Iron in Plant–Pathogen Interactions

Diproline-induced resistance to parasitic nematodes in the same and subsequent rice generations: Roles of iron, nitric oxide and ethylene

Induced resistance (IR) is a plant phenotype characterized by lower susceptibility to biotic challenges upon elicitation by so-called IR stimuli. Earlier, we identified diproline (cyclo(l-Pro-l-Pro)) as IR stimulus that protects rice (Oryza sativa) against the root-knot nematode Meloidogyne graminicola (Mg). In the current study, detailed transcriptome analyses at different time points, and under uninfected and nematode-infected conditions revealed that this rice IR phenotype is correlated with induction of genes related to iron (Fe), ethylene (ET) and reactive oxygen species (ROS)/reactive nitrogen species (RNS) metabolism. An infection experiment under Fe limiting conditions confirmed that diproline-IR is only effective under optimal Fe supply. Although total root Fe levels were not affected in diproline-treated plants, phytosiderophore secretion was found to be induced by this treatment. Experiments on mutant and transgenic rice lines impaired in ET or ROS/RNS metabolism confirmed that these metabolites are involved in diproline-IR. Finally, we provide evidence for transgenerational inheritance of diproline-IR (diproline-TIR), as two successive generations of diproline-treated ancestors exhibited an IR phenotype while themselves never being exposed to diproline. Transcriptome analyses on the offspring plants revealed extensive overlap between the pathways underpinning diproline-IR and diproline-TIR. Although diproline induces significant systemic changes in global DNA methylation levels early after treatment, such changes in DNA methylation were not detected in the descendants of these plants. To our knowledge, this is the first report of TIR in rice and the first transcriptional assessment of TIR in monocots.

Development of siderophore based rhizobacterial consortium for the mitigation of biotic and abiotic environmental stresses in tomatoes: An in vitro and in planta approach

AIM

Tomato associated plant-growth promoting rhizosphere bacteria were screened for effective antagonistic activity against the fungal vascular wilt pathogens; tolerance to heavy metals; and enhancing the bioavailability of iron for tomato plants through in vitro and in vivo approaches.

METHODS AND RESULTS

Among the 121 rhizobacteria screened for siderophores, 25 isolates were observed to be siderophore producers and out of these, seven isolates chelate copper and iron thus exhibiting in vitro antagonism against the virulent strains of Fusarium oxysporum f. sp. lycopersici MTCC10270 (Fol), Fusarium equiseti MFol, and Sarocladium sp. SWL isolated from infected tomatoes. Pseudomonas stutzeri KRP8 was identified to be the most potent strain among the siderophore producers and its siderophores were chemically characterized by mass spectra as metal bound and metal-free forms. Upon bio-inoculation of fortified bacterial consortium (siderozote) into the rhizosphere of vermiculite pot cultured tomatoes supplied with varying concentrations of iron and copper ions, we observed in planta growth improvements, antagonism, enhancement of bioavailability of iron and heavy metal tolerance using Inductively Coupled Plasma-Optical Emission Spectrometry.

CONCLUSION AND SIGNIFICANCE OF THE STUDY

Our rhizobacterial consortium provides an opportunity for soil reclamation through an ecofriendly method for a heavy metal-free agricultural landscape.

Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms

Plants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana, a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogens in the laboratory. We have investigated the interaction between one of the Pseudomonas pathogens and 99 naturally co-occurring commensals, finding plant protection to be common among non-pathogenic Pseudomonas. While protective ability is enriched in one specific lineage, there is also a substantial variation for this trait among isolates of this lineage. These functional differences do not align with core-genome phylogenies, suggesting repeated gene inactivation or loss as causal. Using genome-wide association, we discovered that different bacterial genes are linked to plant protection in each lineage. We validated a protective role of several lineage-specific genes by gene inactivation, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection in this Pseudomonas lineage. Collectively, our work illustrates the importance of functional redundancy in plant protective traits across an important group of commensal bacteria.

Isolation, Identification, Biocontrol Activity, and Plant Growth Promoting Capability of a Superior Streptomyces tricolor Strain HM10

Streptomyces is a genus with known biocontrol activity, producing a broad range of biologically active substances. Our goal was to isolate local Streptomyces species, evaluate their capacity to biocontrol the selected phytopathogens, and promote the plant growth via siderophore and indole acetic acid (IAA) production and phosphate solubilization. Eleven isolates were obtained from local soil samples in Saudi Arabia via the standard serial dilution method and identified morphologically by scanning electron microscope (SEM) and 16S rRNA amplicon sequencing. The biocontrol of phytopathogens was screened against known soil-borne fungi and bacteria. Plant growth promotion capacity was evaluated based on siderophore and IAA production and phosphate solubilization capacity. From eleven isolates obtained, one showed 99.77% homology with the type strain Streptomyces tricolor AS 4.1867, and was designated S. tricolor strain HM10. It showed aerial hyphae in SEM, growth inhibition of ten known phytopathogens in in vitro experiments, and the production of plant growth promoting compounds such as siderophores, IAA, and phosphate solubilization capacity. S. tricolor strain HM10 exhibited high antagonism against the fungi tested (i.e., Colletotrichum gloeosporides with an inhibition zone exceeding 18 mm), whereas the lowest antagonistic effect was against Alternaria solani (an inhibition zone equal to 8 mm). Furthermore, the most efficient siderophore production was recorded to strain HM8, followed by strain HM10 with 64 and 22.56 h/c (halo zone area/colony area), respectively. Concerning IAA production, Streptomyces strain HM10 was the most effective producer with a value of 273.02 μg/ml. An autochthonous strain S. tricolor HM10 should be an important biological agent to control phytopathogens and promote plant growth.

Roles of subcellular metal homeostasis in crop improvement

Improvement of crop production in response to rapidly changing environmental conditions is a serious challenge facing plant breeders and biotechnologists. Iron (Fe), zinc (Zn), manganese (Mn), and copper (Cu) are essential micronutrients for plant growth and reproduction. These minerals are critical to several cellular processes including metabolism, photosynthesis, and cellular respiration. Regulating the uptake and distribution of these minerals could significantly improve plant growth and development, ultimately leading to increased crop production. Plant growth is limited by mineral deficiency, but on the other hand, excess Fe, Mn, Cu, and Zn can be toxic to plants; therefore, their uptake and distribution must be strictly regulated. Moreover, the distribution of these metals among subcellular organelles is extremely important for maintaining optimal cellular metabolism. Understanding the mechanisms controlling subcellular metal distribution and availability would enable development of crop plants that are better adapted to challenging and rapidly changing environmental conditions. Here, we describe advances in understanding of subcellular metal homeostasis, with a particular emphasis on cellular Fe homeostasis in Arabidopsis and rice, and discuss strategies for regulating cellular metabolism to improve plant production.

Iron in plant-pathogen interactions

Iron is an essential element for most organisms. As an indispensable co-factor of many enzymes, iron is involved in various crucial metabolic processes that are required for the survival of plants and pathogens. Conversely, excessive iron produces highly active reactive oxygen species, which are toxic to the cells of plants and pathogens. Therefore, plants and pathogens have evolved sophisticated mechanisms to modulate iron status at a moderate level for maintaining their fitness. Over the past decades, many efforts have been made to reveal these mechanisms, and some progress has been made. In this review, we describe recent advances in understanding the roles of iron in plant-pathogen interactions and propose prospects for future studies.

Host-Pathogen Interactions between Xanthomonas fragariae and Its Host Fragaria × ananassa Investigated with a Dual RNA-Seq Analysis

Strawberry is economically important and widely grown, but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, the gene expression of both plant and bacteria in planta was analyzed at two time points, 12 and 29 days post inoculation, in order to compare the pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28,588 known genes in strawberry and 4046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis-related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most X. fragariae genes involved in host interaction, recognition, and pathogenesis were lower expressed at late-phase infection. This study gives a first insight into the interaction of X. fragariae with its host. The strawberry plant changed gene expression in order to consistently adapt its metabolism with the progression of infection.

Genetic and structural determinants on iron assimilation pathways in the plant pathogen Xanthomonas citri subsp. citri and Xanthomonas sp

Iron is a vital nutrient to bacteria, not only in the basal metabolism but also for virulent species in infection and pathogenicity at their hosts. Despite its relevance, the role of iron in Xanthomonas citri infection, the etiological agent of citrus canker disease, is poorly understood in contrast to other pathogens, including other members of the Xanthomonas genus. In this review, we present iron assimilation pathways in X. citri including the ones for siderophore production and siderophore-iron assimilation, proven to be key factors to virulence in many organisms like Escherichia coli and Xanthomonas campestris. Based on classical iron-related proteins previously characterized in E. coli, Pseudomonas aeruginosa, and also Xanthomonadaceae, we identified orthologs in X. citri and evaluated their sequences, structural characteristics such as functional motifs, and residues that support their putative functions. Among the identified proteins are TonB-dependent receptors, periplasmic-binding proteins, active transporters, efflux pumps, and cytoplasmic enzymes. The role of each protein for the bacterium was analyzed and complemented with proteomics data previously reported. The global view of different aspects of iron regulation and nutrition in X. citri virulence and pathogenesis may help guide future investigations aiming the development of new drug targets against this important phytopathogen.

Intracellular Siderophore Detection in an Egyptian, Cobalt-Treated F. solani Isolate Using SEM-EDX with Reference to its Tolerance

An Egyptian, plant pathogenic Fusarium solani isolate was grown on cobalt concentrations of 0, 50, 200, 500, 800, and 1000 ppm. The isolate survived concentrations up to 800 ppm, however failed to grow at 1000 ppm. Morphology and elemental analysis of the isolate under the investigated Co concentrations were studied using Scanning electron microscopy (SEM) and energy dispersive X-ray microanalysis (EDX). The isolate reserved its morphology up to a concentration of 200 ppm. Morphological distortions were dramatic at 500 and 800 ppm. EDX detected Co uptake through the hyphae, microconidia, macroconidia, and chlamydospores. Iron, calcium, and potassium were also detected. EDX results showed a linear relationship between Co% and Fe% up to a concentration of 500 ppm reflecting the possible ability of the isolate to synthesize intracellular siderophores storing iron and their release from the vacuoles. The participation of such siderophores in conferring tolerance against cobalt is discussed. At 800 ppm, the % of Fe was greatly reduced with an accompanying increase in morphological distortions and absence of microconidia. Increasing the implicated cobalt concentrations resulted in increasing the percentages of the chelated cobalt reflecting the possible implication of the cell wall as well as extracellular siderophores in the uptake of cobalt. The current results recommend the absence of cobalt in any control regime taken to combat the investigated F. solani isolate and highlights the accomplishment of biochemical, ultrastructural, and molecular studies on such isolate to approve the production of siderophores and the role of cell wall in cobalt uptake.

Two NRAMP6 Isoforms Function as Iron and Manganese Transporters and Contribute to Disease Resistance in Rice

Metal ions are essential elements for all living organisms. However, metals can be toxic when present in excess. In plants, metal homeostasis is partly achieved through the function of metal transporters, including the diverse natural resistance-associated macrophage proteins (NRAMP). Among them, the OsNramp6 gene encodes a previously uncharacterized member of the rice NRAMP family that undergoes alternative splicing to produce different NRAMP6 proteins. In this work, we determined the metal transport activity and biological role of the full-length and the shortest NRAMP6 proteins (l-NRAMP6 and s-NRAMP6, respectively). Both l-NRAMP6 and s-NRAMP6 are plasma membrane-localized proteins that function as iron and manganese transporters. The expression of l-Nramp6 and s-Nramp6 is regulated during infection with the fungal pathogen Magnaporthe oryzae, albeit with different kinetics. Rice plants grown under high iron supply show stronger induction of rice defense genes and enhanced resistance to M. oryzae infection. Also, loss of function of OsNramp6 results in enhanced resistance to M. oryzae, supporting the idea that OsNramp6 negatively regulates rice immunity. Furthermore, nramp6 plants showed reduced biomass, pointing to a role of OsNramp6 in plant growth. A better understanding of OsNramp6-mediated mechanisms underlying disease resistance in rice will help in developing appropriate strategies for crop protection.

Effects of iron and boron combinations on the suppression of Fusarium wilt in banana

The effects of mineral nutrient on banana wilt disease, which are the result of a competitive relationship between host plants and pathogens, can affect the interactions of plants with microorganisms. To investigate the mineral nutrient effect, hydroponic experiments were conducted in glasshouse containing combinations of low, medium, and high iron (Fe) and boron (B) concentrations, followed by pathogen inoculation. High Fe and B treatment significantly reduced the disease index and facilitated plants growth. With increasing Fe and B concentrations, more Fe and B accumulated in plants. High Fe and B treatment dramatically reduced the Fusarium oxysporum conidial germination rate and fungal growth compared with the other two treatments, contributing to decreased numbers of the pathogen on infected plants. Furthermore, High Fe and B treatment decreased the fusaric acid production of F. oxysporum in vitro and also increased the mannitol content of the plants, which in turn decreased the phytotoxin production of infected plants and finally reduced the disease index due to the virulence factor of phytotoxin. Taken together, these results indicate that Fe and B play a multifunctional role in reducing the severity of diseases by affecting the growth of F. oxysporum and the responses between plants and pathogens.

Selection of Streptomyces against soil borne fungal pathogens by a standardized dual culture assay and evaluation of their effects on seed germination and plant growth

Background

In the search for new natural resources for crop protection, streptomycetes are gaining interest in agriculture as plant growth promoting bacteria and/or biological control agents. Because of their peculiar life cycle, in which the production of secondary metabolites is synchronized with the development of aerial hyphae and sporulation, the commonly used methods to screen for bacterial antagonists need to be adapted.

Results

The dual culture assay was standardized in terms of inoculation timing of Streptomyces antagonist and pathogen, and growth rate of different fungal pathogens. In case of fast-growing fungi, inoculation of the antagonist 2 or 3 days prior to the pathogen resulted in significantly stronger inhibition of mycelium growth. One hundred and thirty Streptomyces strains were evaluated against six destructive soil borne pathogens. The activity of strains varied from broad-spectrum to highly specific inhibition of individual pathogens. All strains inhibited at least one tested pathogen. Three strains, which combined the largest broad-spectrum with the highest inhibition activity, were selected for further characterization with four vegetable species. All of them were able to colonize seed surface of all tested vegetable crops. They mostly improved radicle and hypocotyl growth in vitro, although no statistically significant enhancement of biomass weight was observed in vivo. Occasionally, transient negative effects on germination and plant growth were observed.

Conclusions

The adapted dual culture assay allowed us to compare the inhibition of individual Streptomyces strains against six fungal soil borne pathogens. The best selected strains were able to colonize the four vegetable crops and have a potential to be developed into biocontrol products. Although they occasionally negatively influenced plant growth, these effects did not persist during the further development. Additional in vivo studies are needed to confirm their potential as biological control or plant growth promoting agents.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0886-1) contains supplementary material, which is available to authorized users.

The effect of peat and iron supplements on the severity of potato common scab and bacterial community in tuberosphere soil

The control of common scab (CS) of potatoes includes resistant cultivars, specific fertilization, increase of soil moisture and chemical treatments. Yet, these management practices do not have common or reproducible results at differing sites. In order to determine the effects of soil organic matter, iron and pH on CS development, peat and DTPA-chelated iron were supplemented to pots filled with soil conducive for CS. All results were compared with the same data obtained for a suppressive soil, which has naturally low severity of CS and occurs nearby. Bacteria, Actinobacteria and the txtB genes from the biosynthetic cluster of thaxtomin, which is responsible for the disease development, were quantified by qPCR in tuberosphere soil and potato periderm. Illumina amplicon sequencing of bacterial 16S rRNA genes was performed for tuberosphere soils. Both peat and iron supplements controlled potato scab, and the combination of the two supplements reduced CS most effectively. The bacterial community was modified by all treatments but the highest number of operational taxonomic units (OTUs) changed towards the suppressive soil after the combined peat and iron treatment. It seemed that iron supplement supported plant defense while both iron and peat additions changed the bacterial community in favor of CS suppression.

Regulating Subcellular Metal Homeostasis: The Key to Crop Improvement

Iron (Fe), zinc (Zn), manganese (Mn), and copper (Cu) are essential micronutrient mineral elements for living organisms, as they regulate essential cellular processes, such as chlorophyll synthesis and photosynthesis (Fe, Cu, and Mn), respiration (Fe and Cu), and transcription (Zn). The storage and distribution of these minerals in various cellular organelles is strictly regulated to ensure optimal metabolic rates. Alteration of the balance in uptake, distribution, and/or storage of these minerals severely impairs cellular metabolism and significantly affects plant growth and development. Thus, any change in the metal profile of a cellular compartment significantly affects metabolism. Different subcellular compartments are suggested to be linked through complex retrograde signaling networks to regulate cellular metal homeostasis. Various genes regulating cellular and subcellular metal distribution have been identified and characterized. Understanding the role of these transporters is extremely important to elaborate the signaling between various subcellular compartments. Moreover, modulation of the proteins involved in cellular metal homeostasis may help in the regulation of metabolism, adaptability to a diverse range of environmental conditions, and biofortification. Here, we review progress in the understanding of different subcellular metal transport components in plants and discuss the prospects of regulating cellular metabolism and strategies to develop biofortified crop plants.

Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas

How pathogens coevolve with and adapt to their hosts are critical to understanding how host jumps and/or acquisition of novel traits can lead to new disease emergences. The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria that collectively infect a broad range of crops and wild plant species. However, individual Xanthomonas strains usually cause disease on only a few plant species and are highly adapted to their hosts, making them pertinent models to study host specificity. This review summarizes our current understanding of the molecular basis of host specificity in the Xanthomonas genus, with a particular focus on the ecology, physiology, and pathogenicity of the bacterium. Despite our limited understanding of the basis of host specificity, type III effectors, microbe-associated molecular patterns, lipopolysaccharides, transcriptional regulators, and chemotactic sensors emerge as key determinants for shaping host specificity.

Plant and pathogen nutrient acquisition strategies

Nutrients are indispensable elements required for the growth of all living organisms including plants and pathogens. Phyllosphere, rhizosphere, apoplast, phloem, xylem, and cell organelles are the nutrient niches in plants that are the target of bacterial pathogens. Depending upon nutrients availability, the pathogen adapts various acquisition strategies and inhabits the specific niche. In this review, we discuss the nutrient composition of different niches in plants, the mechanisms involved in the recognition of nutrient niche and the sophisticated strategies used by the bacterial pathogens for acquiring nutrients. We provide insight into various nutrient acquisition strategies used by necrotrophic, biotrophic, and hemibiotrophic bacteria. Specifically we discuss both modulation of bacterial machinery and manipulation of host machinery. In addition, we highlight the current status of our understanding about the nutrient acquisition strategies used by bacterial pathogens, namely targeting the sugar transporters that are dedicated for the plant's growth and development. Bacterial strategies for altering the plant cell membrane permeability to enhance the release of nutrients are also enumerated along with in-depth analysis of molecular mechanisms behind these strategies. The information presented in this review will be useful to understand the plant-pathogen interaction in nutrient perspective.

Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection

Rice bacterial blight (BB) is a devastating rice disease. The Xa21 gene confers a broad and persistent resistance against BB. We introduced Xa21 into Oryza sativa L ssp indica (rice 9311), through multi-generation backcrossing, and generated a nearly isogenic, blight-resistant 9311/Xa21 rice. Using next-generation sequencing, we profiled the transcriptomes of both varieties before and within four days after infection of bacterium Xanthomonas oryzae pv. oryzae. The identified differentially expressed (DE) genes and signaling pathways revealed insights into the functions of Xa21. Surprisingly, before infection 1,889 genes on 135 of the 316 signaling pathways were DE between the 9311/Xa21 and 9311 plants. These Xa21-mediated basal pathways included mainly those related to the basic material and energy metabolisms and many related to phytohormones such as cytokinin, suggesting that Xa21 triggered redistribution of energy, phytohormones and resources among essential cellular activities before invasion. Counter-intuitively, after infection, the DE genes between the two plants were only one third of that before the infection; other than a few stress-related pathways, the affected pathways after infection constituted a small subset of the Xa21-mediated basal pathways. These results suggested that Xa21 primed critically important genes and signaling pathways, enhancing its resistance against bacterial infection.

Brassica napus L. cultivars show a broad variability in their morphology, physiology and metabolite levels in response to sulfur limitations and to pathogen attack

Under adequate sulfur supply, plants accumulate sulfate in the vacuoles and use sulfur-containing metabolites as storage compounds. Under sulfur-limiting conditions, these pools of stored sulfur-compounds are depleted in order to balance the nitrogen to sulfur ratio for protein synthesis. Stress conditions like sulfur limitation and/or pathogen attack induce changes in the sulfate pool and the levels of sulfur-containing metabolites, which often depend on the ecotypes or cultivars. We are interested in investigating the influence of the genetic background of canola (Brassica napus) cultivars in sulfur-limiting conditions on the resistance against Verticillium longisporum. Therefore, four commercially available B. napus cultivars were analyzed. These high-performing cultivars differ in some characteristics described in their cultivar pass, such as several agronomic traits, differences in the size of the root system, and resistance to certain pathogens, such as Phoma and Verticillium. The objectives of the study were to examine and explore the patterns of morphological, physiological and metabolic diversity in these B. napus cultivars at different sulfur concentrations and in the context of plant defense. Results indicate that the root systems are influenced differently by sulfur deficiency in the cultivars. Total root dry mass and length of root hairs differ not only among the cultivars but also vary in their reaction to sulfur limitation and pathogen attack. As a sensitive indicator of stress, several parameters of photosynthetic activity determined by PAM imaging showed a broad variability among the treatments. These results were supported by thermographic analysis. Levels of sulfur-containing metabolites also showed large variations. The data were interrelated to predict the specific behavior during sulfur limitation and/or pathogen attack. Advice for farming are discussed.