Glomus intraradices induces changes in root system architecture of rice independently of common symbiosis signaling

Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice

Microbes constitute a vital part of the plant holobiont. They establish plant-microbe or microbe-microbe associations, forming a unique microbiota with each plant species and under different environmental conditions. These microbial communities have to adapt to diverse environmental conditions, such as geographical location, climate conditions and soil types, and are subjected to changes in their surrounding environment. Elevated ozone concentration is one of the most important aspects of global change, but its effect on microbial communities living on plant surfaces has barely been investigated. In the current study, we aimed at elucidating the potential effect of elevated ozone concentrations on the phyllosphere (aerial part of the plant) and rhizoplane (surface of the root) microbiota by adopting next-generation 16S rRNA amplicon sequencing. A standard japonica rice cultivar Nipponbare and an ozone-tolerant breeding line L81 (Nipponbare background) were pre-grown in a greenhouse for 10 weeks and then exposed to ozone at 85 ppb for 7 h daily for 30 days in open top chambers. Microbial cells were collected from the phyllosphere and rhizoplane separately. The treatment or different genotypes did not affect various diversity indices. On the other hand, the relative abundance of some bacterial taxa were significantly affected in the rhizoplane community of ozone-treated plants. A significant effect of ozone was detected by homogeneity of molecular variance analysis in the phyllosphere, meaning that the community from ozone-treated phyllosphere samples was more variable than those from control plants. In addition, a weak treatment effect was observed by clustering samples based on the Yue and Clayton and weighted UniFrac distance matrices among samples. We therefore conclude that the elevated ozone concentrations affected the bacterial community structure of the phyllosphere and the rhizosplane as a whole, even though this effect was rather weak and did not lead to changes of the function of the communities.

Improving crop nutrient efficiency through root architecture modifications

Improving crop nutrient efficiency becomes an essential consideration for environmentally friendly and sustainable agriculture. Plant growth and development is dependent on 17 essential nutrient elements, among them, nitrogen (N) and phosphorus (P) are the two most important mineral nutrients. Hence it is not surprising that low N and/or low P availability in soils severely constrains crop growth and productivity, and thereby have become high priority targets for improving nutrient efficiency in crops. Root exploration largely determines the ability of plants to acquire mineral nutrients from soils. Therefore, root architecture, the 3-dimensional configuration of the plant's root system in the soil, is of great importance for improving crop nutrient efficiency. Furthermore, the symbiotic associations between host plants and arbuscular mycorrhiza fungi/rhizobial bacteria, are additional important strategies to enhance nutrient acquisition. In this review, we summarize the recent advances in the current understanding of crop species control of root architecture alterations in response to nutrient availability and root/microbe symbioses, through gene or QTL regulation, which results in enhanced nutrient acquisition.

Does a Common Pathway Transduce Symbiotic Signals in Plant-Microbe Interactions?

Recent years have witnessed major advances in our knowledge of plant mutualistic symbioses such as the rhizobium-legume symbiosis (RLS) and arbuscular mycorrhizas (AM). Some of these findings caused the revision of longstanding hypotheses, but one of the most solid theories is that a conserved set of plant proteins rules the transduction of symbiotic signals from beneficial glomeromycetes and rhizobia in a so-called common symbiotic pathway (CSP). Nevertheless, the picture still misses several elements, and a few crucial points remain unclear. How does one common pathway discriminate between - at least - two symbionts? Can we exclude that microbes other than AM fungi and rhizobia also use this pathway to communicate with their host plants? We here discuss the possibility that our current view is biased by a long-lasting focus on legumes, whose ability to develop both AM and RLS is an exception among plants and a recent innovation in their evolution; investigations in non-legumes are starting to place legume symbiotic signaling in a broader perspective. Furthermore, recent studies suggest that CSP proteins act in a wider scenario of symbiotic and non-symbiotic signaling. Overall, evidence is accumulating in favor of distinct activities for CSP proteins in AM and RLS, depending on the molecular and cellular context where they act.

Effect of volatiles versus exudates released by germinating spores of Gigaspora margarita on lateral root formation

Arbuscular mycorrhizal (AM) fungi influence the root system architecture of their hosts; however, the underlying mechanisms have not been fully elucidated. Ectomycorrhizal fungi influence root architecture via volatiles. To determine whether volatiles also play a role in root system changes in response to AM fungi, spores of the AM fungus Gigaspora margarita were inoculated on the same plate as either wild type (WT) Lotus japonicus, the L. japonicus mutant Ljcastor (which lacks the symbiotic cation channel CASTOR, which is required for inducing nuclear calcium spiking, which is necessary for symbiotic partner recognition), or Arabidopsis thaliana, separated by cellophane membranes (fungal exudates experiment), or on different media but with a shared head space (fungal volatiles experiment). Root development was monitored over time. Both germinating spore exudates (GSEs) and geminated-spore-emitted volatile organic compounds (GVCs) significantly promoted lateral root formation (LRF) in WT L. japonicus. LRF in Ljcastor was significantly enhanced in the presence of GVCs. GVCs stimulated LRF in A. thaliana, whereas GSEs showed an inhibitory effect. The expression profile of the genes involved in mycorrhizal establishment and root development were investigated using quantitative reverse transcription-PCR analysis. Only the expression of the LjCCD7 gene, an important component of the strigolactone synthesis pathway, was differentially expressed following exposure to GVCs. We conclude that volatile organic compounds released by the germinating AM fungal spores may stimulate LRF in a symbiosis signaling pathway (SYM)- and host-independent way, whereas GSEs stimulate LRF in a SYM- and host-dependent way.

Silencing a key gene of the common symbiosis pathway in Nicotiana attenuata specifically impairs arbuscular mycorrhizal infection without influencing the root-associated microbiome or plant growth

While the biochemical function of calcium and calmodulin-dependent protein kinase (CCaMK) is well studied, and plants impaired in the expression of CCaMK are known not to be infected by arbuscular mycorrhizal fungi (AMF) in glasshouse studies, the whole-plant and ecological consequences of CCaMK silencing are not well understood. Here we show that three independently transformed lines of Nicotiana attenuata plants silenced in CCaMK (irCCaMK) are neither infected by Rhizophagus irregularis in the glasshouse nor by native fungal inoculum in the field. The overall fungal community of field-grown roots did not differ significantly among empty vector (EV) and the transgenic lines, and the bacterial communities only showed minor differences, as revealed by the alpha-diversity parameters of bacterial OTUs, which were higher in EV plants compared with two of the three transformed lines, while beta-diversity parameters did not differ. Furthermore, growth and fitness parameters were similar in the glasshouse and field. Herbivory-inducible and basal levels of salicylic acid, jasmonic acid and abscisic acid did not differ among the genotypes, suggesting that activation of the classical defence pathways are not affected by CCaMK silencing. Based on these results, we conclude that silencing of CCaMK has few, if any, non-target effects.

Host and non-host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi

Oryza sativa, a model plant for Arbuscular Mycorrhizal (AM) symbiosis, has both host and non-host roots. Large lateral (LLR) and fine lateral (FLR) roots display opposite responses: LLR support AM colonization, but FLR do not. Our research aimed to study the molecular, morphological and physiological aspects related to the non-host behavior of FLR. RNA-seq analysis revealed that LLR and FLR displayed divergent expression profiles, including changes in many metabolic pathways. Compared with LLR, FLR showed down-regulation of genes instrumental for AM establishment and gibberellin signaling, and a higher expression of nutrient transporters. Consistent with the transcriptomic data, FLR had higher phosphorus content. Light and electron microscopy demonstrated that, surprisingly, in the Selenio cultivar, FLR have a two-layered cortex, which is theoretically compatible with AM colonization. According to RNA-seq, a gibberellin inhibitor treatment increased anticlinal divisions leading to a higher number of cortex cells in FLR. We propose that some of the differentially regulated genes that lead to the anatomical and physiological properties of the two root types also function as genetic factors regulating fungal colonization. The rice root apparatus offers a unique tool to study AM symbiosis, allowing direct comparisons of host and non-host roots in the same individual plant.

Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi

Root systems consist of different root types (RTs) with distinct developmental and functional characteristics. RTs may be individually reprogrammed in response to their microenvironment to maximize adaptive plasticity. Molecular understanding of such specific remodeling--although crucial for crop improvement--is limited. Here, RT-specific transcriptomes of adult rice crown, large and fine lateral roots were assessed, revealing molecular evidence for functional diversity among individual RTs. Of the three rice RTs, crown roots displayed a significant enrichment of transcripts associated with phytohormones and secondary cell wall (SCW) metabolism, whereas lateral RTs showed a greater accumulation of transcripts related to mineral transport. In nature, arbuscular mycorrhizal (AM) symbiosis represents the default state of most root systems and is known to modify root system architecture. Rice RTs become heterogeneously colonized by AM fungi, with large laterals preferentially entering into the association. However, RT-specific transcriptional responses to AM symbiosis were quantitatively most pronounced for crown roots despite their modest physical engagement in the interaction. Furthermore, colonized crown roots adopted an expression profile more related to mycorrhizal large lateral than to noncolonized crown roots, suggesting a fundamental reprogramming of crown root character. Among these changes, a significant reduction in SCW transcripts was observed that was correlated with an alteration of SCW composition as determined by mass spectrometry. The combined change in SCW, hormone- and transport-related transcript profiles across the RTs indicates a previously overlooked switch of functional relationships among RTs during AM symbiosis, with a potential impact on root system architecture and functioning.

Activation of symbiosis signaling by arbuscular mycorrhizal fungi in legumes and rice

Establishment of arbuscular mycorrhizal interactions involves plant recognition of diffusible signals from the fungus, including lipochitooligosaccharides (LCOs) and chitooligosaccharides (COs). Nitrogen-fixing rhizobial bacteria that associate with leguminous plants also signal to their hosts via LCOs, the so-called Nod factors. Here, we have assessed the induction of symbiotic signaling by the arbuscular mycorrhizal (Myc) fungal-produced LCOs and COs in legumes and rice (Oryza sativa). We show that Myc-LCOs and tetra-acetyl chitotetraose (CO4) activate the common symbiosis signaling pathway, with resultant calcium oscillations in root epidermal cells of Medicago truncatula and Lotus japonicus. The nature of the calcium oscillations is similar for LCOs produced by rhizobial bacteria and by mycorrhizal fungi; however, Myc-LCOs activate distinct gene expression. Calcium oscillations were activated in rice atrichoblasts by CO4, but not the Myc-LCOs, whereas a mix of CO4 and Myc-LCOs activated calcium oscillations in rice trichoblasts. In contrast, stimulation of lateral root emergence occurred following treatment with Myc-LCOs, but not CO4, in M. truncatula, whereas both Myc-LCOs and CO4 were active in rice. Our work indicates that legumes and non-legumes differ in their perception of Myc-LCO and CO signals, suggesting that different plant species respond to different components in the mix of signals produced by arbuscular mycorrhizal fungi.

The roots of future rice harvests

Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that can maintain performance by capturing water and nutrient resources unevenly distributed is a major breeding target. Taking advantage of gathering a community of rice root biologists in a Global Rice Science Partnership workshop held in Montpellier, France, we present here the recent progresses accomplished in this area and focal points where an international network of laboratories should direct their efforts.

QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.)

QTL were identified for root architectural traits in maize. Root architectural traits, including the number, length, orientation, and branching of the principal root classes, influence plant function by determining the spatial and temporal domains of soil exploration. To characterize phenotypic patterns and their genetic control, three recombinant inbred populations of maize were grown for 28 days in solid media in a greenhouse and evaluated for 21 root architectural traits, including length, number, diameter, and branching of seminal, primary and nodal roots, dry weight of embryonic and nodal systems, and diameter of the nodal root system. Significant phenotypic variation was observed for all traits. Strong correlations were observed among traits in the same root class, particularly for the length of the main root axis and the length of lateral roots. In a principal component analysis, relationships among traits differed slightly for the three families, though vectors grouped together for traits within a given root class, indicating opportunities for more efficient phenotyping. Allometric analysis showed that trajectories of growth for specific traits differ in the three populations. In total, 15 quantitative trait loci (QTL) were identified. QTL are reported for length in multiple root classes, diameter and number of seminal roots, and dry weight of the embryonic and nodal root systems. Phenotypic variation explained by individual QTL ranged from 0.44% (number of seminal roots, NyH population) to 13.5% (shoot dry weight, OhW population). Identification of QTL for root architectural traits may be useful for developing genotypes that are better suited to specific soil environments.

Auxin perception is required for arbuscule development in arbuscular mycorrhizal symbiosis

Most land plant species live in symbiosis with arbuscular mycorrhizal fungi. These fungi differentiate essential functional structures called arbuscules in root cortical cells from which mineral nutrients are released to the plant. We investigated the role of microRNA393 (miR393), an miRNA that targets several auxin receptors, in arbuscular mycorrhizal root colonization. Expression of the precursors of the miR393 was down-regulated during mycorrhization in three different plant species: Solanum lycopersicum, Medicago truncatula, and Oryza sativa. Treatment of S. lycopersicum, M. truncatula, and O. sativa roots with concentrations of synthetic auxin analogs that did not affect root development stimulated mycorrhization, particularly arbuscule formation. DR5-GUS, a reporter for auxin response, was preferentially expressed in root cells containing arbuscules. Finally, overexpression of miR393 in root tissues resulted in down-regulation of auxin receptor genes (transport inhibitor response1 and auxin-related F box) and underdeveloped arbuscules in all three plant species. These results support the conclusion that miR393 is a negative regulator of arbuscule formation by hampering auxin perception in arbuscule-containing cells.

Earliest colonization events of Rhizophagus irregularis in rice roots occur preferentially in previously uncolonized cells

Arbuscular mycorrhizal (AM) fungi form a symbiotic association with several plant species. An arbuscule, a finely branched structure of AM fungi, is formed in root cells and plays essential roles in resource exchange. Because arbuscules are ephemeral, host cells containing collapsed arbuscules can be recolonized, and a wide region of roots can be continuously colonized by AM fungi, suggesting that repetitive recolonization in root cells is required for continuous mycorrhization. However, recolonization frequency has not been quantified because of the lack of appropriate markers for visualization of the cellular processes after arbuscule collapse; therefore, the nature of the colonization sequence remains uncertain. Here we observed that a green fluorescent protein (GFP)-tagged secretory carrier membrane protein (SCAMP) of rice was expressed even in cells with collapsed arbuscules, allowing live imaging coupled with GFP-SCAMP to evaluate the colonization and recolonization sequences. The average lifetime of intact arbuscules was 1-2 d. Cells with collapsed arbuscules were rarely recolonized and formed a new arbuscule during the observation period of 5 d, whereas de novo colonization occurred even in close proximity to cells containing collapsed arbuscules and contributed to the expansion of the colonized region. Colonization spread into an uncolonized region of roots but sparsely into a previously colonized region having no metabolically active arbuscule but several intercellular hyphae. Therefore, we propose that a previously colonized region tends to be intolerant to new colonization in rice roots. Our observations highlight the overlooked negative impact of the degeneration stage of arbuscules in the colonization sequence.

Transcriptional networks leading to symbiotic nodule organogenesis

The symbiosis with nitrogen-fixing bacteria leading to root nodules is a relatively recent evolutionary innovation and limited to a distinct order of land plants. It has long been a mystery how plants have invented this complex trait. However, recent advances in molecular genetics of model legumes has elucidated genes involved in the development of root nodules, providing insights into this process. Here we discuss how the de novo assembly of transcriptional networks may account for the predisposition to nodulate. Transcriptional networks and modes of gene regulation from the arbuscular mycorrhizal symbiosis, nitrate responses and aspects of lateral root development have likely all contributed to the emergence and development of root nodules.

Signaling events during initiation of arbuscular mycorrhizal symbiosis

Under nutrient-limiting conditions, plants will enter into symbiosis with arbuscular mycorrhizal (AM) fungi for the enhancement of mineral nutrient acquisition from the surrounding soil. AM fungi live in close, intracellular association with plant roots where they transfer phosphate and nitrogen to the plant in exchange for carbon. They are obligate fungi, relying on their host as their only carbon source. Much has been discovered in the last decade concerning the signaling events during initiation of the AM symbiosis, including the identification of signaling molecules generated by both partners. This signaling occurs through symbiosis-specific gene products in the host plant, which are indispensable for normal AM development. At the same time, plants have adapted complex mechanisms for avoiding infection by pathogenic fungi, including an innate immune response to general microbial molecules, such as chitin present in fungal cell walls. How it is that AM fungal colonization is maintained without eliciting a defensive response from the host is still uncertain. In this review, we present a summary of the molecular signals and their elicited responses during initiation of the AM symbiosis, including plant immune responses and their suppression.

Rice flooding negatively impacts root branching and arbuscular mycorrhizal colonization, but not fungal viability

Rice is mostly cultivated in wetlands, where arbuscular mycorrhization (AM) is reported to decrease. The mechanisms regulating such events are largely unknown. Rice uninoculated and inoculated with Rhizophagus irregularis were grown in dry and flooded conditions, allowing also for the transfer of plants from one water regime to the other. Roots were sampled at different times, from 7 to 35 d post-inoculation (dpi). The morphological and molecular parameters (root branching, aerenchyma formation, mycorrhizal colonization, AM marker gene expression) were evaluated. Root branching was more pronounced in dry conditions, and such phenotype was enhanced by the fungus. In wetlands, the colonization level was comparable till 21 dpi, when the mycorrhization then decreased, paralleled by an increase in aerenchyma. Expression of the fungal transporters was comparable under the two conditions. The root apparatus, when shifted from one water regime to the other, rapidly adapted to the new condition, revealing a marked plasticity. The reversibility of the AM rice symbiosis was also mirrored by expression changes of plant marker genes. The results demonstrate that the water regime is the driving force that regulates AM colonization under flooding conditions, by directly influencing root architecture and anatomy, but without impacting the basic AM functionality.

Regulation of root morphogenesis in arbuscular mycorrhizae: what role do fungal exudates, phosphate, sugars and hormones play in lateral root formation?

BACKGROUND

Arbuscular mycorrhizae (AMs) form a widespread root-fungus symbiosis that improves plant phosphate (Pi) acquisition and modifies the physiology and development of host plants. Increased branching is recognized as a general feature of AM roots, and has been interpreted as a means of increasing suitable sites for colonization. Fungal exudates, which are involved in the dialogue between AM fungi and their host during the pre-colonization phase, play a well-documented role in lateral root (LR) formation. In addition, the increased Pi content of AM plants, in relation to Pi-starved controls, as well as changes in the delivery of carbohydrates to the roots and modulation of phytohormone concentration, transport and sensitivity, are probably involved in increasing root system branching.

SCOPE

This review discusses the possible causes of increased branching in AM plants. The differential root responses to Pi, sugars and hormones of potential AM host species are also highlighted and discussed in comparison with those of the non-host Arabidopsis thaliana.

CONCLUSIONS

Fungal exudates are probably the main compounds regulating AM root morphogenesis during the first colonization steps, while a complex network of interactions governs root development in established AMs. Colonization and high Pi act synergistically to increase root branching, and sugar transport towards the arbusculated cells may contribute to LR formation. In addition, AM colonization and high Pi generally increase auxin and cytokinin and decrease ethylene and strigolactone levels. With the exception of cytokinins, which seem to regulate mainly the root:shoot biomass ratio, these hormones play a leading role in governing root morphogenesis, with strigolactones and ethylene blocking LR formation in the non-colonized, Pi-starved plants, and auxin inducing them in colonized plants, or in plants grown under high Pi conditions.

Adventitious roots and lateral roots: similarities and differences

In addition to its role in water and nutrient uptake, the root system is fundamentally important because it anchors a plant to its substrate. Although a wide variety of root systems exist across different species, all plants have a primary root (derived from an embryonic radicle) and different types of lateral roots. Adventitious roots, by comparison, display the same functions as lateral roots but develop from aerial tissues. In addition, they not only develop as an adaptive response to various stresses, such as wounding or flooding, but also are a key limiting component of vegetative propagation. Lateral and adventitious roots share key elements of the genetic and hormonal regulatory networks but are subject to different regulatory mechanisms. In this review, we discuss the developmental processes that give rise to lateral and adventitious roots and highlight knowledge acquired over the past few years about the mechanisms that regulate adventitious root formation.

Cell and developmental biology of arbuscular mycorrhiza symbiosis

The default mineral nutrient acquisition strategy of land plants is the symbiosis with arbuscular mycorrhiza (AM) fungi. Research into the cell and developmental biology of AM revealed fascinating insights into the plasticity of plant cell development and of interorganismic communication. It is driven by the prospect of increased exploitation of AM benefits for sustainable agriculture. The plant cell developmental program for intracellular accommodation of AM fungi is activated by a genetically defined signaling pathway involving calcium spiking in the nucleus as second messenger. Calcium spiking is triggered by chitooligosaccharides released by AM fungi that are probably perceived via LysM domain receptor kinases. Fungal infection and calcium spiking are spatiotemporally coordinated, and only cells committed to accommodating the fungus undergo high-frequency spiking. Delivery of mineral nutrients by AM fungi occurs at tree-shaped hyphal structures, the arbuscules, in plant cortical cells. Nutrients are taken up at a plant-derived periarbuscular membrane, which surrounds fungal hyphae and carries a specific transporter composition that is of direct importance for symbiotic efficiency. An elegant study has unveiled a new and unexpected mechanism for specific protein localization to the periarbuscular membrane, which relies on the timing of gene expression to synchronize protein biosynthesis with a redirection of secretion. The control of AM development by phytohormones is currently subject to active investigation and has led to the rediscovery of strigolactones. Nearly all tested phytohormones regulate AM development, and major insights into the mechanisms of this regulation are expected in the near future.

Polyphony in the rhizosphere: presymbiotic communication in arbuscular mycorrhizal symbiosis

The Arbuscular Mycorrhizal (AM) symbiosis is a ubiquitous relationship established in terrestrial ecosystems between the roots of most plants and fungi of the Glomeromycota. AM fungi occur amongst many other inhabitants of the soil, and successful development of AM symbioses relies on a pre-symbiotic signal exchange that allows mutual recognition and reprogramming for the anticipated physical interaction. The nature of some of the signals has been discovered in recent years, providing a first insight into the type of chemical language spoken between the two symbiotic partners. Importantly, these discoveries suggest that the dialogue is complex and that additional factors and corresponding receptors remain to be unveiled. Here, we explore the latest advances in this pre-symbiotic plant-fungal signal exchange and present the resulting current understanding of rhizosphere communication in AM symbioses.

The impact of beneficial plant-associated microbes on plant phenotypic plasticity

Plants show phenotypic plasticity in response to changing or extreme abiotic environments; but over millions of years they also have co-evolved to respond to the presence of soil microbes. Studies on phenotypic plasticity in plants have focused mainly on the effects of the changing environments on plants' growth and survival. Evidence is now accumulating that the presence of microbes can alter plant phenotypic plasticity in a broad range of traits in response to a changing environment. In this review, we discuss the effects of microbes on plant phenotypic plasticity in response to changing environmental conditions, and how this may affect plant fitness. By using a range of specific plant-microbe interactions as examples, we demonstrate that one way that microbes can alleviate the effect of environmental stress on plants and thus increase plant fitness is to remove the stress, e.g., nutrient limitation, directly. Furthermore, microbes indirectly affect plant phenotypic plasticity and fitness through modulation of plant development and defense responses. In doing so, microbes affect fitness by both increasing or decreasing the degree of phenotypic plasticity, depending on the phenotype and the environmental stress studied, with no clear difference between the effect of prokaryotic and eukaryotic microbes in general. Additionally, plants have the ability to modulate microbial behaviors, suggesting that they manipulate bacteria, enhancing interactions that help them cope with stressful environments. Future challenges remain in the identification of the many microbial signals that modulate phenotypic plasticity, the characterization of plant genes, e.g. receptors, that mediate the microbial effects on plasticity, and the elucidation of the molecular mechanisms that link phenotypic plasticity with fitness. The characterization of plant and microbial mutants defective in signal synthesis or perception, together with carefully designed glasshouse or field experiments that test various environmental stresses will be necessary to understand the link between molecular mechanisms controlling plastic phenotypes with the resulting effects on plant fitness.

Multiple control levels of root system remodeling in arbuscular mycorrhizal symbiosis

In nature, the root systems of most plants develop intimate symbioses with glomeromycotan fungi that assist in the acquisition of mineral nutrients and water through uptake from the soil and direct delivery into the root cortex. Root systems are endowed with a strong, environment-responsive architectural plasticity that also manifests itself during the establishment of arbuscular mycorrhizal (AM) symbioses, predominantly in lateral root proliferation. In this review, we collect evidence for the idea that AM-induced root system remodeling is regulated at several levels: by AM fungal signaling molecules and by changes in plant nutrient status and distribution within the root system.

Getting to the roots of it: Genetic and hormonal control of root architecture

Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.

Involvement of auxin pathways in modulating root architecture during beneficial plant-microorganism interactions

A wide variety of microorganisms known to produce auxin and auxin precursors form beneficial relationships with plants and alter host root development. Moreover, other signals produced by microorganisms affect auxin pathways in host plants. However, the precise role of auxin and auxin-signalling pathways in modulating plant-microbe interactions is unknown. Dissecting out the auxin synthesis, transport and signalling pathways resulting in the characteristic molecular, physiological and developmental response in plants will further illuminate upon how these intriguing inter-species interactions of environmental, ecological and economic significance occur. The present review seeks to survey and summarize the scattered evidence in support of known host root modifications brought about by beneficial microorganisms and implicate the role of auxin synthesis, transport and signal transduction in modulating beneficial effects in plants. Finally, through a synthesis of the current body of work, we present outstanding challenges and potential future research directions on studies related to auxin signalling in plant-microbe interactions.

Isolate identity determines plant tolerance to pathogen attack in assembled mycorrhizal communities

Arbuscular mycorrhizal fungi (AMF) are widespread soil microorganisms that associate mutualistically with plant hosts. AMF receive photosynthates from the host in return for various benefits. One of such benefits is in the form of enhanced pathogen tolerance. However, this aspect of the symbiosis has been understudied compared to effects on plant growth and its ability to acquire nutrients. While it is known that increased AMF species richness positively correlates with plant productivity, the relationship between AMF diversity and host responses to pathogen attack remains obscure. The objective of this study was to test whether AMF isolates can differentially attenuate the deleterious effects of a root pathogen on plant growth, whether the richest assemblage of AMF isolates provides the most tolerance against the pathogen, and whether AMF-induced changes to root architecture serve as a mechanism for improved plant disease tolerance. In a growth chamber study, we exposed the plant oxeye daisy (Leucanthemum vulgare) to all combinations of three AMF isolates and to the plant root pathogen Rhizoctonia solani. We found that the pathogen caused an 81% reduction in shoot and a 70% reduction in root biomass. AMF significantly reduced the highly deleterious effect of the pathogen. Mycorrhizal plants infected with the pathogen produced 91% more dry shoot biomass and 72% more dry root biomass relative to plants solely infected with R. solani. AMF isolate identity was a better predictor of AMF-mediated host tolerance to the pathogen than AMF richness. However, the enhanced tolerance response did not result from AMF-mediated changes to root architecture. Our data indicate that AMF communities can play a major role in alleviating host pathogen attack but this depends primarily on the capacity of individual AMF isolates to provide this benefit.

Getting to the roots of it: Genetic and hormonal control of root architecture

Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.

Getting to the roots of it: Genetic and hormonal control of root architecture

Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.

The microRNA miR171h modulates arbuscular mycorrhizal colonization of Medicago truncatula by targeting NSP2

Most land plants live symbiotically with arbuscular mycorrhizal fungi. Establishment of this symbiosis requires signals produced by both partners: strigolactones in root exudates stimulate pre-symbiotic growth of the fungus, which releases lipochito-oligosaccharides (Myc-LCOs) that prepare the plant for symbiosis. Here, we have investigated the events downstream of this early signaling in the roots. We report that expression of miR171h, a microRNA that targets NSP2, is up-regulated in the elongation zone of the root during colonization by Rhizophagus irregularis (formerly Glomus intraradices) and in response to Myc-LCOs. Fungal colonization was much reduced by over-expressing miR171h in roots, mimicking the phenotype of nsp2 mutants. Conversely, in plants expressing an NSP2 mRNA resistant to miR171h cleavage, fungal colonization was much increased and extended into the elongation zone of the roots. Finally, phylogenetic analyses revealed that miR171h regulation of NSP2 is probably conserved among mycotrophic plants. Our findings suggest a regulatory mechanism, triggered by Myc-LCOs, that prevents over-colonization of roots by arbuscular mycorrhizal fungi by a mechanism involving miRNA-mediated negative regulation of NSP2.

Plant hormones as signals in arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) fungi are non-specific symbionts developing mutual and beneficial symbiosis with most terrestrial plants. Because of the obligatory nature of the symbiosis, the presence of the host plant during the onset and proceeding of symbiosis is necessary. However, AM fungal spores are able to germinate in the absence of the host plant. The fungi detect the presence of the host plant through some signal communications. Among the signal molecules, which can affect mycorrhizal symbiosis are plant hormones, which may positively or adversely affect the symbiosis. In this review article, some of the most recent findings regarding the signaling effects of plant hormones, on mycorrhizal fungal symbiosis are reviewed. This may be useful for the production of plants, which are more responsive to mycorrhizal symbiosis under stress.

Diversity of morphology and function in arbuscular mycorrhizal symbioses in Brachypodium distachyon

Brachypodium distachyon is a grass species that serves as a useful model for wheat and also for many of the grass species proposed as feedstocks for bioenergy production. Here, we monitored B. distachyon symbioses with five different arbuscular mycorrhizal (AM) fungi and identified symbioses that vary functionally with respect to plant performance. Three symbioses promoted significant increases in shoot phosphorus (P) content and shoot growth of Brachypodium, while two associations were neutral. The Brachypodium/Glomus candidum symbiosis showed a classic 'Paris-type' morphology. In the other four AM symbioses, hyphal growth was exclusively intracellular and linear; hyphal coils were not observed and arbuscules were abundant. Expression of the Brachypodium ortholog of the symbiosis-specific phosphate (Pi) transporter MtPT4 did not differ significantly in these five interactions indicating that the lack of apparent functionality did not result from a failure to express this gene or several other AM symbiosis-associated genes. Analysis of the expression patterns of the complete PHT1 Pi transporter gene family and AMT2 gene family in B. distachyon/G. intraradices mycorrhizal roots identified additional family members induced during symbiosis and again, transcript levels were similar in the different Brachypodium AM symbioses. This initial morphological, molecular and functional characterization provides a framework for future studies of functional diversity in AM symbiosis in B. distachyon.

Uptake kinetics of different arsenic species in lowland and upland rice colonized with Glomus intraradices

The effect of Glomus intraradices on four As species (arsenate; arsenite; dimethylarsinic acid, DMA; and monomethylarsonic acid, MMA) uptake by lowland rice and upland rice were investigated based on two experiments: (1) high (0-0.05 mM) and low (0-2.5mM) - affinity uptake kinetics of four As species in the short-term, and (2) As speciation in rice treated with 1mM arsenate, arsenite, DMA or MMA solutions. The results showed that mycorrhizal roots of two rice cultivars reduced the arsenate uptake significantly (P<0.001) in low-affinity uptake system, and decreased the uptake of arsenite and MMA noticeably (P<0.05) in high or low-affinity uptake systems. The four As species influx have significant differences (P<0.05) between two rice varieties in low-affinity uptake systems. In the arsenate treatment, the ratio of arsenate/arsenite reduced in shoots while increased in roots because of G. intraradices presence.

Effect of arbuscular mycorrhizal fungi (Glomus intraradices) on the oviposition of rice water weevil (Lissorhoptrus oryzophilus)

Root-feeding insects are important drivers in ecosystems, and links between aboveground oviposition preference and belowground larval performance have been suggested. The root-colonizing arbuscular mycorrhizal fungi (AMF) play a central role in plant nutrition and are known to change host quality for root-feeding insects. However, it is not known if and how AMF affect the aboveground oviposition of insects whose offspring feed on roots. According to the preference-performance hypothesis, insect herbivores oviposit on plants that will maximize offspring performance. In a greenhouse experiment with rice (Oryza sativa), we investigated the effects of AMF (Glomus intraradices) on aboveground oviposition of rice water weevil (Lissorhoptrus oryzophilus), the larvae of which feed belowground on the roots. Oviposition (i.e., the numbers of eggs laid by weevil females in leaf sheaths) was enhanced when the plants were colonized by AMF. However, the leaf area consumed by adult weevils was not affected. Although AMF reduced plant biomass, it increased nitrogen (N) and phosphorus concentrations in leaves and N in roots. The results suggest that rice water weevil females are able to discriminate plants for oviposition depending on their mycorrhizal status. The discrimination is probably related to AMF-mediated changes in plant quality, i.e., the females choose to oviposit more on plants with higher nutrient concentrations to potentially optimize offspring performance. AMF-mediated change in plant host choice for chewing insect oviposition is a novel aspect of below- and aboveground interactions.

Genetic evidence for auxin involvement in arbuscular mycorrhiza initiation

• Formation of arbuscular mycorrhiza (AM) is controlled by a host of small, diffusible signaling molecules, including phytohormones. To test the hypothesis that the plant hormone auxin controls mycorrhiza development, we assessed mycorrhiza formation in two mutants of tomato (Solanum lycopersicum): diageotropica (dgt), an auxin-resistant mutant, and polycotyledon (pct), a mutant with hyperactive polar auxin transport. • Mutant and wild-type (WT) roots were inoculated with spores of the AM fungus Glomus intraradices. Presymbiotic root-fungus interactions were observed in root organ culture (ROC) and internal fungal colonization was quantified both in ROC and in intact seedlings. • In ROC, G. intraradices stimulated presymbiotic root branching in pct but not in dgt roots. pct roots stimulated production of hyphal fans indicative of appressorium formation and were colonized more rapidly than WT roots. By contrast, approaching hyphae reversed direction to grow away from cultured dgt roots and failed to colonize them. In intact seedlings, pct and dgt roots were colonized poorly, but development of hyphae, arbuscules, and vesicles was morphologically normal within roots of both mutants. • We conclude that auxin signaling within host roots is required for the early stages of AM formation, including during presymbiotic signal exchange.

A holistic view of nitrogen acquisition in plants

Nitrogen (N) is the mineral nutrient required in the greatest amount and its availability is a major factor limiting growth and development of plants. As sessile organisms, plants have evolved different strategies to adapt to changes in the availability and distribution of N in soils. These strategies include mechanisms that act at different levels of biological organization from the molecular to the ecosystem level. At the molecular level, plants can adjust their capacity to acquire different forms of N in a range of concentrations by modulating the expression and function of genes in different N uptake systems. Modulation of plant growth and development, most notably changes in the root system architecture, can also greatly impact plant N acquisition in the soil. At the organism and ecosystem levels, plants establish associations with diverse microorganisms to ensure adequate nutrition and N supply. These different adaptive mechanisms have been traditionally discussed separately in the literature. To understand plant N nutrition in the environment, an integrated view of all pathways contributing to plant N acquisition is required. Towards this goal, in this review the different mechanisms that plants utilize to maintain an adequate N supply are summarized and integrated.

Germinating spore exudates from arbuscular mycorrhizal fungi: molecular and developmental responses in plants and their regulation by ethylene

Arbuscular mycorrhizal (AM) fungi stimulate root development and induce expression of mycorrhization-specific genes in both eudicots and monocots. Diffusible factors released by AM fungi have been shown to elicit similar responses in Medicago truncatula. Colonization of roots by AM fungi is inhibited by ethylene. We compared the effects of germinating spore exudates (GSE) from Glomus intraradices in monocots and in eudicots, their genetic control, and their regulation by ethylene. GSE modify root architecture and induce symbiotic gene expression in both monocots and eudicots. The genetic regulation of root architecture and gene expression was analyzed using M. truncatula and rice symbiotic mutants. These responses are dependent on the common symbiotic pathway as well as another uncharacterized pathway. Significant differences between monocots and eudicots were observed in the genetic control of plant responses to GSE. However, ethylene inhibits GSE-induced symbiotic gene expression and root development in both groups. Our results indicate that GSE signaling shares similarities and differences in monocots versus eudicots, that only a subset of AM signaling pathways has been co-opted in legumes for the establishment of root nodulation with rhizobia, and that regulation of these pathways by ethylene is a feature conserved across higher land plants.

Tissue-adapted invasion strategies of the rice blast fungus Magnaporthe oryzae

Magnaporthe oryzae causes rice blast, the most serious foliar fungal disease of cultivated rice (Oryza sativa). During hemibiotrophic leaf infection, the pathogen simultaneously combines biotrophic and necrotrophic growth. Here, we provide cytological and molecular evidence that, in contrast to leaf tissue infection, the fungus adopts a uniquely biotrophic infection strategy in roots for a prolonged period and spreads without causing a loss of host cell viability. Consistent with a biotrophic lifestyle, intracellularly growing hyphae of M. oryzae are surrounded by a plant-derived membrane. Global, temporal gene expression analysis used to monitor rice responses to progressive root infection revealed a rapid but transient induction of basal defense-related gene transcripts, indicating perception of the pathogen by the rice root. Early defense gene induction was followed by suppression at the onset of intracellular fungal growth, consistent with the biotrophic nature of root invasion. By contrast, during foliar infection, the vast majority of these transcripts continued to accumulate or increased in abundance. Furthermore, induction of necrotrophy-associated genes during early tissue penetration, previously observed in infected leaves, was not seen in roots. Collectively, our results not only report a global characterization of transcriptional root responses to a biotrophic fungal pathogen but also provide initial evidence for tissue-adapted fungal infection strategies.

Membrane steroid-binding protein 1 induced by a diffusible fungal signal is critical for mycorrhization in Medicago truncatula

Arbuscular mycorrhiza (AM) is a mutualistic biotrophic association that requires a complex exchange of signals between plant and fungus to allow accommodation of the mycosymbiont in the root cortex. Signal exchange happens even before physical contact, activating the plant symbiotic program. We investigated very early transcriptional responses in Medicago truncatula to inoculation with Glomus intraradices and identified four genes induced by diffusible AM fungal signals before contact. Three of them were previously shown to be mycorrhiza induced at later stages of the symbiosis, while MtMSBP1, encoding a membrane-bound steroid-binding protein, is a novel mycorrhizal marker. Expression analyses in plants defective in the symbiotic receptor kinase DMI2 allowed discrimination of two different signaling cascades involved in the perception of the diffusible signals. Thus, while some of the genes are activated in a DMI2-dependent manner, the induction of one of them encoding a proteinase inhibitor is DMI2-independent. Downregulation of MtMSBP1 by RNAi led to an aberrant mycorrhizal phenotype with thick and septated appressoria, decrease number of arbuscules and distorted arbuscule morphology. This provides genetic evidence that MtMSBP1 is critical for mycorrhiza development. We hypothesize that MtMSBP1 plays a role in sterol homeostasis in the root.