Intracellular accommodation of microbes by plants: a common developmental program for symbiosis and disease?

Control of Rhizobia Endosymbiosis by Coupling ER Expansion with Enhanced UPR

Legumes establish symbiosis with rhizobia by forming a symbiotic interface that enables cross-kingdom exchanges of signaling molecules and nutrients. However, how host organelles interact with symbiosomes at the symbiotic interface remains elusive during rhizobia endosymbiosis. Here, symbiotic cells are reconstructed using 3D scanning electron microscopy (SEM) and uncover that the host endoplasmic reticulum (ER) undergoes dynamic expansion to gradually enwrap symbiosomes, facilitating their compartmentalization and endosymbiosis. Consistently, altering ER lamellar expansion by overexpressing MtRTNLBs, the reticulons responsible for ER tubulation, impairs rhizobia accommodation and symbiosome development. Intriguingly, unfolded protein response (UPR)-marker genes, bZIP60 and IRE1A/B, show continuously activated expression during nodule development, and the two UPR-deficient mutants, ire1b, and bzip60, exhibit compromised ER biogenesis and defective symbiosome development. Collectively, the findings underpin ER expansion and UPR activation as two key events in rhizobia accommodation and reveal an intrinsic coupling of ER morphology with proper UPR during root nodule symbiosis.

Essential roles of nodule cysteine-rich peptides in maintaining the viability of terminally differentiated bacteroids in legume-rhizobia symbiosis

Investigations into the nitrogen-fixing symbiosis between legumes and rhizobia can yield innovative strategies for sustainable agriculture. Legume species of the Inverted Repeat-Lacking Clade (IRLC) and the Dalbergioids, can utilize nodule cysteine-rich (NCR) peptides, a diverse family of peptides characterized by four or six highly conserved cysteine residues, to communicate with their microbial symbionts. These peptides, many of which exhibit antimicrobial properties, induce profound differentiation of bacteroids (semi-autonomous forms of bacteria) within nodule cells. This terminal differentiation endows the bacteroids with the ability to fix nitrogen, at the expense of their reproductive capacity. Notably, a significant number of NCR peptides is expressed in the nodule fixation zone, where the bacteroids have already reached terminal differentiation. Recent discoveries, through forward genetics approaches, have revealed that the functions of NCR peptides extend beyond antimicrobial effects and the promotion of differentiation. They also play a critical role in sustaining the viability of terminally differentiated bacteroids within nodule cells. These findings underscore the multifaceted functions of NCR peptides and highlight the importance of these peptides in mediating communications between host cells and the terminally differentiated bacteroids.

Brassinosteroids mediate arbuscular mycorrhizal symbiosis through multiple potential pathways and partial identification in tomato

Currently, little is known regarding the specific processes through which brassinosteroids (BR) affect arbuscular mycorrhizal (AM) symbiosis. Understanding this relationship is vital for advancing plant physiology and agricultural applications. In this study, we aimed to elucidate the regulatory mechanisms of BR in AM symbiosis. According to the log2 fold change-value and adjP-value, we integrated the common differentially expressed genes (DEGs) in maize (Zea mays L.) treated with BR and AM, Arabidopsis (Arabidopsis thaliana) mutants deficient in BR receptors, and tomato (Solanum lycopersicum) plants inoculated with AM fungi. In addition, we characterized the symbiotic performance of tomato plants with BR receptor defects and overexpression. The results indicated that the common differential genes induced by BR and AM were involved in metabolic processes, such as cell wall modification, cytoskeleton remodeling, auxin and ethylene signaling, photosynthesis, mineral nutrient transport, and stress defense. Specifically, these include the BR1 gene, which modifies the cell wall. However, the fungal colonization rate of BR receptor-deficient tomato plants was significantly reduced, and the total phosphorus concentration was increased. Conversely, the performance of the overexpressing tomato transformation plants demonstrated a significant contrast. Additionally, the mild rescue of mycorrhizal attenuation in mutants treated with exogenous BR suggests the possibility of direct feedback from BR synthesis to AM. Notably, the cell wall modification gene (SlBR1) and calcium spike gene (SlIPD3) were induced by both BR and AM, suggesting that BR may influence cell penetration during the early stages of AM colonization. Synthesis: Our results demonstrated that BR positively regulates AM symbiosis through multiple pathways. These findings pave the way for future research, including isolation of the individual contributions of each pathway to this complex process and exploration of possible agricultural applications.

Receptor-associated kinases control the lipid provisioning program in plant-fungal symbiosis

The mutualistic association between plants and arbuscular mycorrhizal (AM) fungi requires intracellular accommodation of the fungal symbiont and maintenance by means of lipid provisioning. Symbiosis signaling through lysin motif (LysM) receptor-like kinases and a leucine-rich repeat receptor-like kinase DOES NOT MAKE INFECTIONS 2 (DMI2) activates transcriptional programs that underlie fungal passage through the epidermis and accommodation in cortical cells. We show that two Medicago truncatula cortical cell-specific, membrane-bound proteins of a CYCLIN-DEPENDENT KINASE-LIKE (CKL) family associate with, and are phosphorylation substrates of, DMI2 and a subset of the LysM receptor kinases. CKL1 and CKL2 are required for AM symbiosis and control expression of transcription factors that regulate part of the lipid provisioning program. Onset of lipid provisioning is coupled with arbuscule branching and with the REDUCED ARBUSCULAR MYCORRHIZA 1 (RAM1) regulon for complete endosymbiont accommodation.

Biotrophic Fungal Pathogens: a Critical Overview

Biotrophic fungi are one group of heterogeneous organisms and these fungi differ in their traits like mode of nutrition, types of reproduction, and dispersal systems. Generally, based on the nutritional mode, fungi are classified into three broad categories, viz. biotrophs, necrotrophs, and hemi-biotrophs. Biotrophs derive their nutrients and energy from living plant cells and survive within the interstitial space of the cells. Biotrophic fungi cause serious crop diseases but are highly challenging to investigate and develop a treatment strategy. Blumeria (Erysiphe) graminis, Uromyces fabae, Ustilago maydis, Cladosporium fulvum, Puccinia graminis, and Phytophthora infestans are some of the significant biotrophic fungi that affect mainly plants. One among the biotrophic fungus, Pneumocystis jirovecii (Taphrinomycotina subphylum of the Ascomycota) exclusively a human pathogen, can cause lung diseases such as "pneumocystis." Biotrophic fungus widely parasitizing Solanaceae family crops (Tomato and potato) has done massive damage to the crops and has led to economic impact worldwide. During infection and for nutrient absorption, biotrophs develops external appendages such as appressoria or haustoria. The hyphae or appressorium adheres to the plant cell wall and collapses the layers for their nutrient absorption. The pathogen also secretes effector molecules to escape from the plant defense mechanism. Later, plants activate their primary and secondary defense mechanisms; however, the pathogen induces virulence genes to escape the host immune responses. Obligate biotrophic fungi pathogenicity has not been fully understood at the molecular level because of the complex interaction, recognition, and signaling with the host. This review summarizes the mechanism of infection in the host, and immune response to emphasize the understanding of the biotrophic fungal biology and pathogenesis in crops. Thus, the detailed review will pave the way to design methods to overcome the resistance of biotrophic fungi and develop disease-free crops.

Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi

This review highlights new advances in the emerging field of 'Fungi-on-a-Chip' microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.

Micronutrients in Food Production: What Can We Learn from Natural Ecosystems?

Soil micronutrients limit crop productivity in many regions worldwide, and micronutrient deficiencies affect over two billion people globally. Microbial biofertilizers could combat these issues by inoculating arable soils with microorganisms that mobilize micronutrients, increasing their availability to crop plants in an environmentally sustainable and cost-effective manner. However, the widespread application of biofertilizers is limited by complex micronutrient–microbe–plant interactions, which reduce their effectiveness under field conditions. Here, we review the current state of seven micronutrients in food production. We examine the mechanisms underpinning microbial micronutrient mobilization in natural ecosystems and synthesize the state-of-knowledge to improve our overall understanding of biofertilizers in food crop production. We demonstrate that, although soil micronutrient concentrations are strongly influenced by soil conditions, land management practices can also substantially affect micronutrient availability and uptake by plants. The effectiveness of biofertilizers varies, but several lines of evidence indicate substantial benefits in co-applying biofertilizers with conventional inorganic or organic fertilizers. Studies of micronutrient cycling in natural ecosystems provide examples of microbial taxa capable of mobilizing multiple micronutrients whilst withstanding harsh environmental conditions. Research into the mechanisms of microbial nutrient mobilization in natural ecosystems could, therefore, yield effective biofertilizers to improve crop nutrition under global changes.

Arabidopsis Growth-Promotion and Root Architecture Responses to the Beneficial Rhizobacterium Phyllobacterium brassicacearum Strain STM196 Are Independent of the Nitrate Assimilatory Pathway

Phyllobacterium brassicacearum STM196, a plant growth-promoting rhizobacterium isolated from roots of oilseed rape, stimulates Arabidopsis growth. We have previously shown that the NRT2.5 and NRT2.6 genes are required for this growth promotion response. Since these genes are members of the NRT2 family of nitrate transporters, the nitrogen assimilatory pathway could be involved in growth promotion by STM196. We address this hypothesis using two nitrate reductase mutants, G5 deleted in the major nitrate reductase gene NIA2 and G′4-3 altered in both NIA1 and NIA2 genes. Both mutants had a reduced growth rate and STM196 failed to increase their biomass production on a medium containing NO3− as the sole nitrogen source. However, they both displayed similar growth promotion by STM196 when grown on an NH4+ medium. STM196 was able to stimulate lateral roots development of the mutants under both nutrition conditions. Altogether, our results indicate that the nitrate assimilatory metabolism is not a primary target of STM196 interaction and is not involved in the root developmental response. The NIA1 transcript level was reduced in the shoots of nrt2.5 and nrt2.6 mutants suggesting a role for this nitrate reductase isoform independently from its role in nitrate assimilation.

Exploiting Structural Modelling Tools to Explore Host-Translocated Effector Proteins

Oomycete and fungal interactions with plants can be neutral, symbiotic or pathogenic with different impact on plant health and fitness. Both fungi and oomycetes can generate so-called effector proteins in order to successfully colonize the host plant. These proteins modify stress pathways, developmental processes and the innate immune system to the microbes' benefit, with a very different outcome for the plant. Investigating the biological and functional roles of effectors during plant-microbe interactions are accessible through bioinformatics and experimental approaches. The next generation protein modeling software RoseTTafold and AlphaFold2 have made significant progress in defining the 3D-structure of proteins by utilizing novel machine-learning algorithms using amino acid sequences as their only input. As these two methods rely on super computers, Google Colabfold alternatives have received significant attention, making the approaches more accessible to users. Here, we focus on current structural biology, sequence motif and domain knowledge of effector proteins from filamentous microbes and discuss the broader use of novel modelling strategies, namely AlphaFold2 and RoseTTafold, in the field of effector biology. Finally, we compare the original programs and their Colab versions to assess current strengths, ease of access, limitations and future applications.

Detection of endophytic association between Aeschynomene nodulating Bradyrhizobium sp. and traditional Desariya rice roots under rice-Aeschynomene ecosystem of chaur land, Bihar, India

Engineering diazotrophic rice having either an integral component of diazotrophic microbes or placing microbial origin nif gene to the rice plant is the dream of biotechnologist. Rice-Aeschynomene ecosystem of pristine chaur land provides a suitable niche to search Rhizobium endophytes in rice. Accordingly, the work was initiated to search suitable endophytic Rhizobium strain for artificial symbiosis within the roots of Desariya rice and its source through morphological, biochemical and molecular approaches. Detection of Acetylene reduction assay (ARA) activity in sterilized Desariya rice root confirmed the presence of putative diazotrophic endophytes in rice root. Isolates from Aeschynomene aspera L. nodulating and Desariya rice endophytic Rhizobium were evaluated for growth, IAA, morphological and biochemical features. Carbon profiling pattern of both these isolates indicated that Desariya rice endophytic Rhizobium has its similarity with Aeschynomene aspera L. nodulating Rhizobium. 16S rRNA gene sequencing confirmed the presence of endophytic Bradyrhizobium sp. in Desariya rice roots and its similarity with Aeschynomene aspera L. nodulating Bradyrhizobium. Desariya rice Bradyrhizobium may be an ideal candidate in the future for creating artificial symbiosis in rice due to its similarity with Aeschynomene aspera L. Bradyrhizobium.

Exogenous RNA as a Regulatory Signal during a Plant's Interaction with the Biotic Environment: An Evolutionary Perspective and Future Applications in Agriculture

Environmental RNAi (eRNAi) is a sequence-specific regulation of endogenous gene expression in a responsive organism by exogenous RNA. While exogenous RNA transfer between organisms of different kingdoms of life have been unambiguously identified in nature, our understanding of the biological significance of this phenomenon remains obscure, particularly within an evolutionary context. During the last decade multiple reports utilizing various mechanisms of natural eRNAi phenomena have been attempted to develop new agricultural traits and products including weed, disease and insect control. Although these attempts yielded mixed results, this concept remains extremely attractive for many agricultural applications. To better utilize eRNAi for practical applications, we would like to emphasize the necessity of understanding the biological significance of this phenomenon within an evolutionary context and learn from nature by developing advanced tools to identify and study new cases of exogeneous RNA transfer and eRNAi. In this opinion article we would like to look at the exogeneous RNA transfer from an evolutionary perspective, propose that new cases of exogeneous RNA transfer still remain to be identified in nature, and address a knowledge gap in understanding the biological function and significance of RNA transfer. We believe such approach may eventually result in a more successful use of this phenomenon for practical applications in agriculture.

Plant evolution driven by interactions with symbiotic and pathogenic microbes

During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today's continuum of associations, ranging from parasitism to mutualism. Through phylogenetics, cell biology, and reverse genetics extending beyond flowering plants into bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms used in nonflowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen-resilient crops.

LCO Receptors Involved in Arbuscular Mycorrhiza Are Functional for Rhizobia Perception in Legumes

Bacterial lipo-chitooligosaccharides (LCOs) are key mediators of the nitrogen-fixing root nodule symbiosis (RNS) in legumes. The isolation of LCOs from arbuscular mycorrhizal fungi suggested that LCOs are also signaling molecules in arbuscular mycorrhiza (AM). However, the corresponding plant receptors have remained uncharacterized. Here we show that petunia and tomato mutants in the LysM receptor-like kinases LYK10 are impaired in AM formation. Petunia and tomato LYK10 proteins have a high affinity for LCOs (Kd in the nM range) comparable to that previously reported for a legume LCO receptor essential for the RNS. Interestingly, the tomato and petunia LYK10 promoters, when introduced into a legume, were active in nodules similarly to the promoter of the legume orthologous gene. Moreover, tomato and petunia LYK10 coding sequences restored nodulation in legumes mutated in their orthologs. This combination of genetic and biochemical data clearly pinpoints Solanaceous LYK10 as part of an ancestral LCO perception system involved in AM establishment, which has been directly recruited during evolution of the RNS in legumes.

A Report on Fungal (1→3)-α-d-glucans: Properties, Functions and Application

The cell walls of fungi are composed of glycoproteins, chitin, and α- and β-glucans. Although there are many reports on β-glucans, α-glucan polysaccharides are not yet fully understood. This review characterizes the physicochemical properties and functions of (1→3)-α-d-glucans. Particular attention has been paid to practical application and the effect of glucans in various respects, taking into account unfavourable effects and potential use. The role of α-glucans in plant infection has been proven, and collected facts have confirmed the characteristics of Aspergillus fumigatus infection associated with the presence of glucan in fungal cell wall. Like β-glucans, there are now evidence that α-glucans can also stimulate the immune system. Moreover, α-d-glucans have the ability to induce mutanases and can thus decompose plaque.

Multifunctional aspects of Piriformospora indica in plant endosymbiosis

(Hymenomycetes, Basidiomycota) is an endophytic fungus that colonises plant roots, and was originally isolated from Rajasthan desert. It is comparable to Arbuscular Mycorrhizal (AM) fungi in terms of plant growth promotional effects. P. indica has been used as an ideal example to analyse the mechanisms of mutualistic symbiosis. Major benefit of P. indica over AM fungi is that it is axenically cultivable in different synthetic and complex media. A preliminary attempt was made to scrutinise the role of P. indica co-cultivation on seedling vigour of common vegetables like Cucumis sativus L., Abelmoschus esculentus (L.) Moench, Solanum melongena L. and Capsicum annuum L. The positive effect of P. indica co-culture on seedling performance was compared to the effects of growth hormones like indole acetic acid and benzyl amino purine when supplemented to the MS medium at a concentration of 0.1 mg ml⁻¹. An exogenous supply of auxin resulted in enhanced production of roots and cytokinin supplement favoured shoot production, whereas P. indica co-culture favoured simultaneous production of shoot and root over the control. P. indica colonisation inside the roots of C. sativus L. was also successfully established. These preliminary results indicate the prospective role of P. indica in vegetable farming through its favourable effect on plant growth.

A set of Arabidopsis genes involved in the accommodation of the downy mildew pathogen Hyaloperonospora arabidopsidis

The intracellular accommodation structures formed by plant cells to host arbuscular mycorrhiza fungi and biotrophic hyphal pathogens are cytologically similar. Therefore we investigated whether these interactions build on an overlapping genetic framework. In legumes, the malectin-like domain leucine-rich repeat receptor kinase SYMRK, the cation channel POLLUX and members of the nuclear pore NUP107-160 subcomplex are essential for symbiotic signal transduction and arbuscular mycorrhiza development. We identified members of these three groups in Arabidopsis thaliana and explored their impact on the interaction with the oomycete downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa). We report that mutations in the corresponding genes reduced the reproductive success of Hpa as determined by sporangiophore and spore counts. We discovered that a developmental transition of haustorial shape occurred significantly earlier and at higher frequency in the mutants. Analysis of the multiplication of extracellular bacterial pathogens, Hpa-induced cell death or callose accumulation, as well as Hpa- or flg22-induced defence marker gene expression, did not reveal any traces of constitutive or exacerbated defence responses. These findings point towards an overlap between the plant genetic toolboxes involved in the interaction with biotrophic intracellular hyphal symbionts and pathogens in terms of the gene families involved.

Our work reveals genetic commonalities between biotrophic intracellular interactions with symbiotic and pathogenic hyphal microbes. The majority of land plants engages in arbuscular mycorrhiza (AM) symbiosis with phosphate-acquiring arbuscular mycorrhizal fungi to avoid phosphate starvation. Nutrient exchange in this interaction occurs via arbuscules, tree-shaped fungal structures, hosted within plant root cells. A series of plant genes including the Symbiosis Receptor-like kinase (SYMRK), members of the NUP107-160 subcomplex and nuclear envelope localised cation channels are required for a signalling process leading to the development of AM. The model plant Arabidopsis thaliana lost the ability to form AM. Although the ortholog of SYMRK was deleted during evolution, members of the malectin-like domain leucine-rich repeat receptor kinase (MLD-LRR-RK) gene family, components of the NUP107-160 subcomplex, and an ortholog of the nuclear envelope-localized cation channel POLLUX, are still present in the Arabidopsis genome, and Arabidopsis leaf cells retained the ability to accommodate haustoria, presumed feeding structures of the obligate biotrophic downy mildew pathogen Hyaloperonospora arabidopsidis. We discovered that both of these plant-microbe interactions utilize a corresponding set of genes including the ortholog of POLLUX, members of the NUP107-160 subcomplex and members of the MLD-LRR-RK gene family, thus revealing similarities in the plant program for the intracellular accommodation of biotrophic organisms in symbiosis and disease.

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

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

Influence of fungicides on activities of enzymes of phenolic metabolism in the early stages of formation and functioning of soybean symbiotic apparatus

We studied the effect of complex seed treatment with fungicides and rhizobium culture on the activity of phenolic metabolism enzymes – polyphenol oxidase and guaiacol peroxidase in the early stages of the formation and functioning of various symbiotic systems Glycine max – Bradyrhizobium japonicum. In the research we used microbiological, physiological, biochemical methods, gas chromatography and spectrophotometry. The objects of the study were selected symbiotic systems formed with the participation of soybean (Glycine max (L.) Merr.), Diamond variety, strains Bradyrhizobium japonicum 634b (active, virulent) and 604k (inactive, highly virulent) and fungicides Maxim XL 035 PS (fludioxonil, 25 g/L, metalaxyl, 10 g/L), and Standak Top (fipronil, 250 g/L, thiophanate methyl, 225 g/L, piraclostrobin, 25 g/L). Before sowing, the seeds of soybean were treated with solutions of fungicides, calculated on the basis of one rate of expenditure of the active substance of each preparation indicated by the producer per ton of seed. One part of the seeds treated with fungicides was inoculated with rhizobium culture for 1 h (the titre of bacteria was 108 cells in 1 ml). The other part of the fungicide-treated seeds was not inoculated by rhizobium culture. As a result of the research, it was revealed that an effective symbiotic system formed with the participation of soybean plants and the active strain rhizobia 634b is characterized by a high level of polyphenol oxidase activity and low guaiacol peroxidase in roots and root nodules in the stages of second and third true leaves. Such changes in the activity of enzymes occurred along with the formation of nodules which actively fixed the molecular nitrogen of the atmosphere. An ineffective symbiotic system (strain 604k) is characterized by an elevated level of polyphenol oxidase activity in the roots and guaiacol peroxidase in the root nodules, which is accompanied by activation of the process of nodulation. Treatment of soybean seeds with fungicides in an effective symbiotic system leads to a change in the activity of the enzymes of the phenolic metabolism, which induced adaptive changes in plant metabolism and growth of nitrogenase activity of the root nodules. The recorded changes in the activity of both enzymes for the action of fungicides in the ineffective symbiotic system can be considered as a kind of response of the plant to the treatment and were observed along with the reduction of the processes of nodulation into the stage of the third true leaf.

The host actin cytoskeleton channels rhizobia release and facilitates symbiosome accommodation during nodulation in Medicago truncatula

In plants, the actin cytoskeleton plays a central role in regulating intracellular transport and trafficking in the endomembrane system. Work in legumes suggested that during nodulation, the actin cytoskeleton coordinates numerous cellular processes in the development of nitrogen-fixing nodules. However, we lacked live-cell visualizations demonstrating dynamic remodeling of the actin cytoskeleton during infection droplet release and symbiosome development. Here, we generated transgenic Medicago truncatula lines stably expressing the fluorescent actin marker ABD2-GFP, and utilized live-cell imaging to reveal the architecture and dynamics of the actin cytoskeleton during nodule development. Live-cell observations showed that different zones in nitrogen-fixing nodules exhibit distinct actin architectures and infected cells display five characteristic actin architectures during nodule development. Live-cell imaging combined with three-dimensional reconstruction demonstrated that dense filamentous-actin (F-actin) arrays channel the elongation of infection threads and the release of infection droplets, an F-actin network encircles freshly-released rhizobia, and short F-actin fragments and actin dots around radially distributed symbiosomes. Our findings suggest an important role of the actin cytoskeleton in infection droplet release, symbiosome development and maturation, and provide significant insight into the cellular mechanisms underlying nodule development and nitrogen fixation during legume-rhizobia interactions.

Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae

Ostreococcus tauri, a picoeukaryotic alga that contributes significantly to primary production in oligotrophic waters, has a highly streamlined genome, lacking the genetic capacity to grow without the vitamins thiamine (B₁) and cobalamin (B₁₂)_. Here we demonstrate that the B₁₂ and B₁ auxotrophy of O. tauri can be alleviated by co-culturing with a heterotrophic bacterial partner Dinoroseobacter shibae, a member of the Rhodobacteraceae family of alpha-proteobacteria, genera of which are frequently found associated with marine algae. D. shibae lacks the complete pathway to synthesise three other B-vitamins: niacin (B₃), biotin (B₇), and p-aminobenzoic acid (a precursor for folate, B₉), and the alga is in turn able to satisfy the reciprocal vitamin requirements of its bacterial partner in a stable long-term co-culture. Bioinformatics searches of 197 representative marine bacteria with sequenced genomes identified just nine species that had a similar combination of traits (ability to make vitamin B₁₂, but missing one or more genes for niacin and biotin biosynthesis enzymes), all of which were from the Rhodobacteraceae. Further analysis of 70 species from this family revealed the majority encoded the B₁₂ pathway, but only half were able to make niacin, and fewer than 13% biotin. These characteristics may have either contributed to or resulted from the tendency of members of this lineage to adopt lifestyles in close association with algae. This study provides a nuanced view of bacterial-phytoplankton interactions, emphasising the complexity of the sources, sinks and dynamic cycling between marine microbes of these important organic micronutrients.

Mechanisms Underlying Establishment of Arbuscular Mycorrhizal Symbioses

Most land plants engage in mutually beneficial interactions with arbuscular mycorrhizal (AM) fungi, the fungus providing phosphate and nitrogen in exchange for fixed carbon. During presymbiosis, both organisms communicate via oligosaccharides and butenolides. The requirement for a rice chitin receptor in symbiosis-induced lateral root development suggests that cell division programs operate in inner root tissues during both AM and nodule symbioses. Furthermore, the identification of transcription factors underpinning arbuscule development and degeneration reemphasized the plant's regulatory dominance in AM symbiosis. Finally, the finding that AM fungi, as lipid auxotrophs, depend on plant fatty acids (FAs) to complete their asexual life cycle revealed the basis for fungal biotrophy. Intriguingly, lipid metabolism is also central for asexual reproduction and interaction of the fungal sister clade, the Mucoromycotina, with endobacteria, indicative of an evolutionarily ancient role for lipids in fungal mutualism.

Uptake of bacteria into living plant cells, the unifying and distinct feature of the nitrogen-fixing root nodule symbiosis

Despite the presence of complex microbiota on the surfaces of all plants, the uptake of bacteria into plant cells and the subsequent accommodation in a membrane-enclosed compartment is restricted to the nitrogen-fixing root nodule and the Gunnera-Nostoc symbiosis. The plant cell wall and the outward-directed turgor pressure are major constraints for bacterial uptake because localised lysis of the cell wall endangers the integrity of the protoplast. Host cell integrity is consistently maintained by turgescent neighbours, connected via apoplastic polymers that seal a bacteria-containing extracellular compartment prior to localized cell wall lysis. Its unifying and almost exclusive phylogenetic distribution pinpoints the ability to take up bacteria into living plant cells as a key step during the evolution of the nitrogen-fixing root nodule symbiosis.

Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage

The expansion of plants onto land was a formative event that brought forth profound changes to the earth's geochemistry and biota. Filamentous eukaryotic microbes developed the ability to colonize plant tissues early during the evolution of land plants, as demonstrated by intimate, symbiosis-like associations in >400 million-year-old fossils. However, the degree to which filamentous microbes establish pathogenic interactions with early divergent land plants is unclear. Here, we demonstrate that the broad host-range oomycete pathogen Phytophthora palmivora colonizes liverworts, the earliest divergent land plant lineage. We show that P. palmivora establishes a complex tissue-specific interaction with Marchantia polymorpha, where it completes a full infection cycle within air chambers of the dorsal photosynthetic layer. Remarkably, P. palmivora invaginates M. polymorpha cells with haustoria-like structures that accumulate host cellular trafficking machinery and the membrane syntaxin MpSYP13B, but not the related MpSYP13A. Our results indicate that the intracellular accommodation of filamentous microbes is an ancient plant trait that is successfully exploited by pathogens like P. palmivora.

Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage

Despite the importance of liverworts as the earliest diverging land plant lineage to support fungal symbiosis, it is unknown whether filamentous pathogens can establish intracellular interactions within living cells of these nonvascular plants. Here, we demonstrate that an oomycete pathogen invades Marchantia polymorpha and related liverworts to form intracellular infection structures inside cells of the photosynthetic layer. Plants lacking this tissue layer display enhanced resistance to infection, revealing an architectural susceptibility factor in complex thalloid liverworts. Moreover, we show that dedicated host cellular trafficking proteins are recruited to pathogen interfaces within liverwort cells, supporting the idea that intracellular responses to microbial invasion originated in nonvascular plants.

The expansion of plants onto land was a formative event that brought forth profound changes to the earth’s geochemistry and biota. Filamentous eukaryotic microbes developed the ability to colonize plant tissues early during the evolution of land plants, as demonstrated by intimate, symbiosis-like associations in >400 million-year-old fossils. However, the degree to which filamentous microbes establish pathogenic interactions with early divergent land plants is unclear. Here, we demonstrate that the broad host-range oomycete pathogen Phytophthora palmivora colonizes liverworts, the earliest divergent land plant lineage. We show that P. palmivora establishes a complex tissue-specific interaction with Marchantia polymorpha, where it completes a full infection cycle within air chambers of the dorsal photosynthetic layer. Remarkably, P. palmivora invaginates M. polymorpha cells with haustoria-like structures that accumulate host cellular trafficking machinery and the membrane syntaxin MpSYP13B, but not the related MpSYP13A. Our results indicate that the intracellular accommodation of filamentous microbes is an ancient plant trait that is successfully exploited by pathogens like P. palmivora.

The Role of MPK6 as Mediator of Ethylene/Jasmonic Acid Signaling in Serendipita indica-Colonized Arabidopsis Roots

Serendipita indica is an axenically cultivable fungus, which colonizes a broad range of plant species including the model plant Arabidopsis thaliana. Root colonization by this endophyte leads to enhanced plant fitness and performance and promotes resistance against different biotic and abiotic stresses. The involvement of MPK6 in this mutualistic interaction had been previously shown with an mpk6 A. thaliana mutant, which failed to respond to S. indica colonization. Here, we demonstrate that mpk6 roots are significantly less colonized by S. indica compared to wild-type roots and the foliar application of plant hormones, ethylene, or jasmonic acid, restores the colonization rate at least to the wild-type level. Further, hormone-treated mpk6 plants show typical S. indica-induced growth promotion effects. Moreover, expression levels of several genes related to plant defense and hormone signaling are significantly changed at different colonization phases. Our results demonstrate that the successful root colonization by S. indica depends on efficient suppression of plant immune responses. In A. thaliana, this process relies on intact hormone signaling in which MPK6 seems to play a pivotal role.

Know your enemy, embrace your friend: using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms

Microorganisms, or 'microbes', have formed intimate associations with plants throughout the length of their evolutionary history. In extant plant systems microbes still remain an integral part of the ecological landscape, impacting plant health, productivity and long-term fitness. Therefore, to properly understand the genetic wiring of plants, we must first determine what perception systems plants have evolved to parse beneficial from commensal from pathogenic microbes. In this review, we consider some of the most recent advances in how plants respond at the molecular level to different microbial lifestyles. Further, we cover some of the means by which microbes are able to manipulate plant signaling pathways through altered destructiveness and nutrient sinks, as well as the use of effector proteins and micro-RNAs (miRNAs). We conclude by highlighting some of the major questions still to be answered in the field of plant-microbe research, and suggest some of the key areas that are in greatest need of further research investment. The results of these proposed studies will have impacts in a wide range of plant research disciplines and will, ultimately, translate into stronger agronomic crops and forestry stock, with immune perception and response systems bred to foster beneficial microbial symbioses while repudiating pathogenic symbioses.

A Phenotyping Method of Giant Cells from Root-Knot Nematode Feeding Sites by Confocal Microscopy Highlights a Role for CHITINASE-LIKE 1 in Arabidopsis

Most effective nematicides for the control of root-knot nematodes are banned, which demands a better understanding of the plant-nematode interaction. Understanding how gene expression in the nematode-feeding sites relates to morphological features may assist a better characterization of the interaction. However, nematode-induced galls resulting from cell-proliferation and hypertrophy hinders such observation, which would require tissue sectioning or clearing. We demonstrate that a method based on the green auto-fluorescence produced by glutaraldehyde and the tissue-clearing properties of benzyl-alcohol/benzyl-benzoate preserves the structure of the nematode-feeding sites and the plant-nematode interface with unprecedented resolution quality. This allowed us to obtain detailed measurements of the giant cells’ area in an Arabidopsis line overexpressing CHITINASE-LIKE-1 (CTL1) from optical sections by confocal microscopy, assigning a role for CTL1 and adding essential data to the scarce information of the role of gene repression in giant cells. Furthermore, subcellular structures and features of the nematodes body and tissues from thick organs formed after different biotic interactions, i.e., galls, syncytia, and nodules, were clearly distinguished without embedding or sectioning in different plant species (Arabidopsis, cucumber or Medicago). The combination of this method with molecular studies will be valuable for a better understanding of the plant-biotic interactions.

The Symbiosome: Legume and Rhizobia Co-evolution toward a Nitrogen-Fixing Organelle?

In legume nodules, symbiosomes containing endosymbiotic rhizobial bacteria act as temporary plant organelles that are responsible for nitrogen fixation, these bacteria develop mutual metabolic dependence with the host legume. In most legumes, the rhizobia infect post-mitotic cells that have lost their ability to divide, although in some nodules cells do maintain their mitotic capacity after infection. Here, we review what is currently known about legume symbiosomes from an evolutionary and developmental perspective, and in the context of the different interactions between diazotroph bacteria and eukaryotes. As a result, it can be concluded that the symbiosome possesses organelle-like characteristics due to its metabolic behavior, the composite origin and differentiation of its membrane, the retargeting of host cell proteins, the control of microsymbiont proliferation and differentiation by the host legume, and the cytoskeletal dynamics and symbiosome segregation during the division of rhizobia-infected cells. Different degrees of symbiosome evolution can be defined, specifically in relation to rhizobial infection and to the different types of nodule. Thus, our current understanding of the symbiosome suggests that it might be considered a nitrogen-fixing link in organelle evolution and that the distinct types of legume symbiosomes could represent different evolutionary stages toward the generation of a nitrogen-fixing organelle.

Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi-SlPH tomato line with reduced fruit acidity and higher pH

Background

The destructive phytopathogen Colletotrichum gloeosporioides causes anthracnose disease in fruit. During host colonization, it secretes ammonia, which modulates environmental pH and regulates gene expression, contributing to pathogenicity. However, the effect of host pH environment on pathogen colonization has never been evaluated. Development of an isogenic tomato line with reduced expression of the gene for acidity, SlPH (Solyc10g074790.1.1), enabled this analysis. Total RNA from C. gloeosporioides colonizing wild-type (WT) and RNAi–SlPH tomato lines was sequenced and gene-expression patterns were compared.

Results

C. gloeosporioides inoculation of the RNAi–SlPH line with pH 5.96 compared to the WT line with pH 4.2 showed 30% higher colonization and reduced ammonia accumulation. Large-scale comparative transcriptome analysis of the colonized RNAi–SlPH and WT lines revealed their different mechanisms of colonization-pattern activation: whereas the WT tomato upregulated 13-LOX (lipoxygenase), jasmonic acid and glutamate biosynthesis pathways, it downregulated processes related to chlorogenic acid biosynthesis II, phenylpropanoid biosynthesis and hydroxycinnamic acid tyramine amide biosynthesis; the RNAi–SlPH line upregulated UDP-D-galacturonate biosynthesis I and free phenylpropanoid acid biosynthesis, but mainly downregulated pathways related to sugar metabolism, such as the glyoxylate cycle and L-arabinose degradation II. Comparison of C. gloeosporioides gene expression during colonization of the WT and RNAi–SlPH lines showed that the fungus upregulates ammonia and nitrogen transport and the gamma-aminobutyric acid metabolic process during colonization of the WT, while on the RNAi–SlPH tomato, it mainly upregulates the nitrate metabolic process.

Conclusions

Modulation of tomato acidity and pH had significant phenotypic effects on C. gloeosporioides development. The fungus showed increased colonization on the neutral RNAi–SlPH fruit, and limited colonization on the WT acidic fruit. The change in environmental pH resulted in different defense responses for the two tomato lines. Interestingly, the WT line showed upregulation of jasmonate pathways and glutamate accumulation, supporting the reduced symptom development and increased ammonia accumulation, as the fungus might utilize glutamate to accumulate ammonia and increase environmental pH for better expression of pathogenicity factors. This was not found in the RNAi–SlPH line which downregulated sugar metabolism and upregulated the phenylpropanoid pathway, leading to host susceptibility.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3961-6) contains supplementary material, which is available to authorized users.

Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases

The fungal lineage is one of the three large eukaryotic lineages that dominate terrestrial ecosystems. They share a common ancestor with animals in the eukaryotic supergroup Opisthokonta and have a deeper common ancestry with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among all living organisms. This article provides an overview of some of the most important fungal traits, how they evolve, and what major genes and gene families contribute to their development. The traits highlighted here represent just a sample of the characteristics that have evolved in fungi, including polarized multicellular growth, fruiting body development, dimorphism, secondary metabolism, wood decay, and mycorrhizae. However, a great number of other important traits also underlie the evolution of the taxonomically and phenotypically hyperdiverse fungal kingdom, which could fill up a volume on its own. After reviewing the evolution of these six well-studied traits in fungi, we discuss how the recurrent evolution of phenotypic similarity, that is, convergent evolution in the broad sense, has shaped their phylogenetic distribution in extant species.

The Abundance of Endofungal Bacterium Rhizobium radiobacter (syn. Agrobacterium tumefaciens) Increases in Its Fungal Host Piriformospora indica during the Tripartite Sebacinalean Symbiosis with Higher Plants

Rhizobium radiobacter (syn. Agrobacterium tumefaciens, syn. "Agrobacterium fabrum") is an endofungal bacterium of the fungal mutualist Piriformospora (syn. Serendipita) indica (Basidiomycota), which together form a tripartite Sebacinalean symbiosis with a broad range of plants. R. radiobacter strain F4 (RrF4), isolated from P. indica DSM 11827, induces growth promotion and systemic resistance in cereal crops, including barley and wheat, suggesting that R. radiobacter contributes to a successful symbiosis. Here, we studied the impact of endobacteria on the morphology and the beneficial activity of P. indica during interactions with plants. Low numbers of endobacteria were detected in the axenically grown P. indica (long term lab-cultured, lcPiri) whereas mycelia colonizing the plant root contained increased numbers of bacteria. Higher numbers of endobacteria were also found in axenic cultures of P. indica that was freshly re-isolated (riPiri) from plant roots, though numbers dropped during repeated axenic re-cultivation. Prolonged treatments of P. indica cultures with various antibiotics could not completely eliminate the bacterium, though the number of detectable endobacteria decreased significantly, resulting in partial-cured P. indica (pcPiri). pcPiri showed reduced growth in axenic cultures and poor sporulation. Consistent with this, pcPiri also showed reduced plant growth promotion and reduced systemic resistance against powdery mildew infection as compared with riPiri and lcPiri. These results are consistent with the assumption that the endobacterium R. radiobacter improves P. indica's fitness and thus contributes to the success of the tripartite Sebacinalean symbiosis.

The prediction of a pathogenesis-related secretome of Puccinia helianthi through high-throughput transcriptome analysis

Background

Many plant pathogen secretory proteins are known to be elicitors or pathogenic factors,which play an important role in the host-pathogen interaction process. Bioinformatics approaches make possible the large scale prediction and analysis of secretory proteins from the Puccinia helianthi transcriptome. The internet-based software SignalP v4.1, TargetP v1.01, Big-PI predictor, TMHMM v2.0 and ProtComp v9.0 were utilized to predict the signal peptides and the signal peptide-dependent secreted proteins among the 35,286 ORFs of the P. helianthi transcriptome.

Results

908 ORFs (accounting for 2.6% of the total proteins) were identified as putative secretory proteins containing signal peptides. The length of the majority of proteins ranged from 51 to 300 amino acids (aa), while the signal peptides were from 18 to 20 aa long. Signal peptidase I (SpI) cleavage sites were found in 463 of these putative secretory signal peptides. 55 proteins contained the lipoprotein signal peptide recognition site of signal peptidase II (SpII). Out of 908 secretory proteins, 581 (63.8%) have functions related to signal recognition and transduction, metabolism, transport and catabolism. Additionally, 143 putative secretory proteins were categorized into 27 functional groups based on Gene Ontology terms, including 14 groups in biological process, seven in cellular component, and six in molecular function. Gene ontology analysis of the secretory proteins revealed an enrichment of hydrolase activity. Pathway associations were established for 82 (9.0%) secretory proteins. A number of cell wall degrading enzymes and three homologous proteins specific to Phytophthora sojae effectors were also identified, which may be involved in the pathogenicity of the sunflower rust pathogen.

Conclusions

This investigation proposes a new approach for identifying elicitors and pathogenic factors. The eventual identification and characterization of 908 extracellularly secreted proteins will advance our understanding of the molecular mechanisms of interactions between sunflower and rust pathogen and will enhance our ability to intervene in disease states.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1577-0) contains supplementary material, which is available to authorized users.

Interface Symbiotic Membrane Formation in Root Nodules of Medicago truncatula: the Role of Synaptotagmins MtSyt1, MtSyt2 and MtSyt3

Symbiotic bacteria (rhizobia) are maintained and conditioned to fix atmospheric nitrogen in infected cells of legume root nodules. Rhizobia are confined to the asymmetrical protrusions of plasma membrane (PM): infection threads (IT), cell wall-free unwalled droplets and symbiosomes. These compartments rapidly increase in surface and volume due to the microsymbiont expansion, and remarkably, the membrane resources of the host cells are targeted to interface membrane quite precisely. We hypothesized that the change in the membrane tension around the expanding microsymbionts creates a vector for membrane traffic toward the symbiotic interface. To test this hypothesis, we selected calcium sensors from the group of synaptotagmins: MtSyt1, Medicago truncatula homolog of AtSYT1 from Arabidopsis thaliana known to be involved in membrane repair, and two other homologs expressed in root nodules: MtSyt2 and MtSyt3. Here we show that MtSyt1, MtSyt2, and MtSyt3 are expressed in the expanding cells of the meristem, zone of infection and proximal cell layers of zone of nitrogen fixation (MtSyt1, MtSyt3). All three GFP-tagged proteins delineate the interface membrane of IT and unwalled droplets and create a subcompartments of PM surrounding these structures. The localization of MtSyt1 by EM immunogold labeling has shown the signal on symbiosome membrane and endoplasmic reticulum (ER). To specify the role of synaptotagmins in interface membrane formation, we compared the localization of MtSyt1, MtSyt3 and exocyst subunit EXO70i, involved in the tethering of post-Golgi secretory vesicles and operational in tip growth. The localization of EXO70i in root nodules and arbusculated roots was strictly associated with the tips of IT and the tips of arbuscular fine branches, but the distribution of synaptotagmins on membrane subcompartments was broader and includes lateral parts of IT, the membrane of unwalled droplets as well as the symbiosomes. The double silencing of synaptotagmins caused a delay in rhizobia release and blocks symbiosome maturation confirming the functional role of synaptotagmins.

IN CONCLUSION

synaptotagmin-dependent membrane fusion along with tip-targeted exocytosis is operational in the formation of symbiotic interface.

Structural features of the aromatic/arginine constriction in the aquaglyceroporin GintAQPF2 are responsible for glycerol impermeability in arbuscular mycorrhizal symbiosis

Carbon transport in arbuscular mycorrhizal (AM) symbiosis is of fundamental importance. However, the role of glycerol transport in AM symbiosis has not yet been resolved. Glycerol transport across the cell membrane is mediated by aquaglyceroporins (AQGPs), whereas our previous study revealed that it was disfavoured by GintAQPF2, an AQGP from AM fungi (AMF). Here, we analysed the function of two amino acid residues in the aromatic/arginine (ar/R) constriction known as the major selectivity filter in AQGPs. Replacement of phenylalanine-94 (Phe-94) by alanine (Ala) enlarged the diameter of the ar/R constriction and resulted in an increased intracellular glycerol accumulation and thus survival rate of yeast cells at high glycerol levels, while individual or joint replacement of Phe-94 and Ala-234 by tryptophan and glycine induced a closed state of GintAQPF2, suggesting that the potential double gates (Phe94-Phe243 and arginine-249) of the ar/R constriction also likely determined solute permeability. To figure out whether GintAQPF2 functions were relevant to the establishment of AM symbiosis, genomic analyses of four representative fungi with different lifestyles were performed. We found that glycerol facilitators existed in the facultative fungi (the ectomycorrhizal fungus Laccaria bicolor and hemibiotrophic pathogen Magnaporthe oryzae), but not in the obligatory fungi (the AMF Rhizophagus irregularis and necrotrophic pathogen Fusarium verticillioides), revealing a conserved pattern of glycerol transport in symbionts and pathogens. Our results suggested that glycerol blocks due to the special structural features of the ar/R constriction in the only AMF AQGP could potentially play a role in the establishment of AM symbiosis.

A symbiosis-dedicated SYNTAXIN OF PLANTS 13II isoform controls the formation of a stable host-microbe interface in symbiosis

Arbuscular mycorrhizal (AM) fungi and rhizobium bacteria are accommodated in specialized membrane compartments that form a host-microbe interface. To better understand how these interfaces are made, we studied the regulation of exocytosis during interface formation. We used a phylogenetic approach to identify target soluble N-ethylmaleimide-sensitive factor-attachment protein receptors (t-SNAREs) that are dedicated to symbiosis and used cell-specific expression analysis together with protein localization to identify t-SNAREs that are present on the host-microbe interface in Medicago truncatula. We investigated the role of these t-SNAREs during the formation of a host-microbe interface. We showed that multiple syntaxins are present on the peri-arbuscular membrane. From these, we identified SYNTAXIN OF PLANTS 13II (SYP13II) as a t-SNARE that is essential for the formation of a stable symbiotic interface in both AM and rhizobium symbiosis. In most dicot plants, the SYP13II transcript is alternatively spliced, resulting in two isoforms, SYP13IIα and SYP13IIβ. These splice-forms differentially mark functional and degrading arbuscule branches. Our results show that vesicle traffic to the symbiotic interface is specialized and required for its maintenance. Alternative splicing of SYP13II allows plants to replace a t-SNARE involved in traffic to the plasma membrane with a t-SNARE that is more stringent in its localization to functional arbuscules.

Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus

Crop wild relatives are valuable resources for future genetic improvement. Here, we report the de novo genome assembly of Musa itinerans, a disease-resistant wild banana relative in subtropical China. The assembled genome size was 462.1 Mb, covering 75.2% of the genome (615.2Mb) and containing 32, 456 predicted protein-coding genes. Since the approximate divergence around 5.8 million years ago, the genomes of Musa itinerans and Musa acuminata have shown conserved collinearity. Gene family expansions and contractions enrichment analysis revealed that some pathways were associated with phenotypic or physiological innovations. These include a transition from wood to herbaceous in the ancestral Musaceae, intensification of cold and drought tolerances, and reduced diseases resistance genes for subtropical marginally distributed Musa species. Prevalent purifying selection and transposed duplications were found to facilitate the diversification of NBS-encoding gene families for two Musa species. The population genome history analysis of M. itinerans revealed that the fluctuated population sizes were caused by the Pleistocene climate oscillations, and that the formation of Qiongzhou Strait might facilitate the population downsizing on the isolated Hainan Island about 10.3 Kya. The qualified assembly of the M. itinerans genome provides deep insights into the lineage-specific diversification and also valuable resources for future banana breeding.

Extracellular Recognition of Oomycetes during Biotrophic Infection of Plants

Extracellular recognition of pathogens by plants constitutes an important early detection system in plant immunity. Microbe-derived molecules, also named patterns, can be recognized by pattern recognition receptors (PRRs) on the host cell membrane that trigger plant immune responses. Most knowledge on extracellular pathogen detection by plants comes from research on bacterial and fungal pathogens. For oomycetes, that comprise some of the most destructive plant pathogens, mechanisms of extracellular pattern recognition have only emerged recently. These include newly recognized patterns, e.g., cellulose-binding elicitor lectin, necrosis and ethylene-inducing peptide 1-like proteins (NLPs), and glycoside hydrolase 12, as well as their receptors, e.g., the putative elicitin PRR elicitin response and the NLP PRR receptor-like protein 23. Immunity can also be triggered by the release of endogenous host-derived patterns, as a result of oomycete enzymes or damage. In this review we will describe the types of patterns, both pathogen-derived exogenous and plant-derived endogenous ones, and what is known about their extracellular detection during (hemi-)biotrophic oomycete infection of plants.

Deciphering endophyte behaviour: the link between endophyte biology and efficacious biological control agents

Endophytes associate with the majority of plant species found in natural and managed ecosystems. They are regarded as extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Fossil records of endophytes date back more than 400 million years, implicating these microorganisms in host plant adaptation to habitat transitions. However, it is only recently that endophytes, and their bioactive products, have received meaningful attention from the scientific community. The benefits some endophytes can confer on their hosts include plant growth promotion and survival through the inhibition of pathogenic microorganisms and invertebrate pests, the removal of soil contaminants, improved tolerance of low fertility soils, and increased tolerance of extreme temperatures and low water availability. Endophytes are extremely diverse and can exhibit many different biological behaviours. Not all endophyte technologies have been successfully commercialised. Of interest in the development of the next generation of plant protection products is how much of this is due to the biology of the particular endophytic microorganism. In this review, we highlight selected case studies of endophytes and discuss their lifestyles and behavioural traits, and discuss how these factors contribute towards their effectiveness as biological control agents.

The effector candidate repertoire of the arbuscular mycorrhizal fungus Rhizophagus clarus

Background

Arbuscular mycorrhizal fungi (AMF) form an ecologically important symbiosis with more than two thirds of studied land plants. Recent studies of plant-pathogen interactions showed that effector proteins play a key role in host colonization by controlling the plant immune system. We hypothesise that also for symbiotic-plant interactions the secreted effectome of the fungus is a major component of communication and the conservation level of effector proteins between AMF species may be indicative whether they play a fundamental role.

Results

In this study, we used a bioinformatics pipeline to predict and compare the effector candidate repertoire of the two AMF species, Rhizophagus irregularis and Rhizophagus clarus. Our in silico pipeline revealed a list of 220 R. irregularis candidate effector genes that create a valuable information source to elucidate the mechanism of plant infection and colonization by fungi during AMF symbiotic interaction. While most of the candidate effectors show no homologies to known domains or proteins, the candidates with homologies point to potential roles in signal transduction, cell wall modification or transcription regulation. A remarkable aspect of our work is presence of a large portion of the effector proteins involved in symbiosis, which are not unique to each fungi or plant species, but shared along the Glomeromycota phylum. For 95 % of R. irregularis candidates we found homologs in a R. clarus genome draft generated by Illumina high-throughput sequencing. Interestingly, 9 % of the predicted effectors are at least as conserved between the two Rhizophagus species as proteins with housekeeping functions (similarity > 90 %). Therefore, we state that this group of highly conserved effector proteins between AMF species may play a fundamental role during fungus-plant interaction.

Conclusions

We hypothesise that in symbiotic interactions the secreted effectome of the fungus might be an important component of communication. Identification and functional characterization of the primary AMF effectors that regulate symbiotic development will help in understanding the mechanisms of fungus-plant interaction.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2422-y) contains supplementary material, which is available to authorized users.

Gall-forming root-knot nematodes hijack key plant cellular functions to induce multinucleate and hypertrophied feeding cells

Among plant-parasitic nematodes, the root-knot nematodes (RKNs) of the Meloidogyne spp. are the most economically important genus. RKN are root parasitic worms able to infect nearly all crop species and have a wide geographic distribution. During infection, RKNs establish and maintain an intimate relationship with the host plant. This includes the creation of a specialized nutritional structure composed of multinucleate and hypertrophied giant cells, which result from the redifferentiation of vascular root cells. Giant cells constitute the sole source of nutrients for the nematode and are essential for growth and reproduction. Hyperplasia of surrounding root cells leads to the formation of the gall or root-knot, an easily recognized symptom of plant infection by RKNs. Secreted effectors produced in nematode salivary glands and injected into plant cells through a specialized feeding structure called the stylet play a critical role in the formation of giant cells. Here, we describe the complex interactions between RKNs and their host plants. We highlight progress in understanding host plant responses, focusing on how RKNs manipulate key plant processes and functions, including cell cycle, defence, hormones, cellular scaffold, metabolism and transport.

Haustorium Formation in Medicago truncatula Roots Infected by Phytophthora palmivora Does Not Involve the Common Endosymbiotic Program Shared by Arbuscular Mycorrhizal Fungi and Rhizobia

In biotrophic plant-microbe interactions, microbes infect living plant cells, in which they are hosted in a novel membrane compartment, the host-microbe interface. To create a host-microbe interface, arbuscular mycorrhizal (AM) fungi and rhizobia make use of the same endosymbiotic program. It is a long-standing hypothesis that pathogens make use of plant proteins that are dedicated to mutualistic symbiosis to infect plants and form haustoria. In this report, we developed a Phytophthora palmivora pathosystem to study haustorium formation in Medicago truncatula roots. We show that P. palmivora does not require host genes that are essential for symbiotic infection and host-microbe interface formation to infect Medicago roots and form haustoria. Based on these findings, we conclude that P. palmivora does not hijack the ancient intracellular accommodation program used by symbiotic microbes to form a biotrophic host-microbe interface.

Modulation of host cell biology by plant pathogenic microbes

Plant-pathogen interactions can result in dramatic visual changes in the host, such as galls, phyllody, pseudoflowers, and altered root-system architecture, indicating that the invading microbe has perturbed normal plant growth and development. These effects occur on a cellular level but range up to the organ scale, and they commonly involve attenuation of hormone homeostasis and deployment of effector proteins with varying activities to modify host cell processes. This review focuses on the cellular-reprogramming mechanisms of filamentous and bacterial plant pathogens that exhibit a biotrophic lifestyle for part, if not all, of their lifecycle in association with the host. We also highlight strategies for exploiting our growing knowledge of microbial host reprogramming to study plant processes other than immunity and to explore alternative strategies for durable plant resistance.

Friend or foe: differential responses of rice to invasion by mutualistic or pathogenic fungi revealed by RNAseq and metabolite profiling

The rice endophyte Harpophora oryzae shares a common pathogenic ancestor with the rice blast fungus Magnaporthe oryzae. Direct comparison of the interactions between a single plant species and two closely-related (1) pathogenic and (2) mutualistic fungi species can improve our understanding of the evolution of the interactions between plants and fungi that lead to either mutualistic or pathogenic interactions. Differences in the metabolome and transcriptome of rice in response to challenge by H. or M. oryzae were investigated with GC-MS, RNA-seq, and qRT-PCR. Levels of metabolites of the shikimate and lignin biosynthesis pathways increased continuously in the M. oryzae-challenged rice roots (Mo-roots); these pathways were initially induced, but then suppressed, in the H. oryzae-challenged rice roots (Ho-roots). Compared to control samples, concentrations of sucrose and maltose were reduced in the Ho-roots and Mo-roots. The expression of most genes encoding enzymes involved in glycolysis and the TCA cycle were suppressed in the Ho-roots, but enhanced in the Mo-roots. The suppressed glycolysis in Ho-roots would result in the accumulation of glucose and fructose which was not detected in the Mo-roots. A novel co-evolution pattern of fungi-host interaction is proposed which highlights the importance of plant host in the evolution of fungal symbioses.