Biology subjects

Pieterse, C. M. J.

Publications and source records attributed to Pieterse, C. M. J..

12 recordsLinked to original sources

bioRxiv2026

Nuclear NPR1 Modulates Salicylic Acid/Jasmonic Acid Crosstalk via Transcriptional Control of WRKY Transcription Factors

The plant hormones salicylic acid (SA) and jasmonic acid (JA) are major regulators of plant defense. They can antagonize each other's activity, enabling an optimized defense response. The SA master regulator NPR1 is a key player in this SA/JA crosstalk, although the mechanisms of NPR1-mediated SA/JA crosstalk remain only partly understood, especially regarding the ethylene-coregulated ERF branch of the JA pathway. Here, we investigated the function of NPR1 in SA/JA crosstalk using several Arabidopsis npr1 mutant variants. Assays using the NPR1-HBD and npr1-nls lines, expressing only cytosolic NPR1, revealed that NPR1 has a nuclear role in SA/JA crosstalk. RNA-seq analysis of lines expressing NPR1 mutated in residues Cys82 or Cys216, in which repression of the JA pathway was impaired while SA pathway induction remained mostly intact, identified 32 SA-responsive genes with reduced expression compared to Col-0, including four WRKY transcription factor genes. Of these, WRKY53 and WRKY70 could suppress expression of the JA marker gene PDF1.2 induced by ORA59, the master regulator of the ERF branch of the JA pathway, in a protoplast system. Additional SA-inducible WRKYs (WRKY50, WRKY54, WRKY63, and WRKY67) similarly suppressed ORA59-induced PDF1.2 expression, implicating WRKY63 and WRKY67 for the first time in SA/JA crosstalk and confirming earlier reports on the role of the other WRKY TFs. WRKY53 and WRKY67 were further shown to reduce accumulation of the ORA59 protein in protoplasts. Thus, our study indicated that NPR1 can regulate SA/JA crosstalk in the nucleus via transcriptional activation of genes encoding specific JA-repressing WRKY transcription factors.

molecular biology↗

bioRxiv2026

Coumarins link rhizobacteria perception in roots to systemic resistance in leaves

Induced systemic resistance (ISR) is activated in leaves upon root colonization by beneficial microbes, yet the signals linking rhizosphere perception to shoot immunity remain unknown. In the Arabidopsis thaliana-Pseudomonas simiae WCS417 model interaction, the root-specific transcription factor MYB72 and its target gene BGLU42 regulate ISR and the production, activation, and root secretion of coumarins, specialized metabolites involved in plant iron (Fe) acquisition and rhizosphere microbiome assembly. Overexpression of BGLU42 confers constitutive ISR in leaves, suggesting a link between coumarin metabolism and systemic immunity. Here, two-photon multispectral imaging and targeted metabolite profiling revealed that, under Fe-sufficient conditions, WCS417 induces a distinct spatial pattern of F6H1-dependent coumarin accumulation along the root system. These WCS417-induced coumarin signatures differed from those observed under Fe deficiency, indicating activation of a microbiota-specific coumarin metabolic program. Increased coumarin accumulation in roots was followed by a rise in coumarin levels in shoots. Time-resolved transcriptome profiling supported this metabolic reprogramming, showing rapid activation of Fe acquisition and coumarin biosynthesis genes in roots, including F6H1, MYB72, and BGLU42, followed by delayed but similar transcriptional responses in shoots. Functional analyses demonstrated that coumarin biosynthesis is required for WCS417-ISR: the f6h1 mutant failed to mount systemic resistance, whereas F6H1 overexpression conferred constitutive resistance to bacterial and fungal pathogens. In addition, WCS417-mediated coumarin accumulation systemically modulated flg22-triggered reactive oxygen species production in leaves in an F6H1-dependent manner. Together, our results identify coumarins as key mediators linking rhizobacterial perception in roots to systemic immune signaling and resistance in leaves.

plant biology↗

bioRxiv2026

Pseudomonas volatiles shape the root transcriptome and microbiome to promote plant growth under drought

O_LIVolatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and with plant roots. While their potential as plant-growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remains poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress. C_LIO_LIArabidopsis thaliana plants were exposed to VOCs emitted by Pseudomonas strains under both control and osmotic-stress conditions. VOC exposure generally enhanced plant growth, and this effect was even more pronounced under both drought and salt stress. Transcriptomic analysis revealed that VOC exposure modulates key stress-responsive pathways, including those related to abscisic acid biosynthesis and signalling, sugar transport, iron uptake, aliphatic glucosinolate biosynthesis, and plant defences. Using Arabidopsis mutants, we identified abscisic acid and aliphatic glucosinolates as important components in mediating the plant response to VOCs. SWEET11/12 sugar transporters and ABA signaling genes were downregulated by VOCs exposure, in order to allow for a positive regulation of lateral root numbers (in case of SWEET genes) and plant growth in general under drought stress. In summary, using metabolomics, transcriptomics and functional analysis, we showed a negative cross-talk between the effects of VOCs on plant growth and glucosinolate production, whereas a positive interaction was observed between the biosynthesis of coumarins and VOCs. C_LIO_LINotably, VOCs also improved drought tolerance in soil-grown Brassica oleracea plants. We showed that VOC treatment altered the root-associated microbiome under drought, leading to a community composition more similar to that of well-watered plants. C_LIO_LIOur results show that Pseudomonas emitted VOCs can promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation. C_LI

plant biology↗

bioRxiv2025

Microbiome responses to natural Fusarium infection in field-grown soybean plants

The rhizosphere microbiome influences plant health by mediating plant-pathogen interactions. Plants can recruit protective microbes in response to disease, but the consistency of this process in field conditions is unclear. We examined the rhizosphere microbiome of field-grown soybean (Glycine max L.) naturally infected with root pathogens across three commercial fields in Kentucky, USA. Symptomatic and asymptomatic plants were sampled to assess disease-associated shifts in the rhizosphere microbiome. Amplicon sequencing identified a diverse Fusarium community, with one Fusarium solani amplicon sequence variant (ASV) consistently enriched in diseased plants, identifying it as the likely pathogen. While microbial communities differed between diseased and healthy plants, these shifts were largely field-specific. Several fungal ASVs with known biocontrol potential (Clonostachys rosea, Penicillium, and Trichoderma) were enriched in healthy plants, implying a role in disease suppression. A Sphingomonas ASV, a genus previously linked to plant protection, was more abundant in diseased plant rhizospheres in two fields, suggesting pathogen-triggered recruitment. Conversely, Macrophomina phaseolina, a generalist root pathogen, was enriched in the rhizosphere of diseased plants in all fields, indicating possible co-infection with F. solani. These findings reveal complex pathogen-microbe interactions in field conditions and emphasize the need for field-specific microbiome research to inform sustainable disease management strategies.

plant biology↗

bioRxiv2024

Seed tuber microbiome is a predictor of next-season potato vigor

Potato vigor, an important agronomic trait, is heavily influenced by the field of seed tuber production. Soil microbiota vary significantly between fields, impacting plant health and crop yield. Our study demonstrates that seed potato vigor can be predicted based on microbiota associated with seed tuber eyes, the dormant buds that grow out in the next season. By combining time-resolved drone-imaging of potato crop development with microbiome sequencing of seed tuber eyes from 6 varieties produced in 240 fields, we established correlations between microbiome fingerprints and potato vigor parameters. Employing Random Forest algorithms, we developed a predictive "Potato-Microbiome Informed" model, revealing variety-specific relationships between seed tuber microbiome composition and next seasons potato vigor in trial fields. The model accurately predicted vigor of seed tubers to which the model was naive and pinpointed key microbial indicators of potato vigor. By connecting variety-specific microbiome fingerprints to crop performance in the field, we pave the way for microbiome-informed breeding strategies.

microbiology↗

bioRxiv2023

Seed tuber imprinting shapes the next-generation potato microbiome

Potato seed tubers are colonized and inhabited by soil-borne microbes, some of which can positively or negatively impact the performance of the emerging daughter plant in the next season. In this study, we investigated the intergenerational inheritance of microbiota from seed tubers to next-season daughter plants by amplicon sequencing of bacterial and fungal microbiota associated with tubers and roots of two seed potato genotypes produced in six different fields. We observed that field of production and potato genotype significantly affected the seed tuber microbiome composition and that these differences persisted during winter storage of the seed tubers. When seed tubers from different production fields were planted in a single trial field, the microbiomes of daughter tubers and roots of the emerging plants could still be distinguished according to the field of origin of the seed tuber. Remarkably, we found little evidence of direct vertical inheritance of field-unique microbes from the seed tuber to the daughter tubers or roots. Hence, we hypothesize that this intergenerational "memory" is imprinted in the seed tuber, resulting in differential microbiome assembly strategies depending on the field of production of the seed tuber.

microbiology↗

bioRxiv2022

No priming, just fighting - endophytic yeast attenuates the defense response and the stress induced by Dutch elm disease in Ulmus minor

One century after the first report of Dutch Elm Disease (DED), there is still no practical solution for this problem threatening European and American elms (Ulmus spp.). The long breeding cycles needed to select resistant genotypes and the lack of efficient treatments keep disease incidence at high levels. In the present work, the expression of defense-related genes to the causal agent of DED, Ophiostoma novo-ulmi, were analyzed in in vitro clonal plantlets from two DED-resistant and two DED-susceptible U. minor trees. In addition, the effect of the inoculation of an endophytic pink-pigmented yeast (Cystobasidium sp.) on the plants defense system was tested both individually and in combination with O. novo-ulmi. The multifactorial nature of the resistance to DED was confirmed, as no common molecular response was found in the two resistant genotypes. However, the in vitro experimental system allowed to discriminate the susceptible from the resistant genotypes, showing higher levels of oxidative stress and phenolic compounds in the susceptible genotypes after pathogen inoculation. Inoculation of the endophyte before O. novo-ulmi attenuated the plant molecular response induced by the pathogen and moderated oxidative stress levels. Niche competition, endophyte-pathogen antagonism, and molecular crosstalk between the host and the endophyte are discussed as possible mechanisms of stress reduction. In sum, our results confirm the multifactorial nature of DED resistance mechanisms and highlight the possibility of using certain endophytic yeasts as biological tools to improve tree resilience against biotic stress.

plant biology↗

bioRxiv2021

The beneficial rhizobacterium Bacillus velezensis acquires iron from roots via a type VII secretion system for colonization

Niche colonization is the key for bacterial adaptation to the environment, and competition for iron largely determines root colonization by rhizosphere microbes. Pathogenic and beneficial symbiotic bacteria use various unique secretion systems to support plant colonization or acquire limited resources from the environment. However, ubiquitous nonsymbiotic beneficial rhizobacteria have never been reported to use a unique secretion system to facilitate colonization. Here, we show that the type VII secretion system (T7SS) of the beneficial rhizobacterium Bacillus velezensis SQR9 contributes to root colonization. Knocking out T7SS and the major secreted protein YukE in SQR9 caused a significant decrease in root colonization. Moreover, the T7SS and YukE caused iron loss in plant roots in the early stage after inoculation, which contributed to root colonization by SQR9. Interestingly, purified YukE, but not inactivated YukE, could change the permeability of root cells. We speculated that secreted YukE might be directly inserted into the root cell membrane to cause iron leakage, indicating that the bacterial protein and root cell membrane interact directly. Moreover, a bacterial siderophore and the T7SS may be coordinately involved in iron acquisition by B. velezensis SQR9 for efficient root colonization. We showed that the beneficial rhizobacterium B. velezensis SQR9 could acquire iron from roots via the T7SS for rapid colonization. These findings provide the first insight into the function of the unique secretion system in nonsymbiotic beneficial rhizobacteria and reveal a novel mutualism in which plants and bacteria might share iron in a sequential manner.

microbiology↗

bioRxiv2020

Rapid evolution of bacterial mutualism in the plant rhizosphere

Even though beneficial plant-microbe interactions are commonly observed in nature, direct evidence for the evolution of bacterial mutualism in the rhizosphere remains elusive. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacterium evolves into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition was accompanied with increased mutualist fitness via two mechanisms: i) improved competitiveness for root exudates and ii) enhanced capacity for activating the root-specific transcription factor gene MYB72, which triggers the production of plant-secreted scopoletin antimicrobial for which the mutualists evolved relatively higher tolerance to. Genetically, mutualism was predominantly associated with different mutations in the GacS/GacA two-component regulator system, which conferred high fitness benefits only in the presence of plants. Together, our results show that bacteria can rapidly evolve along the parasitism-mutualism continuum in the plant rhizosphere at an agriculturally relevant evolutionary timescale.

microbiology↗

bioRxiv2020

Role for novel family of pathogen-induced cysteine-rich transmembrane proteins in disease resistance

Plants possess a sophisticated immune system to protect themselves against pathogen attack. The defense hormone salicylic acid (SA) is an important player in the plant immune gene regulatory network. Using RNA-seq time series data of Arabidopsis thaliana leaves treated with SA, we identified a largely uncharacterized SA-responsive gene family of eight members that are all activated in response to various pathogens or their immune elicitors and encode small proteins with cysteine-rich transmembrane domains. Based on their nucleotide similarity and chromosomal position, the designated Pathogen-induced Cysteine-rich transMembrane protein (PCM) genes were subdivided into three subgroups consisting of PCM1-3 (subgroup I), PCM4-6 (subgroup II), and PCM7-8 (subgroup III). Of the PCM genes, only PCM4 (also known as PCC1) has previously been implicated in plant immunity. Transient expression assays in Nicotiana benthamiana indicated that most PCM proteins localize to the plasma membrane. Ectopic overexpression of the PCMs in Arabidopsis resulted in all eight cases in enhanced resistance against the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Additionally, overexpression of PCM subgroup I genes conferred enhanced resistance to the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Ectopic overexpression of the PCMs also affected the expression of genes related to light signaling and development, and accordingly PCM-overexpressing seedlings displayed elongated hypocotyl growth. These results point to a function of PCMs in both disease resistance and photomorphogenesis, connecting both biological processes, possibly via effects on membrane structure or activity of interacting proteins at the plasma membrane.

plant biology↗

bioRxiv2020

Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response in Arabidopsis

Environmentally induced changes in the epigenome help individuals to quickly adapt to fluctuations in the conditions of their habitats. Here we explored those changes in Arabidopsis thaliana plants subjected to multiple biotic and abiotic stresses, and identified transposable element (TE) activation in plants infested with the green peach aphid, Myzus persicae. We performed a genome-wide analysis of DNA methylation, mRNA expression, mRNA degradation and small RNA accumulation. Our results demonstrate that aphid feeding induces loss of methylation of hundreds of loci, mainly TEs. This loss of methylation has the potential to regulate gene expression and we found evidence that it is involved in the control of key plant immunity genes. Accordingly, we find that mutant plants deficient in epigenetic silencing show increased resistance to M.persicae infestation. Collectively, our results show that changes in DNA methylation play a significant role in the regulation of the plant transcriptional response and induction of defense response against aphid feeding.

plant biology↗

bioRxiv2016

Architecture and dynamics of the jasmonic acid gene regulatory network

The phytohormone jasmonic acid (JA) is a critical regulator of plant growth and defense. To significantly advance our understanding of the architecture and dynamics of the JA gene regulatory network, we performed high-resolution RNA-Seq time series analyses of methyl JA-treated Arabidopsis thaliana. Computational analysis unraveled in detail the chronology of events that occur during the early and later phases of the JA response. Several transcription factors, including ERF16 and bHLH27, were uncovered as early components of the JA gene regulatory network with a role in pathogen and insect resistance. Moreover, analysis of subnetworks surrounding the JA-induced transcription factors ORA47, RAP2.6L, and ANAC055 provided novel insights into their regulatory role of defined JA network modules. Collectively, our work illuminates the complexity of the JA gene regulatory network, pinpoints to novel regulators, and provides a valuable resource for future studies on the function of JA signaling components in plant defense and development.

plant biology↗