of the infection in different cell types, focusing both on gene expression in host plants and pathogens. Here, a protocol to apply the LMD approach to study plant and fungal transcript profiles in different cell-type populations is described in detail, from the biological material preparation to RNA extraction and gene expression analyses.

Genome-wide screening and identification of nuclear Factor-Y family genes and exploration their function on regulating abiotic and biotic stress in potato (Solanum tuberosum L.)

The Nuclear Factor-Y (NF-Y) transcription factor (TF), which includes three distinct subunits (NF-YA, NF-YB and NF-YC), is known to manipulate various aspects of plant growth, development, and stress responses. Although the NF-Y gene family was well studied in many species, little is known about their functions in potato. In this study, a total of 37 potato NF-Y genes were identified, including 11 StNF-YAs, 20 StNF-YBs, and 6 StNF-YCs. The genetic features of these StNF-Y genes were investigated by comparing their evolutionary relationship, intron/exon organization and motif distribution pattern. Multiple alignments showed that all StNF-Y proteins possessed clearly conserved core regions that were flanked by non-conserved sequences. Gene duplication analysis indicated that nine StNF-Y genes were subjected to tandem duplication and eight StNF-Ys arose from segmental duplication events. Synteny analysis suggested that most StNF-Y genes (33 of 37) were orthologous to potato's close relative tomato (Solanum lycopersicum L.). Tissue-specific expression of the StNF-Y genes suggested their potential roles in controlling potato growth and development. The role of StNF-Ys in regulating potato responses to abiotic stress (ABA, drought and salinity) was also confirmed: twelve StNF-Y genes were up-regulated and another two were down-regulated under different abiotic treatments. In addition, genes responded differently to pathogen challenges, suggesting that StNF-Y genes may play distinct roles under certain biotic stress. In summary, insights into the evolution of NF-Y family members and their functions in potato development and stress responses are provided.

A roadmap of plant membrane transporters in arbuscular mycorrhizal and legume-rhizobium symbioses

Most land plants live in close contact with beneficial soil microbes: the majority of land plant species establish symbiosis with arbuscular mycorrhizal fungi, while most legumes, the third largest plant family, can form a symbiosis with nitrogen-fixing rhizobia. These microbes contribute to plant nutrition via endosymbiotic processes that require modulating the expression and function of plant transporter systems. The efficient contribution of these symbionts involves precisely controlled integration of transport, which is enabled by the adaptability and plasticity of their transporters. Advances in our understanding of these systems, driven by functional genomics research, are rapidly filling the gap in knowledge about plant membrane transport involved in these plant-microbe interactions. In this review, we synthesize recent findings associated with different stages of these symbioses, from the pre-symbiotic stage to nutrient exchange, and describe the role of host transport systems in both mycorrhizal and legume-rhizobia symbioses.

Distinct genetic basis for root responses to lipo-chitooligosaccharide signal molecules from different microbial origins

Lipo-chitooligosaccharides (LCOs) were originally found as symbiotic signals called Nod Factors (Nod-LCOs) controlling the nodulation of legumes by rhizobia. More recently, LCOs were also found in symbiotic fungi and, more surprisingly, very widely in the kingdom Fungi, including in saprophytic and pathogenic fungi. The LCO-V(C18:1, fucosylated/methyl fucosylated), hereafter called Fung-LCOs, are the LCO structures most commonly found in fungi. This raises the question of how legume plants such as Medicago truncatula can discriminate between Nod-LCOs and Fung-LCOs. To address this question, we performed a genome-wide association study on 173 natural accessions of M. truncatula, using a root branching phenotype and a newly developed local score approach. Both Nod-LCOs and Fung-LCOs stimulated root branching in most accessions, but the root responses to these two types of LCO molecules were not correlated. In addition, the heritability of the root response was higher for Nod-LCOs than for Fung-LCOs. We identified 123 loci for Nod-LCO and 71 for Fung-LCO responses, of which only one was common. This suggests that Nod-LCOs and Fung-LCOs both control root branching but use different molecular mechanisms. The tighter genetic constraint of the root response to Fung-LCOs possibly reflects the ancestral origin of the biological activity of these molecules.

A Transcriptomic Approach Provides Insights on the Mycorrhizal Symbiosis of the Mediterranean Orchid Limodorum abortivum in Nature

The study of orchid mycorrhizal interactions is particularly complex because of the peculiar life cycle of these plants and their diverse trophic strategies. Here, transcriptomics has been applied to investigate gene expression in the mycorrhizal roots of Limodorum abortivum, a terrestrial mixotrophic orchid that associates with ectomycorrhizal fungi in the genus Russula. Our results provide new insights into the mechanisms underlying plant-fungus interactions in adult orchids in nature and in particular into the plant responses to the mycorrhizal symbiont(s) in the roots of mixotrophic orchids. Our results indicate that amino acids may represent the main nitrogen source in mycorrhizal roots of L. abortivum, as already suggested for orchid protocorms and other orchid species. The upregulation, in mycorrhizal L. abortivum roots, of some symbiotic molecular marker genes identified in mycorrhizal roots from other orchids as well as in arbuscular mycorrhiza, may mirror a common core of plant genes involved in endomycorrhizal symbioses. Further efforts will be required to understand whether the specificities of orchid mycorrhiza depend on fine-tuned regulation of these common components, or whether specific additional genes are involved.

Metabolomic adjustments in the orchid mycorrhizal fungus Tulasnella calospora during symbiosis with Serapias vomeracea

All orchids rely on mycorrhizal fungi for organic carbon, at least during early development. In fact, orchid seed germination leads to the formation of a protocorm, a heterotrophic postembryonic structure colonized by intracellular fungal coils, thought to be the site of nutrient transfer. The molecular mechanisms underlying mycorrhizal interactions and metabolic changes induced by this symbiosis in both partners remain mostly unknown. We studied plant-fungus interactions in the mycorrhizal association between the Mediterranean orchid Serapias vomeracea and the basidiomycete Tulasnella calospora using nontargeted metabolomics. Plant and fungal metabolomes obtained from symbiotic structures were compared with those obtained under asymbiotic conditions. Symbiosis induced substantial metabolomic alterations in both partners. In particular, structural and signaling lipid compounds increased markedly in the external fungal mycelium growing near the symbiotic protocorms, whereas chito-oligosaccharides were identified uniquely in symbiotic protocorms. This work represents the first description of metabolic changes occurring in orchid mycorrhiza. These results - combined with previous transcriptomic data - provide novel insights on the mechanisms underlying the orchid mycorrhizal association and open intriguing questions on the role of fungal lipids in this symbiosis.

Biofertilizers as Strategies to Improve Photosynthetic Apparatus, Growth, and Drought Stress Tolerance in the Date Palm

Rainfall regimes are expected to shift on a regional scale as the water cycle intensifies in a warmer climate, resulting in greater extremes in dry versus wet conditions. Such changes are having a strong impact on the agro-physiological functioning of plants that scale up to influence interactions between plants and microorganisms and hence ecosystems. In (semi)-arid ecosystems, the date palm (Phoenix dactylifera L.) -an irreplaceable tree- plays important socio-economic roles. In the current study, we implemeted an adapted management program to improve date palm development and its tolerance to water deficit by using single or multiple combinations of exotic and native arbuscular mycorrhizal fungi (AMF1 and AMF2 respectively), and/or selected consortia of plant growth-promoting rhizobacteria (PGPR: B1 and B2), and/or composts from grasses and green waste (C1 and C2, respectively). We analyzed the potential for physiological functioning (photosynthesis, water status, osmolytes, mineral nutrition) to evolve in response to drought since this will be a key indicator of plant resilience in future environments. As result, under water deficit, the selected biofertilizers enhanced plant growth, leaf water potential, and electrical conductivity parameters. Further, the dual-inoculation of AMF/PGPR amended with composts alone or in combination boosted the biomass under water deficit conditions to a greater extent than in non-inoculated and/or non-amended plants. Both single and dual biofertilizers improved physiological parameters by elevating stomatal conductance, photosynthetic pigments (chlorophyll and carotenoids content), and photosynthetic efficiency. The dual inoculation and compost significantly enhanced, especially under drought stress, the concentrations of sugar and protein content, and antioxidant enzymes (polyphenoloxidase and peroxidase) activities as a defense strategy as compared with controls. Under water stress, we demonstrated that phosphorus was improved in the inoculated and amended plants alone or in combination in leaves (AMF2: 807%, AMF1+B2: 657%, AMF2+C1+B2: 500%, AMF2+C2: 478%, AMF1: 423%) and soil (AMF2: 397%, AMF1+B2: 322%, AMF2+C1+B2: 303%, AMF1: 190%, C1: 188%) in comparison with controls under severe water stress conditions. We summarize the extent to which the dual and multiple combinations of microorganisms can overcome challenges related to drought by enhancing plant physiological responses.

Photosynthetic Traits and Nitrogen Uptake in Crops: Which Is the Role of Arbuscular Mycorrhizal Fungi?

Arbuscular mycorrhizal (AM) fungi are root symbionts that provide mineral nutrients to the host plant in exchange for carbon compounds. AM fungi positively affect several aspects of plant life, improving nutrition and leading to a better growth, stress tolerance, and disease resistance and they interact with most crop plants such as cereals, horticultural species, and fruit trees. For this reason, they receive expanding attention for the potential use in sustainable and climate-smart agriculture context. Although several positive effects have been reported on photosynthetic traits in host plants, showing improved performances under abiotic stresses such as drought, salinity and extreme temperature, the involved mechanisms are still to be fully discovered. In this review, some controversy aspects related to AM symbiosis and photosynthesis performances will be discussed, with a specific focus on nitrogen acquisition-mediated by AM fungi.

Identification of Alternative Mitochondrial Electron Transport Pathway Components in Chickpea Indicates a Differential Response to Salinity Stress between Cultivars

All plants contain an alternative electron transport pathway (AP) in their mitochondria, consisting of the alternative oxidase (AOX) and type 2 NAD(P)H dehydrogenase (ND) families, that are thought to play a role in controlling oxidative stress responses at the cellular level. These alternative electron transport components have been extensively studied in plants like Arabidopsis and stress inducible isoforms identified, but we know very little about them in the important crop plant chickpea. Here we identify AP components in chickpea (Cicer arietinum) and explore their response to stress at the transcript level. Based on sequence similarity with the functionally characterized proteins of Arabidopsis thaliana, five putative internal (matrix)-facing NAD(P)H dehydrogenases (CaNDA1-4 and CaNDC1) and four putative external (inter-membrane space)-facing NAD(P)H dehydrogenases (CaNDB1-4) were identified in chickpea. The corresponding activities were demonstrated for the first time in purified mitochondria of chickpea leaves and roots. Oxidation of matrix NADH generated from malate or glycine in the presence of the Complex I inhibitor rotenone was high compared to other plant species, as was oxidation of exogenous NAD(P)H. In leaf mitochondria, external NADH oxidation was stimulated by exogenous calcium and external NADPH oxidation was essentially calcium dependent. However, in roots these activities were low and largely calcium independent. A salinity experiment with six chickpea cultivars was used to identify salt-responsive alternative oxidase and NAD(P)H dehydrogenase gene transcripts in leaves from a three-point time series. An analysis of the Na:K ratio and Na content separated these cultivars into high and low Na accumulators. In the high Na accumulators, there was a significant up-regulation of CaAOX1, CaNDB2, CaNDB4, CaNDA3 and CaNDC1 in leaf tissue under long term stress, suggesting the formation of a stress-modified form of the mitochondrial electron transport chain (mETC) in leaves of these cultivars. In particular, stress-induced expression of the CaNDB2 gene showed a striking positive correlation with that of CaAOX1 across all genotypes and time points. The coordinated salinity-induced up-regulation of CaAOX1 and CaNDB2 suggests that the mitochondrial alternative pathway of respiration is an important facet of the stress response in chickpea, in high Na accumulators in particular, despite high capacities for both of these activities in leaf mitochondria of non-stressed chickpeas.

Combined effects of phosphorus and magnesium on mycorrhizal symbiosis through altering metabolism and transport of photosynthates in soybean

Arbuscular mycorrhizal (AM) symbiosis plays crucial roles in plant nutrient uptake. However, little is known about the combined effects of phosphorus (P) and magnesium (Mg) on mycorrhizal symbiosis. In the present study, a pot experiment was carried out using two soybean genotypes in the presence or absence of Rhizophagus irregularis inoculation under different P and Mg conditions. The results showed that plant growth promotion by mycorrhizal symbiosis was associated with P-starved nutrition status, high Mg supply augmented the efficiency of AM symbiosis in low P, and high Mg relieved the inhibitory effect of high P availability on AM symbiosis. The P-efficient genotype HN89 was more responsive to Mg application than the P-inefficient genotype HN112 when inoculated with Rhizophagus irregularis. The results from a comparative RNA sequencing analysis of the root transcriptomes showed that several carbon metabolism pathways were enriched in mycorrhizal roots in low P plus high Mg. Accordingly, the expression levels of the key genes related to carbon metabolism and transport were also upregulated in mycorrhizal roots. Conversely, the Mg-deficient mycorrhizal plants showed increased sucrose, glucose, and fructose accumulations in shoots. Overall, the results herein demonstrate that P and Mg interactively affect mycorrhizal responses in plants, and high Mg supply has a profound effect on P-starved mycorrhizal plant growth through promotion of photosynthate metabolism and transport in soybean.

Gene Expression in Nitrogen-Fixing Symbiotic Nodule Cells in Medicago truncatula and Other Nodulating Plants

Root nodules formed by plants of the nitrogen-fixing clade (NFC) are symbiotic organs that function in the maintenance and metabolic integration of large populations of nitrogen-fixing bacteria. These organs feature unique characteristics and processes, including their tissue organization, the presence of specific infection structures called infection threads, endocytotic uptake of bacteria, symbiotic cells carrying thousands of intracellular bacteria without signs of immune responses, and the integration of symbiont and host metabolism. The early stages of nodulation are governed by a few well-defined functions, which together constitute the common symbiosis-signaling pathway (CSSP). The CSSP activates a set of transcription factors (TFs) that orchestrate nodule organogenesis and infection. The later stages of nodule development require the activation of hundreds to thousands of genes, mostly expressed in symbiotic cells. Many of these genes are only active in symbiotic cells, reflecting the unique nature of nodules as plant structures. Although how the nodule-specific transcriptome is activated and connected to early CSSP-signaling is poorly understood, candidate TFs have been identified using transcriptomic approaches, and the importance of epigenetic and chromatin-based regulation has been demonstrated. We discuss how gene regulation analyses have advanced our understanding of nodule organogenesis, the functioning of symbiotic cells, and the evolution of symbiosis in the NFC.

Laser Microdissection as a Useful Tool to Study Gene Expression in Plant and Fungal Partners in AM Symbiosis

Laser microdissection (LMD) technology has been widely applied to plant tissues, offering novel information on the role of different cell-type populations during plant-microbe interactions. In this chapter, protocols to apply the LMD approach to study plant and fungal transcript profiles in different cell-type populations from arbuscular mycorrhizal (AM) roots are described in detail, starting from the biological material preparation to gene expression analyses by RT-PCR and RT-qPCR.

The Evolutionary Aspects of Legume Nitrogen-Fixing Nodule Symbiosis

Nitrogen-fixing root nodule symbiosis can sustain the development of the host plants under nitrogen-limiting conditions. Such symbiosis occurs only in a clade of angiosperms known as the nitrogen-fixing clade (NFC). It has long been proposed that root nodule symbiosis evolved several times (in parallel) in the NFC. Two recent phylogenomic studies compared the genomes of nodulating and related non-nodulating species across the four orders of the NFC and found that genes essential for nodule formation are lost or pseudogenized in the non-nodulating species. As these symbiosis genes are specifically involved in the symbiotic interaction, it means that the presence of pseudogenes and the loss of symbiosis genes strongly suggest that their ancestor, which still had functional genes, most likely had a symbiosis with nitrogen-fixing bacteria. These findings agree with the hypothesis that nodulation evolved once at the common ancestor of the NFC, and challenge the hypothesis of parallel evolution. In this chapter, we will cover the current understandings on actinorhizal-type and legume nodule development, and discuss the evolution of the legume nodule type.

Ray Parenchymal Cells Contribute to Lignification of Tracheids in Developing Xylem of Norway Spruce

A comparative transcriptomic study and a single-cell metabolome analysis were combined to determine whether parenchymal ray cells contribute to the biosynthesis of monolignols in the lignifying xylem of Norway spruce (Picea abies). Ray parenchymal cells may function in the lignification of upright tracheids by supplying monolignols. To test this hypothesis, parenchymal ray cells and upright tracheids were dissected with laser-capture microdissection from tangential cryosections of developing xylem of spruce trees. The transcriptome analysis revealed that among the genes involved in processes typical for vascular tissues, genes encoding cell wall biogenesis-related enzymes were highly expressed in both developing tracheids and ray cells. Interestingly, most of the shikimate and monolignol biosynthesis pathway-related genes were equally expressed in both cell types. Nonetheless, 1,073 differentially expressed genes were detected between developing ray cells and tracheids, among which a set of genes expressed only in ray cells was identified. In situ single cell metabolomics of semi-intact plants by picoliter pressure probe-electrospray ionization-mass spectrometry detected monolignols and their glycoconjugates in both cell types, indicating that the biosynthetic route for monolignols is active in both upright tracheids and parenchymal ray cells. The data strongly support the hypothesis that in developing xylem, ray cells produce monolignols that contribute to lignification of tracheid cell walls.

Sugar transporters in Fabaceae, featuring SUT MST and SWEET families of the model plant Medicago truncatula and the agricultural crop Pisum sativum

Sugar transporters play a crucial role for plant productivity, as they coordinate sugar fluxes from source leaf towards sink organs (seed, fruit, root) and regulate the supply of carbon resources towards the microorganisms of the rhizosphere (bacteria and fungi). Thus, sugar fluxes mediated by SUT (sucrose transporters), MST (monosaccharide transporters) and SWEET (sugar will eventually be exported transporters) families are key determinants of crop yield and shape the microbial communities living in the soil. In this work, we performed a systematic search for sugar transporters in Fabaceae genomes, focusing on model and agronomical plants. Here, we update the inventory of sugar transporter families mining the latest version of the Medicago truncatula genome and identify for the first time SUT MST and SWEET families of the agricultural crop Pisum sativum. The sugar transporter families of these Fabaceae species comprise respectively 7 MtSUT 7 PsSUT, 72 MtMST 59 PsMST and 26 MtSWEET 22 PsSWEET. Our comprehensive phylogenetic analysis sets a milestone for the scientific community, as we propose a new and simple nomenclature to correctly name SUT MST and SWEET families. Then, we searched for transcriptomic data available for our gene repertoire. We show that several clusters of homologous genes are co-expressed in different organs, suggesting that orthologous sugar transporters may have a conserved function. We focused our analysis on gene candidates that may be involved in remobilizing resources during flowering, grain filling and in allocating carbon towards roots colonized by arbuscular mycorrhizal fungi and Rhizobia. Our findings open new perspectives for agroecological applications in legume crops, as for instance improving the yield and quality of seed productions and promoting the use of symbiotic microorganisms.

Transcriptomic Responses to Water Deficit and Nematode Infection in Mycorrhizal Tomato Roots

Climate changes include the intensification of drought in many parts of the world, increasing its frequency, severity and duration. However, under natural conditions, environmental stresses do not occur alone, and, in addition, more stressed plants may become more susceptible to attacks by pests and pathogens. Studies on the impact of the arbuscular mycorrhizal (AM) symbiosis on tomato response to water deficit showed that several drought-responsive genes are differentially regulated in AM-colonized tomato plants (roots and leaves) during water deficit. To date, global changes in mycorrhizal tomato root transcripts under water stress conditions have not been yet investigated. Here, changes in root transcriptome in the presence of an AM fungus, with or without water stress (WS) application, have been evaluated in a commercial tomato cultivar already investigated for the water stress response during AM symbiosis. Since root-knot nematodes (RKNs, Meloidogyne incognita) are obligate endoparasites and cause severe yield losses in tomato, the impact of the AM fungal colonization on RKN infection at 7 days post-inoculation was also evaluated. Results offer new information about the response to AM symbiosis, highlighting a functional redundancy for several tomato gene families, as well as on the tomato and fungal genes involved in WS response during symbiosis, underlying the role of the AM fungus. Changes in the expression of tomato genes related to nematode infection during AM symbiosis highlight a role of AM colonization in triggering defense responses against RKN in tomato. Overall, new datasets on the tomato response to an abiotic and biotic stress during AM symbiosis have been obtained, providing useful data for further researches.

The evolutionary history of LysM-RLKs (LYKs/LYRs) in wild tomatoes

Background

The LysM receptor-like kinases (LysM-RLKs) are important to both plant defense and symbiosis. Previous studies described three clades of LysM-RLKs: LysM-I/LYKs (10+ exons per gene and containing conserved kinase residues), LysM-II/LYRs (1–5 exons per gene, lacking conserved kinase residues), and LysM-III (two exons per gene, with a kinase unlike other LysM-RLK kinases and restricted to legumes). LysM-II gene products are presumably not functional as conventional receptor kinases, but several are known to operate in complexes with other LysM-RLKs. One aim of our study was to take advantage of recently mapped wild tomato transcriptomes to evaluate the evolutionary history of LysM-RLKs within and between species. The second aim was to place these results into a broader phylogenetic context by integrating them into a sequence analysis of LysM-RLKs from other functionally well-characterized model plant species. Furthermore, we sought to assess whether the Group III LysM-RLKs were restricted to the legumes or found more broadly across Angiosperms.

Results

Purifying selection was found to be the prevailing form of natural selection within species at LysM-RLKs. No signatures of balancing selection were found in species-wide samples of two wild tomato species. Most genes showed a greater extent of purifying selection in their intracellular domains, with the exception of SlLYK3 which showed strong purifying selection in both the extracellular and intracellular domains in wild tomato species. The phylogenetic analysis did not reveal a clustering of microbe/functional specificity to groups of closely related proteins. We also discovered new putative LysM-III genes in a range of Rosid species, including Eucalyptus grandis.

Conclusions

The LysM-III genes likely originated before the divergence of E. grandis from other Rosids via a fusion of a Group II LysM triplet and a kinase from another RLK family. SlLYK3 emerges as an especially interesting candidate for further study due to the high protein sequence conservation within species, its position in a clade of LysM-RLKs with distinct LysM domains, and its close evolutionary relationship with LYK3 from Arabidopsis thaliana.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1467-3) contains supplementary material, which is available to authorized users.

Transcriptomic analysis reveals the possible roles of sugar metabolism and export for positive mycorrhizal growth responses in soybean

To elucidate molecular mechanisms controlling differential growth responses to root colonization by arbuscular mycorrhizal (AM) fungi varying in colonization and cooperative behavior, a pot experiment was carried out using two soybean genotypes and three AM inocula. The results showed that inoculation by cooperative Rhizophagus irregularis (Ri) or less cooperative Glomus aggregatum with high AM colonization (Ga-H) significantly promoted plant growth compared with inoculation by G. aggregatum with low AM colonization (Ga-L). A comparative RNA sequencing analysis of the root transcriptomes showed that fatty acid synthesis pathway was significantly enriched in all three AM inoculation roots. However, sugar metabolism and transport were significantly enriched only in Ri and Ga-H inoculation, which was consistent with positive growth responses in these two inoculation treatments. Accordingly, the expression levels of the key genes related to sugar metabolism and transport were also upregulated in Ri and Ga-H roots compared with Ga-L roots. Of them, two sugars will eventually be exported transporters (SWEET) transporter genes, GmSWEET6 (Glyma.04G198600) and GmSWEET15 (Glyma.06G166800), and one invertase (Glyma.17G227900) gene were exclusively induced only in Ri and Ga-H roots. Promoter analyses in transgenic soybean roots further demonstrated that GUS driven by the GmSWEET6 promoter was highly expressed in arbuscule-containing cortical cells. Additionally, Ri and Ga-H inoculation increased the contents of sucrose, glucose and fructose in both shoots and roots compared with those of Ga-L and non-mycorrhizal. These results imply that positive mycorrhizal growth responses in plants might mostly be due to the stimulation of photosynthate metabolism and transport by AM fungal inoculum with high colonization capabilities.

Transcriptome analysis of soybean (Glycine max) root genes differentially expressed in rhizobial, arbuscular mycorrhizal, and dual symbiosis

Soybean (Glycine max) roots establish associations with nodule-inducing rhizobia and arbuscular mycorrhizal (AM) fungi. Both rhizobia and AM fungi have been shown to affect the activity of and colonization by the other, and their interactions can be detected within host plants. Here, we report the transcription profiles of genes differentially expressed in soybean roots in the presence of rhizobial, AM, or rhizobial-AM dual symbiosis, compared with those in control (uninoculated) roots. Following inoculation, soybean plants were grown in a glasshouse for 6 weeks; thereafter their root transcriptomes were analyzed using an oligo DNA microarray. Among the four treatments, the root nodule number and host plant growth were highest in plants with dual symbiosis. We observed that the expression of 187, 441, and 548 host genes was up-regulated and 119, 1,439, and 1,298 host genes were down-regulated during rhizobial, AM, and dual symbiosis, respectively. The expression of 34 host genes was up-regulated in each of the three symbioses. These 34 genes encoded several membrane transporters, type 1 metallothionein, and transcription factors in the MYB and bHLH families. We identified 56 host genes that were specifically up-regulated during dual symbiosis. These genes encoded several nodulin proteins, phenylpropanoid metabolism-related proteins, and carbonic anhydrase. The nodulin genes up-regulated by the AM fungal colonization probably led to the observed increases in root nodule number and host plant growth. Some other nodulin genes were down-regulated specifically during AM symbiosis. Based on the results above, we suggest that the contribution of AM fungal colonization is crucial to biological N2-fixation and host growth in soybean with rhizobial-AM dual symbiosis.

A purple acid phosphatase, GmPAP33, participates in arbuscule degeneration during arbuscular mycorrhizal symbiosis in soybean

Arbuscules are the central structures of the symbiotic association between terrestrial plants and arbuscular mycorrhizal (AM) fungi. However, arbuscules are also ephemeral structures, and following development, these structures are soon digested and ultimately disappear. Currently, little is known regarding the mechanism underlying the digestion of senescent arbuscules. Here, biochemical and functional analyses were integrated to test the hypothesis that a purple acid phosphatase, GmPAP33, controls the hydrolysis of phospholipids during arbuscule degeneration. The expression of GmPAP33 was enhanced by AM fungal inoculation independent of the P conditions in soybean roots. Promoter-β-glucuronidase (GUS) reporter assays revealed that the expression of GmPAP33 was mainly localized to arbuscule-containing cells during symbiosis. The recombinant GmPAP33 exhibited high hydrolytic activity towards phospholipids, phosphatidylcholine, and phosphatidic acid. Furthermore, soybean plants overexpressing GmPAP33 exhibited increased percentages of large arbuscules and improved yield and P content compared with wild-type plants when inoculated with AM fungi. Mycorrhizal RNAi plants had high phospholipid levels and a large percentage of small arbuscules. These results in combination with the subcellular localization of GmPAP33 at the plasma membrane indicate that GmPAP33 participates in arbuscule degeneration during AM symbiosis via involvement in phospholipid hydrolysis.

Insights into the complex role of GRAS transcription factors in the arbuscular mycorrhiza symbiosis

To improve access to limiting nutrients, the vast majority of land plants forms arbuscular mycorrhizal (AM) symbioses with Glomeromycota fungi. We show here that AM-related GRAS transcription factors from different subgroups are upregulated during a time course of mycorrhization. Based on expression studies in mutants defective in arbuscule branching (ram1-1, with a deleted MtRam1 GRAS transcription factor gene) or in the formation of functional arbuscules (pt4-2, mutated in the phosphate transporter gene MtPt4), we demonstrate that the five AM-related GRAS transcription factor genes MtGras1, MtGras4, MtGras6, MtGras7, and MtRad1 can be differentiated by their dependency on MtRAM1 and MtPT4, indicating that the network of AM-related GRAS transcription factors consists of at least two regulatory modules. One module involves the MtRAM1- and MtPT4-independent transcription factor MtGRAS4 that activates MtGras7. Another module is controlled by the MtRAM1- and MtPT4-dependent transcription factor MtGRAS1. Genome-wide expression profiles of mycorrhized MtGras1 knockdown and ram1-1 roots differ substantially, indicating different targets. Although an MtGras1 knockdown reduces transcription of AM-related GRAS transcription factor genes including MtRam1 and MtGras7, MtGras1 overexpression alone is not sufficient to activate MtGras genes. MtGras1 knockdown roots display normal fungal colonization, with a trend towards the formation of smaller arbuscules.

Arbuscular mycorrhizal fungi induce the expression of specific retrotransposons in roots of sunflower (Helianthus annuus L.)

Retrotransposon expression during arbuscular mycorrhizal (AM) fungal colonisation of sunflower roots (Helianthus annuus) was analysed using Illumina RNA-Seq, in order to verify whether mycorrhizal symbiosis can activate retrotransposable elements. Illumina cDNA libraries were produced from RNAs isolated from the roots of sunflower plants at 4 and 16 days after inoculation with the AM fungus Rhizoglomus irregulare and from their respective control plants. Illumina reads were mapped to a library of reverse transcriptase-encoding sequences, putatively belonging to long terminal repeat retrotransposons of Gypsy and Copia superfamilies. Forty-six different reverse transcriptase sequences were transcribed, although at a low rate, in mycorrhizal or control roots and only four were significantly over-expressed at day 16, compared with control roots. Almost all expressed or over-expressed sequences belonged to low-copy elements, mostly, of the Copia superfamily. A meta-analysis, using publicly available Illumina cDNA libraries obtained from sunflower plants treated with different hormones and chemicals, mimicking stimuli produced by abiotic and biotic stresses, was also conducted. Such analyses indicated that the four reverse transcriptase sequences over-expressed in mycorrhizal roots were explicitly induced only by AM symbiosis, showing the specificity of AM stimuli compared to that of other fungal/plant interactions.

Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis

Plant root symbiosis with Arbuscular mycorrhizal (AM) fungi improves uptake of water and mineral nutrients, improving plant development under stressful conditions. Unraveling the unified transcriptomic signature of a successful colonization provides a better understanding of symbiosis. We developed a framework for finding the transcriptomic signature of Arbuscular mycorrhiza colonization and its regulating transcription factors in roots of Medicago truncatula. Expression profiles of roots in response to AM species were collected from four separate studies and were combined by direct merging meta-analysis. Batch effect, the major concern in expression meta-analysis, was reduced by three normalization steps: Robust Multi-array Average algorithm, Z-standardization, and quartiling normalization. Then, expression profile of 33685 genes in 18 root samples of Medicago as numerical features, as well as study ID and Arbuscular mycorrhiza type as categorical features, were mined by seven models: RELIEF, UNCERTAINTY, GINI INDEX, Chi Squared, RULE, INFO GAIN, and INFO GAIN RATIO. In total, 73 genes selected by machine learning models were up-regulated in response to AM (Z-value difference > 0.5). Feature weighting models also documented that this signature is independent from study (batch) effect. The AM inoculation signature obtained was able to differentiate efficiently between AM inoculated and non-inoculated samples. The AP2 domain class transcription factor, GRAS family transcription factors, and cyclin-dependent kinase were among the highly expressed meta-genes identified in the signature. We found high correspondence between the AM colonization signature obtained in this study and independent RNA-seq experiments on AM colonization, validating the repeatability of the colonization signature. Promoter analysis of upregulated genes in the transcriptomic signature led to the key regulators of AM colonization, including the essential transcription factors for endosymbiosis establishment and development such as NF-YA factors. The approach developed in this study offers three distinct novel features: (I) it improves direct merging meta-analysis by integrating supervised machine learning models and normalization steps to reduce study-specific batch effects; (II) seven attribute weighting models assessed the suitability of each gene for the transcriptomic signature which contributes to robustness of the signature (III) the approach is justifiable, easy to apply, and useful in practice. Our integrative framework of meta-analysis, promoter analysis, and machine learning provides a foundation to reveal the transcriptomic signature and regulatory circuits governing Arbuscular mycorrhizal symbiosis and is transferable to the other biological settings.

Comparative transcriptome analysis of Poncirus trifoliata identifies a core set of genes involved in arbuscular mycorrhizal symbiosis

The perennial woody plants of citrus are one of the most important fruit crops in the world and largely depends on arbuscular mycorrhizal symbiosis (AMS) to obtain essential nutrients from soil. However, the molecular aspects of AMS in citrus and perennial woody plants in general have largely been understudied. We used RNA-sequencing to identify differentially expressed genes in roots of Poncirus trifoliata upon mycorrhization by the AM fungus Glomus versiforme and evaluated their conservation by comparative transcriptome analyses with four herbaceous model plants. We identified 282 differentially expressed genes in P. trifoliata, including orthologs of 21 genes with characterized roles in AMS and 83 genes that are considered to be conserved in AM-host plants. Comparative transcriptome analysis revealed a 'core set' of 156 genes from P. trifoliata whose orthologous genes from at least three of the five species also exhibited similar transcriptional changes during AMS. Functional analysis of one of these conserved AM-induced genes, a 3-keto-acyl-ACP reductase (FatG) involved in fatty acid biosynthesis, confirmed its involvement in AMS in Medicago truncatula. Our results identify a core transcriptional program for AMS that is largely conserved between P. trifoliata and other plants. The comparative transcriptomics approach adds to previous phylogenomics studies to identify conserved genes required for AMS.

Fixation and Laser Capture Microdissection of Plant Tissue for RNA Extraction and RNASeq Library Preparation

In order to study the transcriptome of individual plant cells at specific points in time, we developed protocols for fixation, embedding, and sectioning of plant tissue followed by laser capture microdissection (LCM) and processing for RNA recovery. LCM allows the isolation of individual cell types from heterogeneous tissue sections and is particularly suited to plant processing because it does not require the breakdown of cell walls. This approach allows accurate separation of a small volume of cells that can be used to study gene expression profiles in different tissues or cell layers. The technique does not require separation of cells by enzymatic digestion of any kind, does not require cell-specific reporter genes, and allows storage of fixed and embedded tissue for months before capture. The methods for fixation, embedding, sectioning, and capture of plant cells that we describe yield high-quality RNA suitable for making libraries for RNASeq. © 2018 by John Wiley & Sons, Inc.

Arbuscular Mycorrhizal Symbiosis Leads to Differential Regulation of Drought-Responsive Genes in Tissue-Specific Root Cells of Common Bean

Arbuscular mycorrhizal fungi (AMF) colonization in plants promotes both local and systemic changes in the gene expression profiles of the host that might be relevant for drought-stress perception and response. Drought-tolerant common bean plants (cv. BAT 477), colonized by a mixture of AMF (Glomus clarum, Acaulospora scrobiculata, and Gigaspora rosea), were exposed to a water deprivation regime of 96 h during pre-flowering. Root transcriptomes were accessed through RNA-Seq revealing a set of 9,965 transcripts with significant differential regulation in inoculated plants during a water deficit event, and 10,569 in non-inoculated. These data include 1,589 transcripts that are exclusively regulated by AMF-inoculation, and 2,313 under non-inoculation conditions. Relative gene expression analyses of nine aquaporin-related transcripts were performed in roots and leaves of plants harvested at initial stages of treatment. Significant shifts in gene expression were detected in AM water deficit-treated roots, in relation to non-inoculated, between 48 and 72 h. Leaves also showed significant mycorrhizal influence in gene expression, especially after 96 h. Root cortical cells, harboring or not arbuscules, were collected from both inoculation treatments through a laser microdissection-based technique. This allowed the identification of transcripts, such as the aquaporin PvPIP2;3 and Glucan 1,3 β-Glucosidase, that are unique to arbuscule-containing cells. During the water deficit treatment, AMF colonization exerted a fine-tune regulation in the expression of genes in the host. That seemed to initiate in arbuscule-containing cells and, as the stressful condition persisted, propagated to the whole-plant through secondary signaling events. Collectively, these results demonstrate that arbuscular mycorrhization leads to shifts in common bean's transcriptome that could potentially impact its adaptation capacity during water deficit events.

Transcriptional Regulation of Arbuscular Mycorrhiza Development

Arbuscular mycorrhiza (AM) is an ancient symbiosis between land plants and fungi of the glomeromycotina that is widespread in the plant kingdom. AM improves plant nutrition, stress resistance and general plant performance, and thus represents a promising addition to sustainable agricultural practices. In return for delivering mineral nutrients, the obligate biotrophic AM fungi receive up to 20% of the photosynthetically fixed carbon from the plant. AM fungi colonize the inside of roots and form highly branched tree-shaped structures, called arbuscules, in cortex cells. The pair of the arbuscule and its host cell is considered the central functional unit of the symbiosis as it mediates the bidirectional nutrient exchange between the symbionts. The development and spread of AM fungi within the root is predominantly under the control of the host plant and depends on its developmental and physiological status. Intracellular accommodation of fungal structures is enabled by the remarkable plasticity of plant cells, which undergo drastic subcellular rearrangements. These are promoted and accompanied by cell-autonomous transcriptional reprogramming. AM development can be dissected into distinct stages using plant mutants. Progress in the application of laser dissection technology has allowed the assignment of transcriptional responses to specific stages and cell types. The first transcription factors controlling AM-specific gene expression and AM development have been discovered, and cis-elements required for AM-responsive promoter activity have been identified. An understanding of their connectivity and elucidation of transcriptional networks orchestrating AM development can be expected in the near future.

Revealing proteins associated with symbiotic germination of Gastrodia elata by proteomic analysis

BACKGROUND

Gastrodia elata, a mycoheterotrophic orchid, is a well-known medicinal herb. In nature, the seed germination of G. elata requires proper fungal association, because of the absence of endosperm. To germinate successfully, G. elata obtains nutrition from mycorrhizal fungi such as Mycena. However, Mycena is not able to supply nutrition for the further development and enlargement of protocorms into tubers, flowering and fruit setting of G. elata. To date, current genomic studies on this topic are limited. Here we used the proteomic approach to explore changes in G. elata at different stages of symbiotic germination.

RESULTS

Using mass spectrometry, 3787 unique proteins were identified, of which 599 were classified as differentially accumulated proteins. Most of these differentially accumulated proteins were putatively involved in energy metabolism, plant defense, molecular signaling, and secondary metabolism. Among them, the defense genes (e.g., pathogenesis-/wound-related proteins, peroxidases, and serine/threonine-protein kinase) were highly expressed in late-stage protocorms, suggesting that fungal colonization triggered the significant defense responses of G. elata.

CONCLUSIONS

The present study indicated the metabolic change and defensive reaction could disrupt the balance between Mycena and G. elata during mycorrhizal symbiotic germination.

Strigolactone Biosynthesis Genes of Rice are Required for the Punctual Entry of Arbuscular Mycorrhizal Fungi into the Roots

Arbuscular mycorrhiza (AM) is a mutualistic association between most plant species and the ancient fungal phylum Glomeromycota in roots, and it plays a key role in a plant's nutrient uptake from the soil. Roots synthesize strigolactones (SLs), derivatives of carotenoids, and exude them to induce energy metabolism and hyphal branching of AM fungi. Despite the well-documented roles of SLs in the pre-symbiotic phase, little is known about the role of SLs in the process of root colonization. Here we show that the expansion of root colonization is suppressed in the mutants of rice (Oryza sativa) SL biosynthesis genes, carotenoid cleavage dioxygenase D10 and more severely in D17. Interestingly, most of the colonization process is normal, i.e. AM fungal hyphae approach the roots and cling around them, and epidermal penetration, arbuscule size, arbuscule number per hyphopodium and metabolic activity of the intraradical mycelium are not affected in d10 and d17 mutants. In contrast, hyphopodium formation is severely attenuated. Our observations establish the requirement for SL biosynthesis genes for efficient hyphopodium formation, suggesting that SLs are required in this process. Efficient hyphopodium formation is required for the punctual internalization of hyphae into roots and maintaining the expansion of colonization.