5,287 research outputs found
The rhizosphere microbiome and plant health
No full textThe diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant–microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit
protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production
Plant basal resistance: genetics, biochemistry, and impacts on plant-biotic interactions
No full textBasal resistance depends largely on a diverse range of defence mechanisms that become active upon attack by pathogens or insects. These mechanisms range from rapid stomatal closure and production of reactive oxygen species, to callose deposition and defence gene induction. It is commonly assumed that the speed and intensity of these inducible defences determines the effectiveness of basal resistance. The present dissertation describes different aspects of basal resistance in Arabidopsis thaliana and Zea mays. Chapter 2 of the dissertation describes natural variation between Arabidopsis accessions in basal defence responsiveness to pathogen-associated molecular patterns (PAMPs) and the defence hormone salicylic acid (SA). Quantitative trait loci (QTL) analysis identified different loci regulating the sensitivity of PAMP-induced callose and SA-induced defence gene expression. One QTL controlling SA responsiveness was found to contribute to basal resistance against Pseudomonas syringae pv. tomato. In Chapter 3, the contribution of benzoxazinoids (BXs) in basal resistance of maize is described, using maize bx1 mutant lines that are impaired in the first dedicated step of BX biosynthesis. Compared to wild-type lines, bx1 lines displayed reduced penetration resistance against aphids and fungus. Furthermore, infestation of wild-type plants by aphids and fungi stimulated the conversion of DIMBOA-glucoside into HDMBOA-glucoside and DIMBOA, which was most pronounced in the apoplast of challenged tissues. Interestingly, these events preceded major tissue damage or symptom development, suggesting that BX-dependent basal resistance does not necessarily depend on tissue damage. Upon further investigation of wild-type and bx1 mutant lines, we observed significantly reduced callose deposition in bx1 plants after PAMP treatment. Furthermore, DIMBOA infiltration of the apoplast mimicked PAMP-induced callose in wild-type plants. Hence, DIMBOA acts as a regulatory signal in the expression of cell wall-based basal resistance of maize. BXs have also been reported to act as allelopathic signals belowground, which are further investigated in Chapter 4. Chromatographic analysis revealed that DIMBOA is the dominant BX species in root exudates of maize. To investigate the impact of BXs on root-colonizing rhizobacteria, transcriptome analysis was performed of DIMBOA-treated Pseudomonas putida KT2440. This global analysis pointed towards increased transcription of bacterial genes that are involved in break-down of aromatic metabolites and chemotaxis. The latter response was confirmed by in vitro assays, which demonstrated chemotaxis of the bacteria towards DIMBOA. Furthermore, root colonisation assays with GFP-expressing P. putida KT2440 revealed that wild-type plants allowed more bacterial colonization than BX-deficient bx1 plants, indicating that BXs can recruit rhizobacteria from the soil. Preliminary results that are presented in Chapter 5 show that root colonization by P. putida KT2440 primes aboveground basal defences against herbivores, thereby further highlighting the central and multifaceted function of DIMBOA in maize basal resistance
Analysis of rhizosphere bacterial communities in Arabidopsis: impact of plant defense signaling
No full textIn the rhizosphere, numerous microbial and plant-microbe interactions occur. Of special interest is the ability of specific rhizosphere bacteria to elicit induced systemic resistance (ISR), a state of enhanced defensive capacity of the plant that is effective against a wide range of pathogens. The goal to minimize the use of agrochemicals in crop protection stimulates the development of practical applications of ISR-eliciting bacteria as an environmentally friendly alternative. However, application of these bacteria on a large scale and at high densities may perturb the indigenous microflora. This thesis is focused on effects of plant defense signaling on the indigenous bacterial rhizosphere microflora. Population densities of the bacterial and Pseudomonas spp. microflora were determined by selective dilution plating, whereas bacterial community structures were studied by DGGE analysis of amplified 16S rDNA, obtained from DNA directly extracted from rhizosphere and bulk soil. As model plant we used Arabidopsis thaliana accession Col-0, since numerous defense signaling mutants and transgenic lines are available and rhizobacteria-mediated ISR has been characterized in detail in this species. To determine if the indigenous bacterial microflora in the rhizosphere is affected by plant defenses, Arabidopsis genotypes with altered defense signaling were used. Whereas no differences were observed on microbial community structures, in some defense signal-transduction mutants rhizosphere population densities of culturable bacteria or Pseudomonas spp. were different from those of the parent Col-0. These differences were observed only in one type of soil. Apparently, soil is a predominant factor shaping microbial communities. In a complementary approach, jasmonic acid (JA)- or salicylic acid (SA)-dependent defenses were chemically activated by application of these hormones. Neither the abundance, nor the community structure of the bacterial rhizosphere microflora was affected by activation of the JA- or SA-dependent responses. Whereas Pseudomonas putida WCS358r and Pseudomonas fluorescens WCS417r elicit ISR against the bacterial leaf pathogen Pseudomonas syringae pv. tomato (Pst) in Arabidopsis, P. fluorescens WCS374r does not. The root-colonizing capacity of these three bacterial strains was studied on wild-type Arabidopsis and on a non ISR-expressing mutant, myb72. Whereas WCS358r and WCS417r proliferated on the roots of the wild type, this was not the case for WCS374r. However, none of the strains proliferated on the roots of the myb72 mutant. Apparently, MYB72 is not only essential for the expression of ISR, but also influences root colonization by rhizobacteria. Metabolic profiling revealed that treatment of wild-type plants and the myb72 mutant with the Pseudomonas spp. strains significantly altered the amounts of sugars, organic acids and amino acids. Most annotated metabolite fragments could be linked to known plant-microbe or plant-pathogen interactions, but not to the expression of ISR. Finally, population densities of total culturable bacteria and Pseudomonas spp. in the phyllosphere were determined upon infection with Pst. Arabidopsis mutants differed in their sensitivity to Pst and the most sensitive mutants also had the highest bacterial and Pseudomonas spp. populations on their leaves. Collectively, these results suggest that control of plant diseases by elicitation of induced systemic resistance will not significantly affect the indigenous rhizosphere bacterial microflora
Microbiome-on-a-Chip: New Frontiers in Plant-Microbiota Research
No full textAn enigmatic concoction of interactions between microbes and hosts takes place below ground, yet the function(s) of the individual components in this complex playground are far from understood. This Forum article highlights how microfluidic - or 'Microbiome-on-a-Chip' - technology could help to shed light on such relationships, opening new frontiers in plant-microbiota research
Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development
No full textPlants have incredible developmental plasticity, enabling them to respond to a wide range of environmental conditions. Among these conditions is the presence of plant growth-promoting rhizobacteria (PGPR) in the soil. Recent studies show that PGPR affect Arabidopsis thaliana root growth and development by modulating cell division and differentiation in the primary root and influencing lateral root development. These effects lead to dramatic changes in root system architecture that significantly impact aboveground plant growth. Thus, PGPR may promote shoot growth via their effect on root developmental programs. This review focuses on contextualizing root developmental changes elicited by PGPR in light of our understanding of plant-microbe interactions and root developmental biology
Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere
No full textDespite significant advances in crop protection, plant diseases cause a 20% yield loss in food and cash crops worldwide. Therefore, interactions between plants and pathogens have been studied in great detail. In contrast, the interplay between plants and non-pathogenic microorganisms has received scant attention, and differential responses of plants to pathogenic and non-pathogenic microorganisms are as yet not well understood. Plants affect their rhizosphere microbial communities that can contain beneficial, neutral and pathogenic elements. Interactions between the different elements of these communities have been studied in relation to biological control of plant pathogens. One of the mechanisms of disease control is induced systemic resistance (ISR). Studies on biological control of plant diseases have focused on ISR the last decade, because ISR is effective against a wide range of pathogens and thus offers serious potential for practical applications in crop protection. Such applications may however affect microbial communities associated with plant roots and interfere with the functioning of the root microbiota. Here, we review the possible impact of plant defense signaling on bacterial communities in the rhizosphere. To better assess implications of shifts in the rhizosphere microflora we first review effects of root exudates on soil microbial communities. Current knowledge on inducible defense signaling in plants is discussed in the context of recognition and systemic responses to pathogenic and beneficial microorganisms. Finally, the as yet limited knowledge on effects of plant defense on rhizosphere microbial communities is reviewed and we discuss future directions of research that will contribute to unravel the molecular interplay of plants and their beneficial microflora
Modulation of plant immunity by atmospheric CO2
No full textThe continuously increasing CO2 levels in the atmosphere is considered to be core among climate changes and is expected to affect plant diseases in the future, posing a new challenge for future strategies in plant protection. In this thesis we explore signaling mechanisms underlying atmospheric CO2-modulated defense responses in Arabidopsis plants. We demonstrate that the disease resistance against the hemi-biotroph Pseudomonas syringae pv. tomato DC3000 (Pst) decreases and the disease resistance against the necrotroph Botrytis cinerea increases as the level of atmopheric CO2 increases. By employing genetic, physiological and biochemical analysis, we further demonstrated that ABA signaling plays a central role in CO2-regulated defense against Pst. The CO2-controlled stomatal reopening is dependent on ABA signaling in the plant, whereby the low ABA concentration under a low CO2 regime leads to prolonged closure of the stomata after infection with Pst. This ABA-dependent effect on the opening of the stomata is correlated with an increased resistance against this pathogen that invades the plant through the stomata. Together, our findings highlight the importance of ABA signaling for fine tuning atmospheric CO2-regulated defense responses. In a search for potential components involved in CO2-modulated defense responses, we reveal that two carbonic anhydrases (CAs), CA1 and CA4, are important regulators in pathogen associated molecular patterns (PAMPs)-triggered immunity (PTI). We demonstrate that these CAs have an antagonizing effect on the SA signaling pathway. We further propose a model for the function of CAs in mediating PTI. Upon recognition of PAMPs, CA1 and CA4 are down-regulated in plants, resulting in enhanced ROS production and increased defense-related gene expression. This ultimately leads to enhanced SA-dependent defenses and inhibition of pathogen growth. Moreover, we show that these two CA genes play a role in atmospheric CO2-regulated defense against Pst. These results together suggest that CAs might serve as an important node connecting CO2 and plant defense signaling. Finally, our results reveal that changes in atmospheric CO2 do not significantly influence soil-borne diseases caused by Rhizoctonia solani and Fusarium oxysporum f.sp. raphani in Arabidopsis. Possibly, this is caused by the fact that CO2 levels in the soil are ready much higher than in the atmosphere. In conclusion, our research demonstrates that hormonal signaling pathways and CAs are important regulators in CO2-modulated defense responses. This knowledge provides a new perspective on future investigations into the functioning of the plant immune system under changed atmospheric CO2 conditions and ultimately can be utilized to improve crop protection and crop breeding in the face of changing climate change
Molecular aspects of plant disease susceptibility: Arabidopsis genes affecting downy mildew infection
No full textInteractions of plants with pathogenic microorganisms are influenced by multiple biotic and abiotic factors. The host immune system can detect pathogens and restrict their growth and development, but also non-immunity related host factors and processes can contribute to pathogenesis by attracting pathogens, stimulating their development and providing nutrition. We use the model plant species Arabidopsis thaliana and its biotrophic pathogen Hyaloperonospora arabidopsidis (Hpa), causing downy mildew, to study the role of immunity and non-immunity related host processes in plant disease susceptibility. The work described in this thesis was aimed at identifying Arabidopsis genes that alter susceptibility to the downy mildew pathogen. In Chapters 2, 3 and 4, results of studies on susceptibility of natural Arabidopsis accessions to Hpa are presented. The Arabidopsis line C24 is resistant to all downy mildew isolates tested so far, however, genetic mechanisms of this broad-spectrum resistance (BSR) were unknown. Using segregation analysis and quantitative trait loci mapping, we found that BSR is multigenic and mediated by different combinations of isolate-specific resistance loci, some of which confer only partial resistance. In Chapter 3, quantitative resistance of C24 to the Hpa isolate Waco9 was studied in more details. Backcross mapping facilitated by whole-genome sequencing revealed two major loci, which interact to confer strong quantitative resistance to Hpa. To identify Arabidopsis genes which contribute to susceptibility to downy mildew in a non-isolate specific manner, we performed association mapping in the core Arabidopsis HapMap population of susceptibility to a mixture of four Hpa isolates (Chapter 4). Natural variation at three loci, CYTOKININ RESPONSE FACTOR 1 (CRF1), STOMATAL CARPENTER 1 (SCAP1), and the unknown gene At5g53750, was associated with susceptibility to Hpa. Analysis of mutants and silencing lines indicated that SCAP1 and CRF2, the close homolog of CRF1, could play a role in the Arabidopsis-downy mildew interaction. However, functions of these genes in Arabidopsis susceptibility remain unknown. The downy mildew pathogen forms specialized infectious structures called haustoria, which penetrate plant cell wall but remain separated from host plasma membrane. To gain insight the molecular events occurring specifically in the Hpa-infected cells of Arabidopsis, we used an N-glycotagging approach coupled to label-free quantitative proteomics (described in Chapter 5). We found 18 candidate complex N-glycoproteins of Arabidopsis associated with downy mildew infection. Analysis of mutants in the corresponding genes suggested that Arabidopsis PLASMODESMATA GERMIN-LIKE PROTEIN 1 (PDGLP1) and the subtilase ATSBT3.5 are involved in regulating the host susceptibility to Hpa. Functions of the identified novel putative players in the interaction between Arabidopsis and downy mildew are largely unknown, but their further characterization might point to new processes contributing to plant susceptibility to (hemi-)biotrophic pathogen
Beneficial microbes in a changing environment: are they always helping plants to deal with insects?
No full textPlants have a complex immune system that defends them against attackers (e.g. herbivores and microbial pathogens) but that also regulates the interactions with mutualistic organisms (e.g. mycorrhizal fungi and plant growth-promoting rhizobacteria). Plants have to respond to multiple environmental challenges, so they need to integrate both signals associated with biotic and abiotic stresses in the most appropriate response to survive. Beneficial microbes such as rhizobacteria and mycorrhizal fungi can help plants to deal' with pathogens and herbivorous insects as well as to tolerate abiotic stress. Therefore, beneficial microbes may play an important role in a changing environment, where abiotic and biotic stresses on plants are expected to increase. The effects of beneficial microbes on herbivores are highly context-dependent, but little is known on what is driving such dependency. Recent evidence shows that abiotic stresses such as changes in soil nutrients, drought and salt stress, as well as ozone can modify the outcome of plantmicrobeinsect interactions. Here, we review how abiotic stress can affect plantmicrobe, plantinsect and plantmicrobeinsect interactions, and the role of the network of plant signal-transduction pathways in regulating such interactions. Most of the studies on the effects of abiotic stress on plantmicrobeinsect interactions show that the effects of microbes on herbivores (positive or negative) are strengthened under stressful conditions. We propose that, at least in part, this is due to the crosstalk of the different plant signalling pathways triggered by each stress individually. By understanding the cross-regulation mechanisms we may be able to predict the possible outcomes of plant-microbeinsect interactions under particular abiotic stress conditions. We also propose that microbes can help plants to deal with insects mainly under conditions that compromise efficient activation of plant defences. In the context of global change, it is crucial to understand how abiotic stresses will affect species interactions, especially those interactions that are beneficial for plants. The final aim of this review is to stimulate studies unravelling when these beneficial' microbes really benefit a plant
Signals from the underground and their interplay with plant immunity
No full textThe interface between roots and their adjacent soil layer, the rhizosphere, constitutes a hotspot of microbial activity and represents one of the most diverse ecosystems on Earth. The root-associated microbial community, the microbiome, contains rhizobacteria that can change the phenotypic plasticity of their hosts and trigger a broad-spectrum form of systemic immunity, known as induced systemic resistance (ISR). Although the effect of beneficial rhizobacteria on plant growth and plant health is relatively well studied, very little is known about the early molecular processes that occur at the root-microbiome interface. In this thesis, we investigated early changes in the root transcriptome and metabolome of plant roots in response to colonization of the roots by beneficial ISR-inducing Pseudomonas rhizobacteria. We discovered that ISR-inducing rhizobacteria suppress host immune responses that are triggered by their general microbial elicitors to subsequently allow root colonization and promotion of plant growth and protection. Moreover, we uncovered the iron-mobilizing coumarin scopoletin as a major player in the chemical dialogue between plants roots and ISR-inducing members in the root microbiome. Collectively, our results show that beneficial rhizobacteria are capable of suppressing root immune responses that are activated by their general elicitors, possibly via the action of immune-suppressive effectors. This paves the way to colonize the roots and provide beneficial functions to the host plant, such as enhanced growth and protection. Within the root, the transcription factor MYB72 regulates the biosynthesis of coumarins, such as scopolin. Due to the action of the MYB72-regulated β-glucosidase BGLU42, scopolin is hydrolyzed into scopoletin, which facilitates the excretion of this metabolite into the rhizosphere. Scopoletin has a differential antimicrobial activity to which ISR-inducing rhizobacteria WCS417 and WCS358 are insensitive, but which impacts the performance of selected soil-borne pathogens. Analysis of the root-associated microbiomes of Arabidopsis roots with different scopoletin exudation patterns demonstrated a role for scopoletin in microbiome assembly. Knowledge on the molecular mechanisms that play a role in the interaction between plant roots and beneficial members of the root microbiome is essential for the development of durable biological control strategies and crops with traits that can maximize the profitable functions the root microbiome
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