New insights into the signaling pathways controlling defense gene expression in rice roots during the arbuscular mycorrhizal symbiosis

Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi

The synergy between bacteria and fungi is a key determinant of soil health and have a positive effect on plant development under drought conditions, with the potentially enhancing the sustainability of amending soil with natural materials. However, identifying how soil amendments influence plant growth is often difficult due to the complexity of microorganisms and their links with different soil amendment types and environmental factors. To address this, we conducted a field experiment to examine the impact of soil amendments (biochar, Bacillus mucilaginosus, Bacillus subtilis and super absorbent polymer) on plant growth. We also assessed variations in microbial community, links between fungi and bacteria, and soil available nutrients, while exploring how the synergistic effects between fungus and bacteria influenced the response of soil amendments to plant growth. This study revealed that soil amendments reduced soil bacterial diversity but increased the proportion of the family Enterobacteriaceae, Nitrosomonadaceae, and also increased soil fungal diversity and the proportion of the sum of the family Lasiosphaeriaceae, Chaetomiaceae, Pleosporaceae. Changes in soil microbial communities lead to increase the complexity of microbial co-occurrence networks. Furthermore, this heightened network complexity enhanced the synergy of soil bacteria and fungi, supporting bacterial functions related to soil nutrient cycling, such as metabolic functions and genetic, environmental, and cellular processes. Hence, the BC and BS had 3.0-fold and 0.5-fold greater root length densities than CK and apple tree shoot growth were increased by 62.14 %,50.53 % relative to CK, respectively. In sum, our results suggest that the synergistic effect of bacteria and fungi impacted apple tree growth indirectly by modulating soil nutrient cycling. These findings offer a new strategy for enhancing the quality of arable land in arid and semi-arid regions.

Organ-specific responses during acclimation of mycorrhizal and non-mycorrhizal tomato plants to a mild water stress reveal differential local and systemic hormonal and nutritional adjustments

MAIN CONCLUSION

Tomato plant acclimation to a mild water stress implied tissue-specific hormonal and nutrient adjustments, being the root one of the main modulators of this response. Phytohormones are key regulators of plant acclimation to water stress. However, it is not yet clear if these hormonal responses follow specific patterns depending on the plant tissue. In this study, we evaluated the organ-specific physiological and hormonal responses to a 14 day-long mild water stress in tomato plants (Solanum lycopersicum cv. Moneymaker) in the presence or absence of the arbuscular mycorrhizal fungus Rhizoglomus irregulare, a frequently used microorganism in agriculture. Several physiological, production, and nutritional parameters were evaluated throughout the experiments. Additionally, endogenous hormone levels in roots, leaves, and fruits at different developmental stages were quantified by ultrahigh-performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS). Water deficit drastically reduced shoot growth, while it did not affect fruit production. In contrast, fruit production was enhanced by mycorrhization regardless of the water treatment. The main tissue affected by water stress was the root system, where huge rearrangements in different nutrients and stress-related and growth hormones took place. Abscisic acid content increased in every tissue and fruit developmental stage, suggesting a systemic response to drought. On the other hand, jasmonate and cytokinin levels were generally reduced upon water stress, although this response was dependent on the tissue and the hormonal form. Finally, mycorrhization improved plant nutritional status content of certain macro and microelements, specially at the roots and ripe fruits, while it affected jasmonate response in the roots. Altogether, our results suggest a complex response to drought that consists in systemic and local combined hormonal and nutrient responses.

A transcriptional activator from Rhizophagus irregularis regulates phosphate uptake and homeostasis in AM symbiosis during phosphorous starvation

Introduction

Phosphorus (P) is one of the most important nutrient elements for plant growth and development. Under P starvation, arbuscular mycorrhizal (AM) fungi can promote phosphate (Pi) uptake and homeostasis within host plants. However, the underlying mechanisms by which AM fungal symbiont regulates the AM symbiotic Pi acquisition from soil under P starvation are largely unknown. Here, we identify a HLH domain containing transcription factor RiPho4 from Rhizophagus irregularis.

Methods

To investigate the biological functions of the RiPho4, we combined the subcellular localization and Yeast One-Hybrid (Y1H) experiments in yeasts with gene expression and virus-induced gene silencing approach during AM symbiosis.

Results

The approach during AM symbiosis. The results indicated that RiPho4 encodes a conserved transcription factor among different fungi and is induced during the in planta phase. The transcription of RiPho4 is significantly up-regulated by P starvation. The subcellular localization analysis revealed that RiPho4 is located in the nuclei of yeast cells during P starvation. Moreover, knock-down of RiPho4 inhibits the arbuscule development and mycorrhizal Pi uptake under low Pi conditions. Importantly, RiPho4 can positively regulate the downstream components of the phosphate (PHO) pathway in R. irregularis.

Discussion

In summary, these new findings reveal that RiPho4 acts as a transcriptional activator in AM fungus to maintain arbuscule development and regulate Pi uptake and homeostasis in the AM symbiosis during Pi starvation.

Effect of Glyphosate and Carbaryl Applications on Okra (Abelmoschus esculentus) Biomass and Arbuscular Mycorrhizal Fungi (AMF) Root Colonization in Organic Soil

Pesticide application in horticultural crops has recently multiplied to increase crop yields and boost economic return. Consequently, the effects of pesticides on soil organisms and plant symbionts is an evolving subject of research. In this short-term study, we evaluated the effects of glyphosate (herbicide) and carbaryl (insecticide) on okra biomass and AMF root colonization in both shade house and field settings. An additional treatment, the combination of glyphosate and carbaryl, was applied in the field trial. Soil and root samples were collected three times during the experiment: 30 days after planting (before first spray, or T0), 45 days after planting (before second spray, or T1), and at full maturity (at 66 days after planting, or T2). Our results indicate that glyphosate and combined treatments were most effective in controlling weeds and produced almost 40% higher okra biomass than the control. There was a ~40% increase in AMF root colonization in glyphosate-treated plots from T0 to T1. This result was likely due to high initial soil P content, high soil temperature, and low rainfall, which aided in the rapid degradation of glyphosate in the soil. However, at T2 (second spray), high rainfall and the presence of excess glyphosate resulted in a 15% reduction in AMF root colonization when compared to T1. We found carbaryl had little to negligible effect on AMF root colonization.

Effects of nitrogen deposition and phosphorus addition on arbuscular mycorrhizal fungi of Chinese fir (Cunninghamia lanceolata)

Nitrogen (N) deposition is a key factor that affects terrestrial biogeochemical cycles with a growing trend, especially in the southeast region of China, where shortage of available phosphorus (P) is particularly acute and P has become a major factor limiting plant growth and productivity. Arbuscular mycorrhizal fungi (AMF) establish a mutualistic symbiosis with plants, and play an important role in enhancing plant stress resistance. However, the response of AMF to the combined effects of N deposition and P additions is poorly understood. Thus, in this study, a field experiment was conducted in 10-year Chinese fir forests to estimate the effects of simulated nitrogen (N) deposition (low-N, 30 kg ha-1 year-1 and high-N, 60 kg ha-1 year-1) and phosphorus (P) addition treatments (low-P, 20 mg kg-1 and high-P, 40 mg kg-1) on AMF since April 2017, which was reflected in AMF root colonization rates and spore density of rhizosphere soil. Our results showed that N deposition significantly decreased AMF root colonization rates and spore density. In N-free plots, P addition significantly decreased AMF root colonization rates, but did not significantly alter spore density. In low-N plots, colonization rates significantly decreased under low P addition, but significantly increased under high P addition, and spore density exhibited a significant decline under high P additions. In high-N plots, colonization rates and spore density significantly increased under P additions. Interactive effects of simulated N deposition and P addition on both colonization rates and spore density were significant. Moderate N deposition or P addition can weaken the symbiotic relationship between plants and AMF, significantly reducing AMF colonization rates and inhibiting spore production. However, a moderate addition of P greatly enhances spore yield. In the case of interactive effects, the AMF colonization rates and spore density are affected by the relative content of N and P in the soil.

Omics approaches revealed how arbuscular mycorrhizal symbiosis enhances yield and resistance to leaf pathogen in wheat

Besides improved mineral nutrition, plants colonised by arbuscular mycorrhizal (AM) fungi often display increased biomass and higher tolerance to biotic and abiotic stresses. Notwithstanding the global importance of wheat as an agricultural crop, its response to AM symbiosis has been poorly investigated. We focused on the role of an AM fungus on mineral nutrition of wheat, and on its potential protective effect against Xanthomonas translucens. To address these issues, phenotypical, molecular and metabolomic approaches were combined. Morphological observations highlighted that AM wheat plants displayed an increased biomass and grain yield, as well as a reduction in lesion area following pathogen infection. To elucidate the molecular mechanisms underlying the mycorrhizal phenotype, we investigated changes of transcripts and proteins in roots and leaves during the double (wheat-AM fungus) and tripartite (wheat-AM fungus-pathogen) interaction. Transcriptomic and proteomic profiling identified the main pathways involved in enhancing plant biomass, mineral nutrition and in promoting the bio-protective effect against the leaf pathogen. Mineral and amino acid contents in roots, leaves and seeds, and protein oxidation profiles in leaves, supported the omics data, providing new insight into the mechanisms exerted by AM symbiosis to confer stronger productivity and enhanced resistance to X. translucens in wheat.

The enhancement by arbuscular mycorrhizal fungi of the Cd remediation ability and bioenergy quality-related factors of five switchgrass cultivars in Cd-contaminated soil

A greenhouse experiment was carried out to investigate the effects of arbuscular mycorrhizal fungi (AMF) on the growth, P and Cd concentrations and bioenergy quality-related factors of five cultivars of switchgrass, including three lowland cultivars (Alamo (Ala), Kanlow (Kan), Performer (Per)) and two highland cultivars (Blackwell (Bw), Summer (Sum)), with 0, 1 and 10 mg/kg Cd addition levels. The results showed that AMF inoculation notably increased the biomass and P concentrations of all the cultivars. The Cd concentrations in the roots were higher than those in the shoots of all cultivars irrespective of inoculation, but the AMF had different effects on Cd accumulation in highland and lowland cultivars. AMF inoculation decreased the shoot and root concentrations in Ala and Kan, increased the shoot and root concentrations of Cd in Bw and Sum, and increased shoot Cd concentrations and decreased root Cd concentrations in Per. The highest Cd concentrations were detected in the roots of Bw and in the shoots of Sum with AMF symbiosis. Bw contained the highest total extracted Cd which was primarily in the roots. Ala had the second highest extracted Cd in the shoots, reaching 32% with 1 mg/kg of added Cd, whereas Sum had the lowest extracted Cd. AMF symbiosis had varied effects on bioenergy quality-related factors: for example, AMF decreased the ash lignin content in Ala and the C/N in Sum, increased the nitrogen, gross calorie values, and maintained the hemicellulose and cellulose contents in all cultivars with all tested concentrations of Cd. A principal component analysis (PCA) showed that AMF inoculation could enhance, weaken or transform (positive-negative, PC1-PC2) the correlations of these factors with the principle components under Cd stress. Therefore, AMF symbiosis enhanced the growth of different cultivars of switchgrass, increased/decreased Cd accumulation, promoted Cd extraction, and regulated the bioenergy quality-related factors in Cd-polluted areas. Bw is a suitable cultivar for phytostabilization due to high root Cd stabilization, whereas Ala is an appropriate cultivar for phytoremediation of less polluted areas because of its high Cd extraction and excellent bioenergy quality.

The Nitrogen Availability Interferes with Mycorrhiza-Induced Resistance against Botrytis cinerea in Tomato

Mycorrhizal plants are generally quite efficient in coping with environmental challenges. It has been shown that the symbiosis with arbuscular mycorrhizal fungi (AMF) can confer resistance against root and foliar pathogens, although the molecular mechanisms underlying such mycorrhiza-induced resistance (MIR) are poorly understood. Tomato plants colonized with the AMF Rhizophagus irregularis display enhanced resistance against the necrotrophic foliar pathogen Botrytis cinerea. Leaves from arbuscular mycorrhizal (AM) plants develop smaller necrotic lesions, mirrored also by a reduced levels of fungal biomass. A plethora of metabolic changes takes place in AMF colonized plants upon infection. Certain changes located in the oxylipin pathway indicate that several intermediaries are over-accumulated in the AM upon infection. AM plants react by accumulating higher levels of the vitamins folic acid and riboflavin, indolic derivatives and phenolic compounds such as ferulic acid and chlorogenic acid. Transcriptional analysis support the key role played by the LOX pathway in the shoots associated with MIR against B. cinerea. Interestingly, plants that have suffered a short period of nitrogen starvation appear to react by reprogramming their metabolic and genetic responses by prioritizing abiotic stress tolerance. Consequently, plants subjected to a transient nitrogen depletion become more susceptible to B. cinerea. Under these experimental conditions, MIR is severely affected although still functional. Many metabolic and transcriptional responses which are accumulated or activated by MIR such NRT2 transcript induction and OPDA and most Trp and indolic derivatives accumulation during MIR were repressed or reduced when tomato plants were depleted of N for 48 h prior infection. These results highlight the beneficial roles of AMF in crop protection by promoting induced resistance not only under optimal nutritional conditions but also buffering the susceptibility triggered by transient N depletion.

Contrasting Regulation of NO and ROS in Potato Defense-Associated Metabolism in Response to Pathogens of Different Lifestyles

Our research provides new insights into how the low and steady-state levels of nitric oxide (NO) and reactive oxygen species (ROS) in potato leaves are altered after the challenge with the hemibiotroph Phytophthora infestans or the necrotroph Botrytis cinerea, with the subsequent rapid and invader-dependent modification of defense responses with opposite effects. Mainly in the avirulent (avr) P. infestans–potato system, NO well balanced with the superoxide level was tuned with a battery of SA-dependent defense genes, leading to the establishment of the hypersensitive response (HR) successfully arresting the pathogen. Relatively high levels of S-nitrosoglutathione and S-nitrosothiols concentrated in the main vein of potato leaves indicated the mobile function of these compounds as a reservoir of NO bioactivity. In contrast, low-level production of NO and ROS during virulent (vr) P. infestans-potato interactions might be crucial in the delayed up-regulation of PR-1 and PR-3 genes and compromised resistance to the hemibiotrophic pathogen. In turn, B. cinerea triggered huge NO overproduction and governed inhibition of superoxide production by blunting NADPH oxidase. Nevertheless, a relatively high level of H₂O₂ was found owing to the germin-like activity in cooperation with NO-mediated HR-like cell death in potato genotypes favorable to the necrotrophic pathogen. Moreover, B. cinerea not only provoked cell death, but also modulated the host redox milieu by boosting protein nitration, which attenuated SA production but not SA-dependent defense gene expression. Finally, based on obtained data the organismal cost of having machinery for HR in plant resistance to biotrophs is also discussed, while emphasizing new efforts to identify other components of the NO/ROS cell death pathway and improve plant protection against pathogens of different lifestyles.

Stress promotes Arabidopsis - Piriformospora indica interaction

The endophytic fungus Piriformospora indica colonizes Arabidopsis thaliana roots and promotes plant performance, growth and resistance/tolerance against abiotic and biotic stress. Here we demonstrate that the benefits for the plant increase when the two partners are co-cultivated under stress (limited access to nutrient, exposure to heavy metals and salt, light and osmotic stress, pathogen infection). Moreover, physical contact between P. indica and Arabidopsis roots is necessary for optimal growth promotion, and chemical communication cannot replace the physical contact. Lower nutrient availability down-regulates and higher nutrient availability up-regulates the plant defense system including the expression of pathogenesis-related genes in roots. High light, osmotic and salt stresses support the beneficial interaction between the plant and the fungus. P. indica reduces stomata closure and H2O2 production after Alternaria brassicae infection in leaves and suppresses the defense-related accumulation of the phytohormone jasmonic acid. Thus, shifting the growth conditions toward a stress promotes the mutualistic interaction, while optimal supply with nutrients or low stress diminishes the benefits for the plant in the symbiosis.

The interaction of Arabidopsis with Piriformospora indica shifts from initial transient stress induced by fungus-released chemical mediators to a mutualistic interaction after physical contact of the two symbionts

BACKGROUND

Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of many plant species including Arabidopsis thaliana. The symbiotic interaction promotes plant performance, growth and resistance/tolerance against abiotic and biotic stress.

RESULTS

We demonstrate that exudated compounds from the fungus activate stress and defense responses in the Arabidopsis roots and shoots before the two partners are in physical contact. They induce stomata closure, stimulate reactive oxygen species (ROS) production, stress-related phytohormone accumulation and activate defense and stress genes in the roots and/or shoots. Once a physical contact is established, the stomata re-open, ROS and phytohormone levels decline, and the number and expression level of defense/stress-related genes decreases.

CONCLUSIONS

We propose that exudated compounds from P. indica induce stress and defense responses in the host. Root colonization results in the down-regulation of defense responses and the activation of genes involved in promoting plant growth, metabolism and performance.

Defense related phytohormones regulation in arbuscular mycorrhizal symbioses depends on the partner genotypes

Arbuscular mycorrhizal (AM) symbioses are mutualistic associations between soil fungi and most vascular plants. Modulation of the hormonal and transcriptional profiles, including changes related to defense signalling, has been reported in many host plants during AM symbioses. These changes have been often related to the improved stress tolerance common in mycorrhizal plants. However, results on the alterations in phytohormones content and their role on the symbiosis are controversial. Here, an integrative analysis of the response of phylogenetically diverse plants (i.e., tomato, soybean, and maize) to two mycorrhizal fungi -Funneliformis mosseae and Rhizophagus irregularis- was performed. The analysis of the defense-related hormones salicylic acid, abscisic acid, and jasmonates, and the expression of marker genes of the pathways they regulate, revealed significant changes in the roots of mycorrhizal plants. These changes depended on both the plant and the AM fungus (AMF) involved. However, general trends can be identified: roots associated with the most effective colonizer R. irregularis showed fewer changes in these defense-related traits, while the colonization by F. mosseae led to significant modifications in all plants tested. The up-regulation of the jasmonate pathway by F. mosseae was found to be highly conserved among the different plant species, suggesting an important role of jasmonates during this AM interaction. Our study evidences a strong influence of the AMF genotype on the modulation of host defense signalling, and offers hints on the role of these changes in the symbiosis.

Gene expression in mycorrhizal orchid protocorms suggests a friendly plant-fungus relationship

Orchids fully depend on symbiotic interactions with specific soil fungi for seed germination and early development. Germinated seeds give rise to a protocorm, a heterotrophic organ that acquires nutrients, including organic carbon, from the mycorrhizal partner. It has long been debated if this interaction is mutualistic or antagonistic. To investigate the molecular bases of the orchid response to mycorrhizal invasion, we developed a symbiotic in vitro system between Serapias vomeracea, a Mediterranean green meadow orchid, and the rhizoctonia-like fungus Tulasnella calospora. 454 pyrosequencing was used to generate an inventory of plant and fungal genes expressed in mycorrhizal protocorms, and plant genes could be reliably identified with a customized bioinformatic pipeline. A small panel of plant genes was selected and expression was assessed by real-time quantitative PCR in mycorrhizal and non-mycorrhizal protocorm tissues. Among these genes were some markers of mutualistic (e.g. nodulins) as well as antagonistic (e.g. pathogenesis-related and wound/stress-induced) genes. None of the pathogenesis or wound/stress-related genes were significantly up-regulated in mycorrhizal tissues, suggesting that fungal colonization does not trigger strong plant defence responses. In addition, the highest expression fold change in mycorrhizal tissues was found for a nodulin-like gene similar to the plastocyanin domain-containing ENOD55. Another nodulin-like gene significantly more expressed in the symbiotic tissues of mycorrhizal protocorms was similar to a sugar transporter of the SWEET family. Two genes coding for mannose-binding lectins were significantly up-regulated in the presence of the mycorrhizal fungus, but their role in the symbiosis is unclear.

Growth of Arabidopsis seedlings on high fungal doses of Piriformospora indica has little effect on plant performance, stress, and defense gene expression in spite of elevated jasmonic acid and jasmonic acid-isoleucine levels in the roots

The endophytic fungus Piriformospora indica colonizes the roots of many plant species including Arabidopsis and promotes their performance, biomass, and seed production as well as resistance against biotic and abiotic stress. Imbalances in the symbiotic interaction such as uncontrolled fungal growth result in the loss of benefits for the plants and activation of defense responses against the microbe. We exposed Arabidopsis seedlings to a dense hyphal lawn of P. indica. The seedlings continue to grow, accumulate normal amounts of chlorophyll, and the photosynthetic parameters demonstrate that they perform well. In spite of high fungal doses around the roots, the fungal material inside the roots was not significantly higher when compared with roots that live in a beneficial symbiosis with P. indica. Fifteen defense- and stress-related genes including PR2, PR3, PAL2, and ERF1 are only moderately upregulated in the roots on the fungal lawn, and the seedlings did not accumulate H2O2/radical oxygen species. However, accumulation of anthocyanin in P. indica-exposed seedlings indicates stress symptoms. Furthermore, the jasmonic acid (JA) and jasmonic acid-isoleucine (JA-Ile) levels were increased in the roots, and consequently PDF1.2 and a newly characterized gene for a 2-oxoglurate and Fe2+ -dependent oxygenase were upregulated more than 7-fold on the dense fungal lawn, in a JAR1- and EIN3-dependent manner. We conclude that growth of A. thaliana seedlings on high fungal doses of P. indica has little effect on the overall performance of the plants although elevated JA and JA-Ile levels in the roots induce a mild stress or defense response.

Cropping practices modulate the impact of glyphosate on arbuscular mycorrhizal fungi and rhizosphere bacteria in agroecosystems of the semiarid prairie

A growing body of evidence obtained from studies performed under controlled conditions suggests that glyphosate use can modify microbial community assemblages. However, few studies have examined the influence of glyphosate in agroecosystems. We examined 4 wheat-based production systems typical of the Canadian prairie over 2 years to answer the following question: Does preseeding of glyphosate impact soil rhizosphere microorganisms? If so, do cropping practices influence this impact? Glyphosate caused a shift in the species dominating the arbuscular mycorrhizal fungal community in the rhizosphere, possibly through the modification of host plant physiology. Glyphosate stimulated rhizobacterial growth while having no influence on saprotrophic fungi, suggesting a greater abundance of glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in bacteria than in fungi. Glyphosate stimulated rhizosphere bacteria in pea but not in urea-fertilized durum wheat, which is consistent with inhibition of EPSPS tolerance to residual glyphosate through high ammonium levels. Mitigation of the effects of glyphosate on rhizosphere bacteria through tillage suggests a reduction in residual glyphosate activity through increased adsorption to soil binding sites upon soil mixing. The influence of glyphosate on Gram-negative bacteria was mitigated under drought conditions in 2007. Our experiment suggests that interactions between soil fertility, tillage, and cropping practices shape the influence of glyphosate use on rhizosphere microorganisms.