A rice Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal symbiosis at the peri-arbuscular membrane

The costs and benefits of symbiotic interactions: variable effects of rhizobia and arbuscular mycorrhizae on Vigna radiata accessions

BACKGROUND

The symbiosis among plants, rhizobia, and arbuscular mycorrhizal fungi (AMF) is one of the most well-known symbiotic relationships in nature. However, it is still unclear how bilateral/tripartite symbiosis works under resource-limited conditions and the diverse genetic backgrounds of the host.

RESULTS

Using a full factorial design, we manipulated mungbean accessions/subspecies, rhizobia, and AMF to test their effects on each other. Rhizobia functions as a typical facilitator by increasing plant nitrogen content, plant weight, chlorophyll content, and AMF colonization. In contrast, AMF resulted in a tradeoff in plants (reducing biomass for phosphorus acquisition) and behaved as a competitor in reducing rhizobia fitness (nodule weight). Plant genotype did not have a significant effect on AMF fitness, but different mungbean accessions had distinct rhizobia affinities. In contrast to previous studies, the positive relationship between plant and rhizobia fitness was attenuated in the presence of AMF, with wild mungbean being more responsive to the beneficial effect of rhizobia and attenuation by AMF.

CONCLUSIONS

We showed that this complex tripartite relationship does not unconditionally benefit all parties. Moreover, rhizobia species and host genetic background affect the symbiotic relationship significantly. This study provides a new opportunity to re-evaluate the relationships between legume plants and their symbiotic partners.

The receptor-like kinase ARK controls symbiotic balance across land plants

The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago and is still widely found in all major land plant lineages. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. The ARBUSCULAR RECEPTOR-LIKE KINASE (ARK) is required for sustaining AM symbiosis in distantly related angiosperms. Here, we demonstrate that ARK has an equivalent role in symbiosis maintenance in the bryophyte Marchantia paleacea and is part of a broad AM genetic program conserved among land plants. In addition, our comparative transcriptome analysis identified evolutionarily conserved expression patterns for several genes in the core symbiotic program required for presymbiotic signaling, intracellular colonization, and nutrient exchange. This study provides insights into the molecular pathways that consistently associate with AM symbiosis across land plants and identifies an ancestral role for ARK in governing symbiotic balance.

Walking on a tightrope: cell wall-associated kinases act as sensors and regulators of immunity and symbiosis

This article is a Commentary on Zhang et al. (2024), 242: 2180–2194.

A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction between fungi and most land plants that is underpinned by a bidirectional exchange of nutrients. AM development is a tightly regulated process that encompasses molecular communication for reciprocal recognition, fungal accommodation in root tissues and activation of symbiotic function. As such, a complex network of transcriptional regulation and molecular signaling underlies the cellular and metabolic reprogramming of host cells upon AM fungal colonization. In addition to transcription factors, small RNAs (sRNAs) are emerging as important regulators embedded in the gene network that orchestrates AM development. In addition to controlling cell-autonomous processes, plant sRNAs also function as mobile signals capable of moving to different organs and even to different plants or organisms that interact with plants. AM fungi also produce sRNAs; however, their function in the AM symbiosis remains largely unknown. Here, we discuss the contribution of host sRNAs in the development of AM symbiosis by considering their role in the transcriptional reprogramming of AM fungal colonized cells. We also describe the characteristics of AM fungal-derived sRNAs and emerging evidence for the bidirectional transfer of functional sRNAs between the two partners to mutually modulate gene expression and control the symbiosis.

Molecular and Systems Biology Approaches for Harnessing the Symbiotic Interaction in Mycorrhizal Symbiosis for Grain and Oil Crop Cultivation

Mycorrhizal symbiosis, the mutually beneficial association between plants and fungi, has gained significant attention in recent years due to its widespread significance in agricultural productivity. Specifically, arbuscular mycorrhizal fungi (AMF) provide a range of benefits to grain and oil crops, including improved nutrient uptake, growth, and resistance to (a)biotic stressors. Harnessing this symbiotic interaction using molecular and systems biology approaches presents promising opportunities for sustainable and economically-viable agricultural practices. Research in this area aims to identify and manipulate specific genes and pathways involved in the symbiotic interaction, leading to improved cereal and oilseed crop yields and nutrient acquisition. This review provides an overview of the research frontier on utilizing molecular and systems biology approaches for harnessing the symbiotic interaction in mycorrhizal symbiosis for grain and oil crop cultivation. Moreover, we address the mechanistic insights and molecular determinants underpinning this exchange. We conclude with an overview of current efforts to harness mycorrhizal diversity to improve cereal and oilseed health through systems biology.

Comparative RNA sequencing-based transcriptome profiling of ten grapevine rootstocks: shared and specific sets of genes respond to mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis improves water and nutrient uptake by plants and provides them other ecosystem services. Grapevine is one of the major crops in the world. Vitis vinifera scions generally are grafted onto a variety of rootstocks that confer different levels of resistance against different pests, tolerance to environmental stress, and influence the physiology of the scions. Arbuscular mycorrhizal fungi are involved in the root architecture and in the immune response to soil-borne pathogens. However, the fine-tuned regulation and the transcriptomic plasticity of rootstocks in response to mycorrhization are still unknown. We compared the responses of 10 different grapevine rootstocks to arbuscular mycorrhizal symbiosis (AMS) formed with Rhizophagus irregularis DAOM197198 using RNA sequencing-based transcriptome profiling. We have highlighted a few shared regulation mechanisms, but also specific rootstock responses to R. irregularis colonization. A set of 353 genes was regulated by AMS in all ten rootstocks. We also compared the expression level of this set of genes to more than 2000 transcriptome profiles from various grapevine varieties and tissues to identify a class of transcripts related to mycorrhizal associations in these 10 rootstocks. Then, we compared the response of the 351 genes upregulated by mycorrhiza in grapevine to their Medicago truncatula homologs in response to mycorrhizal colonization based on available transcriptomic studies. More than 97% of the 351 M. truncatula-homologous grapevine genes were expressed in at least one mycorrhizal transcriptomic study, and 64% in every single RNAseq dataset. At the intra-specific level, we described, for the first time, shared and specific grapevine rootstock genes in response to R. irregularis symbiosis. At the inter-specific level, we defined a shared subset of mycorrhiza-responsive genes.

Microbiome specificity and fluxes between two distant plant taxa in Iberian forests

BACKGROUND

Plant-associated microbial communities play important roles in host nutrition, development and defence. In particular, the microbes living within internal plant tissues can affect plant metabolism in a more intimate way. Understanding the factors that shape plant microbial composition and discovering enriched microbes within endophytic compartments would thus be valuable to gain knowledge on potential plant-microbial coevolutions. However, these interactions are usually studied through reductionist approaches (in vitro models or crop controlled systems). Here, we investigate these ecological factors in wild forest niches using proximally located plants from two distant taxa (blueberry and blackberry) as a model.

RESULTS

Although the microbial communities were quite similar in both plants, we found that sampling site had a high influence on them; specifically, its impact on the rhizosphere communities was higher than that on the roots. Plant species and sample type (root vs. rhizosphere) affected the bacterial communities more than the fungal communities. For instance, Xanthobacteraceae and Helotiales taxa were more enriched in roots, while the abundance of Gemmatimonadetes was higher in rhizospheres. Acidobacteria abundance within the endosphere of blueberry was similar to that in soil. Several taxa were significantly associated with either blackberry or blueberry samples regardless of the sampling site. For instance, we found a significant endospheric enrichment of Nevskia in blueberry and of Sphingobium, Novosphingobium and Steroidobacter in blackberry.

CONCLUSIONS

There are selective enrichment and exclusion processes in the roots of plants that shapes a differential composition between plant species and sample types (root endosphere-rhizosphere). The special enrichment of some microbial taxa in each plant species might suggest the presence of ancient selection and/or speciation processes and might imply specific symbiosis. The selection of fungi by the host is more pronounced when considering the fungal trait rather than the taxonomy. This work helps to understand plant-microbial interactions in natural ecosystems and the microbiome features of plants.

ARBUSCULAR MYCORRHIZA-INDUCED KINASES AMK8 and AMK24 associate with the receptor-like kinase KINASE3 to regulate arbuscular mycorrhizal symbiosis in Lotus japonicus

Arbuscular mycorrhizal (AM) symbiosis is a widespread, ancient mutualistic association between plants and fungi, and facilitates nutrient uptake into plants. Cell surface receptor-like kinases (RLKs) and receptor-like cytoplasmic kinases (RLCKs) play pivotal roles in transmembrane signaling, while few RLCKs are known to function in AM symbiosis. Here, we show that 27 out of 40 AM-induced kinases (AMKs) are transcriptionally upregulated by key AM transcription factors in Lotus japonicus. Nine AMKs are only conserved in AM-host lineages, among which the SPARK-RLK-encoding gene KINASE3 (KIN3) and the RLCK paralogues AMK8 and AMK24 are required for AM symbiosis. KIN3 expression is directly regulated by the AP2 transcription factor CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), which regulates the reciprocal exchange of nutrients in AM symbiosis, via the AW-box motif in the KIN3 promoter. Loss of function mutations in KIN3, AMK8, or AMK24 result in reduced mycorrhizal colonization in L. japonicus. AMK8 and AMK24 physically interact with KIN3. KIN3 and AMK24 are active kinases and AMK24 directly phosphorylates KIN3 in vitro. Moreover, CRISPR-Cas9-mediated mutagenesis of OsRLCK171, the sole homolog of AMK8 and AMK24 in rice (Oryza sativa), leads to diminished mycorrhization with stunted arbuscules. Overall, our results reveal a crucial role of the CBX1-driven RLK/RLCK complex in the evolutionarily conserved signaling pathway enabling arbuscule formation.

A glycan receptor kinase facilitates intracellular accommodation of arbuscular mycorrhiza and symbiotic rhizobia in the legume Lotus japonicus

Receptors that distinguish the multitude of microbes surrounding plants in the environment enable dynamic responses to the biotic and abiotic conditions encountered. In this study, we identify and characterise a glycan receptor kinase, EPR3a, closely related to the exopolysaccharide receptor EPR3. Epr3a is up-regulated in roots colonised by arbuscular mycorrhizal (AM) fungi and is able to bind glucans with a branching pattern characteristic of surface-exposed fungal glucans. Expression studies with cellular resolution show localised activation of the Epr3a promoter in cortical root cells containing arbuscules. Fungal infection and intracellular arbuscule formation are reduced in epr3a mutants. In vitro, the EPR3a ectodomain binds cell wall glucans in affinity gel electrophoresis assays. In microscale thermophoresis (MST) assays, rhizobial exopolysaccharide binding is detected with affinities comparable to those observed for EPR3, and both EPR3a and EPR3 bind a well-defined β-1,3/β-1,6 decasaccharide derived from exopolysaccharides of endophytic and pathogenic fungi. Both EPR3a and EPR3 function in the intracellular accommodation of microbes. However, contrasting expression patterns and divergent ligand affinities result in distinct functions in AM colonisation and rhizobial infection in Lotus japonicus. The presence of Epr3a and Epr3 genes in both eudicot and monocot plant genomes suggest a conserved function of these receptor kinases in glycan perception.

A New Classification of Lysin Motif Receptor-Like Kinases in Lotus japonicus

Lysin motif receptor-like kinases (LysM-RLKs) are a plant-specific receptor protein family that sense components from soil microorganisms, regulating innate immunity and symbiosis. Every plant species possesses multiple LysM-RLKs in order to interact with a variety of soil microorganisms; however, most receptors have not been characterized yet. Therefore, we tried to identify LysM-RLKs from diverse plant species and proposed a new classification to indicate their evolution and characteristics, as well as to predict new functions. In this study, we have attempted to explore and update LysM-RLKs in Lotus japonicus using the latest genome sequencing and divided 20 LysM-RLKs into 11 clades based on homolog identity and phylogenetic analysis. We further identified 193 LysM-RLKs from 16 Spermatophyta species including L. japonicus and divided these receptors into 14 clades and one out-group special receptor based on the classification of L. japonicus LysM-RLKs. All plant species not only have clade I receptors such as Nod factor or chitin receptors but also have clade III receptors where most of the receptors are uncharacterized. We also identified dicotyledon- and monocotyledon-specific clades and predicted evolutionary trends in LysM-RLKs. In addition, we found a strong correlation between plant species that did not possess clade II receptors and those that lost symbiosis with arbuscular mycorrhizal fungi. A clade II receptor in L. japonicus Lys8 was predicted to express during arbuscular mycorrhizal symbiosis. Our proposed new inventory classification suggests the evolutionary pattern of LysM-RLKs and might help in elucidating novel receptor functions in various plant species.

The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network

Arbuscular mycorrhizal symbiosis (AMS) is an ancient plant-fungus relationship that is widely distributed in terrestrial plants. The formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous genes. However, the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly understood. In this study, a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato, an emerging AMS model. The annotation of the tomato genome was improved by a multiple-platform sequencing strategy. A total of 3,174 protein-coding genes were upregulated during AMS, 42% of which were alternatively spliced. Comparative-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant angiosperms. Seven additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host plants. However, these orthogroups were absent or not induced in monocots and/or non-AMS hosts, suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory module. Additionally, we detected 587 lncRNAs, ten miRNAs, and 146 circRNAs that responded to AMS, which were incorporated to establish a tomato AMS-responsive, competing RNA-responsive endogenous RNA (ceRNA) network. Finally, a tomato symbiotic transcriptome database (TSTD, https://efg.nju.edu.cn/TSTD) was constructed to serve as a resource for deep deciphering of the AMS regulatory network. These results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.

Quantitative Proteomics at Early Stages of the Symbiotic Interaction Between Oryza sativa and Nostoc punctiforme Reveals Novel Proteins Involved in the Symbiotic Crosstalk

Symbiosis between cyanobacteria and plants is considered pivotal for biological nitrogen deposition in terrestrial ecosystems. Despite extensive knowledge of the ecology of plant-cyanobacterium symbioses, little is known about the molecular mechanisms involved in recognition between partners. Here, we conducted a quantitative sequential window acquisition of all theoretical fragment ion spectra mass spectrometry pipeline to analyze protein changes in Oryza sativa and Nostoc punctiforme during early events of symbiosis. We found differentially expressed proteins in both organisms linked to several biological functions, including signal transduction, adhesion, defense-related proteins and cell wall modification. In N. punctiforme we found increased expression of 62 proteins that have been previously described in other Nostoc-plant symbioses, reinforcing the robustness of our study. Our findings reveal new proteins activated in the early stages of the Nostoc-Oryza symbiosis that might be important for the recognition between the plant and the host. Oryza mutants in genes in the common symbiosis signaling pathway (CSSP) show reduced colonization efficiency, providing first insights on the involvement of the CSSP for the accommodation of N. punctiforme inside the plant cells. This information may have long-term implications for a greater understanding of the symbiotic interaction between Nostoc and land plants.

Functions of Lipids in Development and Reproduction of Arbuscular Mycorrhizal Fungi

Arbuscular mycorrhizal fungi (AMF) form mutualistic associations with most land plants. The symbiosis is based on the exchange of nutrients: AMF receive photosynthetically fixed carbon from the plants and deliver mineral nutrients in return. Lipids are important players in the symbiosis. They act as components of the plant-derived membrane surrounding arbuscules, as carbon sources transferred from plants to AMF, as a major form of carbon storage in AMF and as triggers of developmental responses in AMF. In this review, we describe the role of lipids in arbuscular mycorrhizal symbiosis and AMF development.

Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2

Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals.

Plant Foraging Strategies Driven by Distinct Genetic Modules: Cross-Ecosystem Transcriptomics Approach

Plants have evolved diverse strategies for foraging, e.g., mycorrhizae, modification of root system architecture, and secretion of phosphatase. Despite extensive molecular/physiological studies on individual strategies under laboratory/greenhouse conditions, there is little information about how plants orchestrate these strategies in the field. We hypothesized that individual strategies are independently driven by corresponding genetic modules in response to deficiency/unbalance in nutrients. Roots colonized by mycorrhizal fungi, leaves, and root-zone soils were collected from 251 maize plants grown across the United States Corn Belt and Japan, which provided a large gradient of soil characteristics/agricultural practice and thus gene expression for foraging. RNA was extracted from the roots, sequenced, and subjected to gene coexpression network analysis. Nineteen genetic modules were defined and functionally characterized, from which three genetic modules, mycorrhiza formation, phosphate starvation response (PSR), and root development, were selected as those directly involved in foraging. The mycorrhizal module consists of genes responsible for mycorrhiza formation and was upregulated by both phosphorus and nitrogen deficiencies. The PSR module that consists of genes encoding phosphate transporter, secreted acid phosphatase, and enzymes involved in internal-phosphate recycling was regulated independent of the mycorrhizal module and strongly upregulated by phosphorus deficiency relative to nitrogen. The root development module that consists of regulatory genes for root development and cellulose biogenesis was upregulated by phosphorus and nitrogen enrichment. The expression of this module was negatively correlated with that of the mycorrhizal module, suggesting that root development is intrinsically an opposite strategy of mycorrhizae. Our approach provides new insights into understanding plant foraging strategies in complex environments at the molecular level.

Molecular Regulation of Arbuscular Mycorrhizal Symbiosis

Plant-microorganism interactions at the rhizosphere level have a major impact on plant growth and plant tolerance and/or resistance to biotic and abiotic stresses. Of particular importance for forestry and agricultural systems is the cooperative and mutualistic interaction between plant roots and arbuscular mycorrhizal (AM) fungi from the phylum Glomeromycotina, since about 80% of terrestrial plant species can form AM symbiosis. The interaction is tightly regulated by both partners at the cellular, molecular and genetic levels, and it is highly dependent on environmental and biological variables. Recent studies have shown how fungal signals and their corresponding host plant receptor-mediated signalling regulate AM symbiosis. Host-generated symbiotic responses have been characterized and the molecular mechanisms enabling the regulation of fungal colonization and symbiosis functionality have been investigated. This review summarizes these and other recent relevant findings focusing on the molecular players and the signalling that regulate AM symbiosis. Future progress and knowledge about the underlying mechanisms for AM symbiosis regulation will be useful to facilitate agro-biotechnological procedures to improve AM colonization and/or efficiency.

Dual Roles of OsGH3.2 in Modulating Rice Root Morphology and Affecting Arbuscular Mycorrhizal Symbiosis

Several angiosperm GRETCHEN HAGEN 3 (GH3) genes, including tomato SlGH3.4 and rice OsGH3.2 are induced during arbuscular mycorrhizal (AM) symbiosis, but their functions remain largely unclear. Recently, tomato SlGH3.4 was suggested to negatively regulate arbuscule incidence via decreasing auxin levels in colonized cells. In this study, by acquiring rice OsGH3.2pro:β-glucuronidase (GUS) transgenic plants and generating Osgh3.2 mutants via CRISPR/Cas9 technique, the roles of OsGH3.2 in modulating rice root morphology and affecting AM symbiosis were investigated through time course experiments. Unlike SlGH3.4, OsGH3.2 showed asymbiotic expression in rice young lateral roots, and its mutation resulted in a "shallow" root architecture. Such root morphological change was also observed under symbiotic condition and it likely promoted AM fungal colonization, as the mutants exhibited higher colonization levels and arbuscule incidence than wild-type at early stages. Similar to SlGH3.4, OsGH3.2 showed symbiotic expression in cortical cells that have formed mature arbuscules. At late stages of symbiosis, Osgh3.2 mutants showed elongated cortical cells and larger arbuscules than wild-type, indicating elevated auxin level in the colonized cells. Together, these results revealed both asymbiotic and symbiotic roles of OsGH3.2 in modulating rice root architecture and controlling auxin levels in arbusculated cells, which further affected colonization rate and arbuscule phenotype.

KIN3 impacts arbuscular mycorrhizal symbiosis and promotes fungal colonisation in Medicago truncatula

Arbuscular mycorrhizal fungi help their host plant in the acquisition of nutrients, and this association is itself impacted by soil nutrient levels. High phosphorus levels inhibit the symbiosis, whereas high nitrogen levels enhance it. The genetic mechanisms regulating the symbiosis in response to soil nutrients are poorly understood. Here, we characterised the symbiotic phenotypes in four Medicago truncatula Tnt1-insertion mutants affected in arbuscular mycorrhizal colonisation. We located their Tnt1 insertions and identified alleles for two genes known to be involved in mycorrhization, RAM1 and KIN3. We compared the effects of the kin3-2 and ram1-4 mutations on gene expression, revealing that the two genes alter the expression of overlapping but not identical gene sets, suggesting that RAM1 acts upstream of KIN3. Additionally, KIN3 appears to be involved in the suppression of plant defences in response to the fungal symbiont. KIN3 is located on the endoplasmic reticulum of arbuscule-containing cortical cells, and kin3-2 mutants plants hosted significantly fewer arbuscules than the wild type. KIN3 plays an essential role in the symbiotic response to soil nitrogen levels, as, contrary to wild-type plants, the kin3-2 mutant did not exhibit increased root colonisation under high nitrogen.

OsADK1, a novel kinase regulating arbuscular mycorrhizal symbiosis in rice

Arbuscular mycorrhizal (AM) symbiosis relies on the formation of arbuscules for efficient nutrient exchange between plants and AM fungi. In this study, we identified a novel kinase gene in rice named OsADK1 (Arbuscule Development Kinase 1) that is required for arbuscule development. By obtaining OsADK1pro::GUS transgenic rice plants and also generating Osadk1 mutants via CRISPR/Cas9 technique, OsADK1 was revealed to be specifically induced in the arbusculated cortical cells and mutations in OsADK1 resulted in an extremely low colonisation rate (c. 3%) of rice roots by AM fungus Rhizophagus irregularis. In the mutant roots, the very few observed arbuscules nearly all arrested at an early 'trunk-forming' phase without forming any branches. Increasing the inoculum strength of AM fungus or cocultivation with a wild-type nurse plant did not result in the rescue of the arbuscule phenotype. Transcriptome sequencing of both nursed and un-nursed Osadk1 mutants then revealed that the mutation of OsADK1 could greatly affect the AM symbiotic programme, including many key transcription factors such as RAM1 and WRI5. OsADK1 therefore represents a new rice kinase that is required for arbuscule branching. Its identification opens a new window to explore the elaborate signal transduction pathway that determines arbuscule development during plant-fungus symbiosis.

OsRAM2 Function in Lipid Biosynthesis Is Required for Arbuscular Mycorrhizal Symbiosis in Rice

Arbuscular mycorrhiza (AM) is a mutualistic symbiosis formed between most land plants and Glomeromycotina fungi. During symbiosis, plants provide organic carbon to fungi in exchange for mineral nutrients. Previous legume studies showed that the required for arbuscular mycorrhization2 (RAM2) gene is necessary for transferring lipids from plants to AM fungi (AMF) and is also likely to play a "signaling" role at the root surface. To further explore RAM2 functions in other plant lineages, in this study, two rice (Oryza sativa) genes, OsRAM2 and OsRAM2L, were identified as orthologs of legume RAM2. Examining their expression patterns during symbiosis revealed that only OsRAM2 was strongly upregulated upon AMF inoculation. CRISPR/Cas9 mutagenesis was then performed to obtain three Osram2 mutant lines (-1, -2, and -3). After inoculation by AMF Rhizophagus irregularis or Funneliformis mosseae, all of the mutant lines showed extremely low colonization rates and the rarely observed arbuscules were all defective, thus supporting a conserved "nutritional" role of RAM2 between monocot and dicot lineages. As for the signaling role, although the hyphopodia numbers formed by both AMF on Osram2 mutants were indeed reduced, their morphology showed no abnormality, with fungal hyphae invading roots successfully. Promoter activities further indicated that OsRAM2 was not expressed in epidermal cells below hyphopodia or outer cortical cells enclosing fungal hyphae but instead expressed exclusively in cortical cells containing arbuscules. Therefore, this suggested an indirect role of RAM2 rather than a direct involvement in determining the symbiosis signals at the root surface.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

A Label-Free Proteomic and Complementary Metabolomic Analysis of Leaves of the Resurrection Plant Xerophytaschlechteri during Dehydration

Vegetative desiccation tolerance, or the ability to survive the loss of ~95% relative water content (RWC), is rare in angiosperms, with these being commonly called resurrection plants. It is a complex multigenic and multi-factorial trait, with its understanding requiring a comprehensive systems biology approach. The aim of the current study was to conduct a label-free proteomic analysis of leaves of the resurrection plant Xerophyta schlechteri in response to desiccation. A targeted metabolomics approach was validated and correlated to the proteomics, contributing the missing link in studies on this species. Three physiological stages were identified: an early response to drying, during which the leaf tissues declined from full turgor to a RWC of ~80–70%, a mid-response in which the RWC declined to 40% and a late response where the tissues declined to 10% RWC. We identified 517 distinct proteins that were differentially expressed, of which 253 proteins were upregulated and 264 were downregulated in response to the three drying stages. Metabolomics analyses, which included monitoring the levels of a selection of phytohormones, amino acids, sugars, sugar alcohols, fatty acids and organic acids in response to dehydration, correlated with some of the proteomic differences, giving insight into the biological processes apparently involved in desiccation tolerance in this species.

Visualising an invisible symbiosis

Despite the vast abundance and global importance of plant and microbial species, the large majority go unnoticed and unappreciated by humans, contributing to pressing issues including the neglect of study and research of these organisms, the lack of interest and support for their protection and conservation, low microbial and botanical literacy in society, and a growing disconnect between people and nature. The invisibility of many of these organisms is a key factor in their oversight by society, but also points to a solution: sharing the wealth of visual data produced during scientific research with a broader audience. Here, we discuss how the invisible can be visualised for a public audience, and the benefits it can bring.

SUMMARY

Whether too small, slow or concealed, the majority of species on Earth go unseen by humans. One such rather unobservable group of organisms are the arbuscular mycorrhizal (AM) fungi, who form beneficial symbioses with plants. AM symbiosis is ubiquitous and vitally important globally in ecosystem functioning, but partly as a consequence of its invisibility, it receives disproportionally little attention and appreciation. Yet AM fungi, and other unseen organisms, need not remain overlooked: from decades of scientific research there exists a goldmine of visual data, which if shared effectively we believe can alleviate the issues of low awareness. Here, we use examples from our experience of public engagement with AM symbiosis as well as evidence from the literature to outline the diverse ways in which invisible organisms can be visualised for a broad audience. We highlight outcomes and knock-on consequences of this visualisation, ranging from improved human mental health to environmental protection, making the case for researchers to share their images more widely for the benefit of plants (and fungi and other overlooked organisms), people and planet.

A mycorrhiza-associated receptor-like kinase with an ancient origin in the green lineage

Receptor-like kinases (RLKs) are key cell signaling components. The rice ARBUSCULAR RECEPTOR-LIKE KINASE 1 (OsARK1) regulates the arbuscular mycorrhizal (AM) association postarbuscule development and belongs to an undefined subfamily of RLKs. Our phylogenetic analysis revealed that ARK1 has an ancient paralogue in spermatophytes, ARK2 Single ark2 and ark1/ark2 double mutants in rice showed a nonredundant AM symbiotic function for OsARK2 Global transcriptomics identified a set of genes coregulated by the two RLKs, suggesting that OsARK1 and OsARK2 orchestrate symbiosis in a common pathway. ARK lineage proteins harbor a newly identified SPARK domain in their extracellular regions, which underwent parallel losses in ARK1 and ARK2 in monocots. This protein domain has ancient origins in streptophyte algae and defines additional overlooked groups of putative cell surface receptors.

Invasion and Colonization Pattern of Fusarium fujikuroi in Rice

Bakanae disease in rice can cause abnormal elongation of the stem and leaves, development of adventitious roots, a larger leaf angle, and even death. Little is known about the infection, colonization, and distribution of Fusarium fujikuroi in rice plants across different growth stages. In this study, microscopic observation and quantitative real-time PCR were combined to investigate the pathogenesis of bakanae, using artificially inoculated seedlings of a susceptible rice cultivar, Zerawchanica karatals (ZK), a resistant cultivar, Tainung 67 (TNG67), naturally infected adult field plants (cultivars Kaohsiung 139, Taikeng 2, and Tainan 11), and an F. fujikuroi isolate expressing green fluorescent protein. In rice seedlings, F. fujikuroi hyphae were found to directly penetrate the epidermis of basal stems and roots, then extend inter- and intracellularly to invade the vascular bundles. Occlusion of vascular bundles and radial hyphal expansion from vascular bundles to surrounding parenchyma were observed in adult plants. Analysis of consecutive 3-cm segments of the whole plant revealed that F. fujikuroi was largely confined to the embryo, basal stem, and basal roots in seedlings, and distributed unevenly in the lower aerial parts (including nodes and internodes) of adult plants. The elongation and development of adventitious roots did not necessarily correlate with the amount of F. fujikuroi in diseased plants. Treatment of rice seeds with gibberellic acid-3 (GA₃) at 0.5 mg/liter resulted in significantly more elongation of ZK than TNG67 seedlings, suggesting that the susceptibility of ZK to bakanae is associated with its higher sensitivity to GA₃.

The Arabidopsis V-ATPase is localized to the TGN/EE via a seed plant-specific motif

The V-ATPase is a versatile proton-pump found in a range of endomembrane compartments yet the mechanisms governing its differential targeting remain to be determined. In Arabidopsis, VHA-a1 targets the V-ATPase to the TGN/EE whereas VHA-a2 and VHA-a3 are localized to the tonoplast. We report here that the VHA-a1 targeting domain serves as both an ER-exit and as a TGN/EE-retention motif and is conserved among seed plants. In contrast, Marchantia encodes a single VHA-isoform that localizes to the TGN/EE and the tonoplast in Arabidopsis. Analysis of CRISPR/Cas9 generated null alleles revealed that VHA-a1 has an essential function for male gametophyte development but acts redundantly with the tonoplast isoforms during vegetative growth. We propose that in the absence of VHA-a1, VHA-a3 is partially re-routed to the TGN/EE. Our findings contribute to understanding the evolutionary origin of V-ATPase targeting and provide a striking example that differential localization does not preclude functional redundancy.

Proteomics Analysis of Plasma Membrane Fractions of the Root, Leaf, and Flower of Rice

The plasma membrane regulates biological processes such as ion transport, signal transduction, endocytosis, and cell differentiation/proliferation. To understand the functional characteristics and organ specificity of plasma membranes, plasma membrane protein fractions from rice root, etiolated leaf, green leaf, developing leaf sheath, and flower were analyzed by proteomics. Among the proteins identified, 511 were commonly accumulated in the five organs, whereas 270, 132, 359, 146, and 149 proteins were specifically accumulated in the root, etiolated leaf, green leaf, developing leaf sheath, and developing flower, respectively. The principle component analysis revealed that the functions of the plasma membrane in the root was different from those of green and etiolated leaves and that the plasma membrane protein composition of the leaf sheath was similar to that of the flower, but not that of the green leaf. Functional classification revealed that the root plasma membrane has more transport-related proteins than the leaf plasma membrane. Furthermore, the leaf sheath and flower plasma membranes were found to be richer in proteins involved in signaling and cell function than the green leaf plasma membrane. To validate the proteomics data, immunoblot analysis was carried out, focusing on four heterotrimeric G protein subunits, Gα, Gβ, Gγ1, and Gγ2. All subunits could be detected by both methods and, in particular, Gγ1 and Gγ2 required concentration by immunoprecipitation for mass spectrometry detection.

The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice

Most plants associate with beneficial arbuscular mycorrhizal (AM) fungi that facilitate soil nutrient acquisition. Prior to contact, partner recognition triggers reciprocal genetic remodelling to enable colonisation. The plant Dwarf14-Like (D14L) receptor conditions pre-symbiotic perception of AM fungi, and also detects the smoke constituent karrikin. D14L-dependent signalling mechanisms, underpinning AM symbiosis are unknown. Here, we present the identification of a negative regulator from rice, which operates downstream of the D14L receptor, corresponding to the homologue of the Arabidopsis thaliana Suppressor of MAX2-1 (AtSMAX1) that functions in karrikin signalling. We demonstrate that rice SMAX1 is a suppressor of AM symbiosis, negatively regulating fungal colonisation and transcription of crucial signalling components and conserved symbiosis genes. Similarly, rice SMAX1 negatively controls strigolactone biosynthesis, demonstrating an unexpected crosstalk between the strigolactone and karrikin signalling pathways. We conclude that removal of SMAX1, resulting from D14L signalling activation, de-represses essential symbiotic programmes and increases strigolactone hormone production.

Signaling via the D14L karrikin receptor conditions rice roots for association with arbuscular mycorrhizal fungi. Here, Choi et al. show that SMAX1, a rice homolog of an Arabidopsis repressor of karrikin signaling, acts downstream of D14L to suppress mycorrhizal symbiosis and strigolactone biosynthesis.

Receptor-Like Kinases Sustain Symbiotic Scrutiny

Plant receptor-like kinases (RLKs) control the initiation, development, and maintenance of symbioses with beneficial mycorrhizal fungi and nitrogen-fixing bacteria. Carbohydrate perception activates symbiosis signaling via Lysin-motif RLKs and subsequently the common symbiosis signaling pathway. As the receptors activated are often also immune receptors in multiple species, exactly how carbohydrate identities avoid immune activation and drive symbiotic outcome is still not fully understood. This may involve the coincident detection of additional signaling molecules that provide specificity. Because of the metabolic costs of supporting symbionts, the level of symbiosis development is fine-tuned by a range of local and mobile signals that are activated by various RLKs. Beyond early, precontact symbiotic signaling, signal exchanges ensue throughout infection, nutrient exchange, and turnover of symbiosis. Here, we review the latest understanding of plant symbiosis signaling from the perspective of RLK-mediated pathways.

A Flexible, Low-Cost Hydroponic Co-Cultivation System for Studying Arbuscular Mycorrhiza Symbiosis

Arbuscular mycorrhiza (AM) is a widespread symbiosis between plant roots and fungi of the Glomeromycotina, which improves nutrient uptake by plants. The molecular mechanisms underlying development and function of the symbiosis are subject to increasing research activity. Since AM occurs in the soil, most studies targeting a molecular understanding of AM development and function, use solid substrates for co-cultivating plants and AM fungi. However, for some experiments very clean roots, highly controlled nutrient conditions or applications of defined concentrations of signaling molecules (such as hormones) or other small chemicals (such as synthetic inhibitors or signaling agonists) are needed. To this end, hydroponics has been widely used in research on mechanisms of plant nutrition and some hydroponic systems were developed for AM fungal spore amplification. Here, we present a hydroponics set-up, which can be successfully utilized for experimental root colonization assays. We established a "tip-wick" system based on pipette tips and rock wool wicks for co-cultivation of AM fungi with small model plants such as Lotus japonicus. A larger "Falcon-wick" system using Falcon tubes and rockwool wicks was developed for larger model plants such as rice. The hydroponic system can also be employed for growing L. japonicus hairy roots after transformation by Agrobacterium rhizogenes, thus circumventing the laborious cultivation on agar medium-containing Petri dishes during hairy root development. The tip-wick and Falcon-wick systems are easy to use and can be built with low cost, conventional and reusable lab plastic ware and a simple aquarium pump.

Ramf: An Open-Source R Package for Statistical Analysis and Display of Quantitative Root Colonization by Arbuscular Mycorrhiza Fungi

Data analysis and graphical representation form an essential part of scientific research dissemination. The life-science community is moving towards a more transparent presentation of single data points or data distributions and away from mean values displayed as bar charts. To facilitate transparent data display to the mycorrhiza community, we present "Ramf" an open-source R package for statistical analysis and preparation of a variety of publication-ready plots, custom-made for analyzing and displaying quantitative root colonization by arbuscular mycorrhiza fungi or any kind of data to be displayed in the same format. Ramf replaces the scripting needed for data analysis and can be readily used by researchers not acquainted with R. In addition, the package is open to improvements by the community. Ramf is available at https://github.com/mchiapello/Ramf.

Phytohormones, miRNAs, and peptide signals integrate plant phosphorus status with arbuscular mycorrhizal symbiosis

Most land plant species engage in a beneficial interaction with arbuscular mycorrhizal fungi in order to increase mineral nutrient acquisition, in particular the major macronutrient phosphorus (P). Initiation, development, and maintenance of the symbiosis are largely under the control of the host plant and strongly influenced by the plants' P status. Recent advances reveal that phytohormones, microRNAs, and secreted peptides all regulate and integrate development of arbuscular mycorrhizal (AM) symbiosis with the P status of the plant. This occurs through a complex, multi-layered signaling network with crosstalk between phosphate (Pi) starvation signaling pathways and AM symbiosis signaling, and also via direct effects on the AM fungal symbiont. Multiple checkpoints allow the plant to fine-tune symbiosis based on its P status.

Mechanisms and Impact of Symbiotic Phosphate Acquisition

Phosphorous is important for life but often limiting for plants. The symbiotic pathway of phosphate uptake via arbuscular mycorrhizal fungi (AMF) is evolutionarily ancient and today occurs in natural and agricultural ecosystems alike. Plants capable of this symbiosis can obtain up to all of the phosphate from symbiotic fungi, and this offers potential means to develop crops less dependent on unsustainable P fertilizers. Here, we review the mechanisms and insights gleaned from the fine-tuned signal exchanges that orchestrate the intimate mutualistic symbiosis between plants and AMF. As the currency of trade, nutrients have signaling functions beyond being the nutritional goal of mutualism. We propose that such signaling roles and metabolic reprogramming may represent commitments for a mutualistic symbiosis that act across the stages of symbiosis development.

Proteomics Analysis to Identify Proteins and Pathways Associated with the Novel Lesion Mimic Mutant E40 in Rice Using iTRAQ-Based Strategy

A novel rice lesion mimic mutant (LMM) was isolated from the mutant population of Japonica rice cultivar Hitomebore generated by ethyl methane sulfonate (EMS) treatment. Compared with the wild-type (WT), the mutant, tentatively designated E40, developed necrotic lesions over the whole growth period along with detectable changes in several important agronomic traits including lower height, fewer tillers, lower yield, and premature death. To understand the molecular mechanism of mutation-induced phenotypic differences in E40, a proteomics-based approach was used to identify differentially accumulated proteins between E40 and WT. Proteomic data from isobaric tags for relative and absolute quantitation (iTRAQ) showed that 233 proteins were significantly up- or down-regulated in E40 compared with WT. These proteins are involved in diverse biological processes, but phenylpropanoid biosynthesis was the only up-regulated pathway. Differential expression of the genes encoding some candidate proteins with significant up- or down-regulation in E40 were further verified by qPCR. Consistent with the proteomic results, substance and energy flow in E40 shifted from basic metabolism to secondary metabolism, mainly phenylpropanoid biosynthesis, which is likely involved in the formation of leaf spots.

Pyrophosphate modulates plant stress responses via SUMOylation

Pyrophosphate (PPi), a byproduct of macromolecule biosynthesis is maintained at low levels by soluble inorganic pyrophosphatases (sPPase) found in all eukaryotes. In plants, H⁺-pumping pyrophosphatases (H⁺-PPase) convert the substantial energy present in PPi into an electrochemical gradient. We show here, that both cold- and heat stress sensitivity of fugu5 mutants lacking the major H⁺-PPase isoform AVP1 is correlated with reduced SUMOylation. In addition, we show that increased PPi concentrations interfere with SUMOylation in yeast and we provide evidence that SUMO activating E1-enzymes are inhibited by micromolar concentrations of PPi in a non-competitive manner. Taken together, our results do not only provide a mechanistic explanation for the beneficial effects of AVP1 overexpression in plants but they also highlight PPi as an important integrator of metabolism and stress tolerance.