PHYTOPATHOGENIC BACTERIA

Group leader: Emilia López Solanilla - Professor
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Personnel:

 

 

 

 

Plant diseases caused by bacteria are responsible of considerable economic losses associated with crop production. Phytopathogenic bacteria colonize plant surfaces and can multiply epiphytically and saprophytically before entering the plant tissue. When conditions are favorable, bacteria enter through natural openings or wounds and multiply in plant apoplast activating virulence mechanisms and inducing the symptoms associated with the disease. In this scenario, both survival in the phyllosphere, and the entry into the plant are critical stages that determine the occurrence and spread of the disease.

New sustainable strategies to prevent or restrict bacterial disease arise as an urgent demand in plant protection field. Our work has been centered over the last years in gaining knowledge on the vulnerable stages of pathogenic bacterial life cycle during the onset of infection.

Despite the pathogenic style of plant bacterial pathogens, both the adaptation to the plant surface and the switching between the epiphytic to the pathogenic stage are common themes which have deserved our attention. Our aim is to understand the relevance in disease production of the mechanisms underlying the perception and response to plant and environmental signals in two models of phytopathogenic bacteria which represent different pathogenic styles: the hemibiotrophic bacteria Pseudomonas syringae pv tomato DC3000 (PsPto), which is the causal agent of bacterial speck in tomato and Dickeya dandantii 3937 (Dd3937), a necrotroph soft-rot enterobacterium which has a broad-host range.


Simplified scheme of plant infection by phytopatogenic bacteria. Survival on the phyllosphere and entry into the plant are critical stages that determine the occurrence and spread of the disease. Bacterial cells live as epiphytes on the lea ves. Eventually, when conditions are favorable, bacteria move attracted by plant-derived compounds and penetra te into the plant apoplast through open stomata or wounds. The encircled panel represents a cross-section of a leaf showing bacteria colonizing the plant apoplast. The pathogen multiplies in the leaf apoplast activating virulence mechanisms and inducing visible disease-associated symptoms.



Our group is working on analyzing specific mechanisms operating during the first stages of the infection in these two model phytopathogenic bacteria. Specifically, we are interested in the involvement of light perception and chemotaxis in the regulation of the entry process and establishment of infection into the host.


CHEMOTAXIS AND CHEMORECEPTORS

Chemotaxis is based on the action of chemosensory pathways: signaling is initiated by the recognition of signals, known as chemoeffectors, by chemoreceptors, or methyl accepting chemotaxis proteins (MCP). Chemoreceptors differ in topology, sensing mode, cellular location, and the type of ligand binding domain (LBD). The number of chemoreceptors depends on bacterial lifestyle. Moreover, many bacterial genomes encode multiple chemosensory pathways. In the case of most phytopathogenic bacteria the number of chemoreceptors is significantly high.

Our results highlight the role of motility and chemotaxis in the pathogenicity of PsPto and Dd3937. In the case of Dd3937, genes involved in the chemotaxis transduction system (cheW, B, Y and Z) and in the structure of the flagellar motor (motA) are required for swimming and entry into Arabidopsis leaves. These functions mediate chemoattraction and chemorepellance in response to compounds such as cell wall-derived sugars, amino acids and plant hormones, like jasmonic acid (JA) (Río-Alvarez et al., 2014a).


Quantitative chemotaxis assays of Dd3937 strains towards jasmonic acid (JA) and xylose. Bars represent the chemotaxis index (CI) for wi/d-type (WT) and different mutant strains towards 1 mM JA (A) and 1 mM xylose (8). Values of CI greater than 1.0 are considered as chemoattraction and values less than 1.0 as chemorepulsion. Asterisk indicates significant differences. Dd3937 chemoreceptors contribute in a different manner to entry into Arabidopsis thaliana leaves. Entry of Dd3937 WT and mutant strains in A. thaliana leaves (C). Entry of Dd3937 WT and two complemented strains in A. thaliana leaves (E). Cells were placed on a wound and bacterial populations inside the leaf were estimated after 2 h (cfu, colony-forming units). Entry-dependent colonization assays of WT or mutant (20167 and 46680) strains in A. thaliana leaves (D). Non-entry-dependent pathogenicity assay in A. thaliana lea ves. WT or 20167 cells were infiltrated into the abaxial side of leaves (F). Bacterial populations inside the leaf were estimated after 24 h.



We are interested in the characterization, in our model bacteria, of chemoreceptors involved in relevant perception mechanisms during the infection. The ultimate aim is the design of interfering strategies of the chemotactic signaling pathways which could lead to efficient control of bacterial pathogenesis. We combine bioinformatics, biochemical and in vivo analysis to approach this study. Results obtained through these approaches allow us to identify the chemoeffectors recognized by specific chemoreceptors whose function controls key aspects of the pathogenic process.


LIGHT PERCEPTION

Light has revealed as a key signal controlling fitness and pathogenicity features in PsPto. The PsPto genome encodes a single blue light-sensing LOV-domain protein and two red light-sensing bacteriophytochromes. In previous works, we have described that PsPto light perception affects motility, attachment to plant leaves and virulence, and these phenotypes require the LOV photoreceptor. Interestingly, light impacted these plant-based pathogen behaviors when the pathogen was exposed to the light signal for only 10 minutes prior to inoculation onto tomato leaves. This discovery illustrates that light can evoke changes in pathogen traits or behavior that are detectable after the initial light stimulus is gone (Río-Alvarez et al., 2014b).


Exploitation of cues based on the presence, absence and quality of light to optimize leaf invasion. Model illustrating the impact of PsPto light-sensing at various times through the diurnal light cycle on virulence and colonization of tomato leaves (A). Light induces gene-expression reprogramming in PsPto. The data show the functional categories that are overrepresented among the differentially-expressed genes responding toa 10-min treatment with white (B), blue (C) or red (D) light. Red and green colors indicate the number of up-regulated and down-regulated genes, respectively, within each functional category. The percentage of overrepresented indicates the percentage of observed genes out of the total number of genes annotated in each functional category.



We have also explored the interplay among light-mediated impacts on plant-bacteria interaction, PsPto global gene expression patterns, PsPto photoreceptors, and PsPto virulence. Light induces genetic reprogramming in PsPto that involves large-scale changes in stress tolerance- and virulence-related traits. Blue light mediated up-regulation of T3SS genes and red light mediated down-regulation of coronatine biosynthesis genes. These changes are accompanied by changes in virulence output that varied depending on the wavelength to which the bacteria were exposed before inoculation and the physiological stage of the plants with respect to the diurnal cycle. Moreover, PsPto expresses selected virulence-related traits in the absence of light, which provides evidence that this nocturnal priming optimizes bacterial entry through the stomata at dawn. The behavior of mutants altered in the PsPto photoreceptors corroborates the role of light perception during the early stages of infection, likely at the point of bacterial entry (Santamaría-Hernando et al. 2018). In depth study of traits regulated by light during the epiphytic stage will help us to determine the factors involved in the switching to a pathogenic style.


BIOINFORMATICS APPROACH

In parallel, we are trying to underpin the concept of bacterial pathogenicity towards plants at the genomic level, using a machine learning approach. To do so, we have developed a bioinformatics tool which identifies known pathogenicity factors from a bacterial genome. This tool, named PIFAR, is available on-line and can applied to any number of novel genomes. Using the results provided by PIFAR we have trained a supervised machine-learning classification machine that allows the identification of plant-associated bacteria with a precision of ∼93%. The application of our method to approximately 9,500 genomes predicted several unknown interactions between well-known human pathogens and plants, and it also confirmed several cases for which evidence has been reported. We observed that factors involved in adhesion, deconstruction of the plant cell wall, and detoxifying activities were highlighted as the most predictive features. The application of our strategy to sequenced strains that are involved in food poisoning, for example, can be used as a primary screening tool to determine the possible causes of contaminations (Martínez-García et al. 2016). We have also developed another bioinformatics tool to identify and analyze type 3, 4 and 6 secretion systems in bacterial genomes. These secretion mechanisms have been involved in key steps during bacterial interaction with plants (Martínez-García et al. 2015a).


Schematic representation of the bioinformatics pipeline used for the generation of the training set. (A) The genomes of a selection of bacterial strains were retrieved from NCBI and classified according to three categories (PP, PANP and NPA). (B) PIFAR annotation tool was used to screen these strains for factors in the database. T346Hunter was used to identify the genomic clusters encoding T3SS, T4SS and T6SS. (C) The results from above searches were used to crea te vectors containing the repertoire of factors of each genome. (D) A subset of vectors was /eft out for validation purposes. (E) Each vector was /abeled as PP, PANP or NPA, and a matrix was created. (F) The matrix was used as the training set for three random forests classifiers. (G) Ranking with the importance measure assigned to each of the fea tu res in the PA-NPA classifier. The factor types with the most importance are those related to bacterial adhesion.




Moreover, we work in the development of an object-oriented programming tool to study and classify MCP chemoreceptors and light receptors from bacterial genomes. The ultimately objective is to determine the relations between these traits and the plant-pathogenic life style. Furthermore, we are collaborating with other groups, providing bioinformatics expertise to analyze different problems in bacterial-plant interactions (Martínez-García et al. 2015b; Martínez-García et al. 2015c; Bardají et al., 2017; Arrebola et al., 2015; Magno_Pérez-Bryan et al., 2015; Pérez-Bueno et al., 2016; Santander et al., 2016).


OTHER RESEARCH LINES:

Genomics and molecular biology of bacterial pathogens of woody hosts

We collaborate with Dr. Cayo Ramos' group in University of Málaga, Spain, in studying the differential features that enable bacterial pathogens to attack woody hosts. In the context of this collaboration we performed several years ago the annotation and bioinformatics analysis of the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 genome, a tumor-inducing pathogen of olive tree. Over the last years, we have been actively involved in the functional characterization of effector proteins in this bacterium (Matas et al., 2014; Castañeda-Ojeda et al. 2017a and 2017b).


Research lines on the frame of the CBGP Transversal Scientific Program (TSP) on Plant Response to Biotic Stresses

  1. Interactions between bacteria and viruses in co-infected hosts. In collaboration with Dr. García-Arenal´s group (CBGP) we are leading an initiative with the aim of understanding the effects of interactions between viruses and bacteria, in co-infected plants, on plant resistance and on the pathogen infectivity and virulence.

  2. Perception of cell wall-derived glycans by bacteria. These activities are in the frame of the project “Balancing plant disease resistance and pathogen virulence by sensing plant cell wall-derived glycans” in collaboration with Dr. Molina´s group.

  3. Effects of combined mite and bacterial stresses in plants. We collaborate in this research line led by Dr. Diaz´s group (CBGP). The aim of this line is to unveil if phytopathogenic bacteria with different lifestyles interact in different ways with mite stressor. These activities are part of the project “Molecular insights on the effects of combined mite and bacterial stresses in plants”.

 


Representative Publications

Contreras, E., Rodriguez-Herva, J.J., Diaz, I., Lopez-Solanilla, E., Martinez, M. 2023. Previous interaction with phytopathogenic bacteria alters the response of Arabidopsis against Tetranychus urticae herbivory. Journal of Plant Interactions 18, 2144651. DOI: 10.1080/17429145.2022.2144651

Gálvez-Roldán, C., Cerna-Vargas, J.P., Rodriguez Herva, J.J., Krell, T., Santamaria-Hernando, S., López-Solanilla, E. 2022. A NIT sensor domain containing chemoreceptor is required for a successful entry and virulence of Dickeya dadantii 3937 in potato plants. Phytopathology®. DOI: 10.1094/PHYTO-10-22-0367-R

Santamaría-Hernando, S., López-Maroto, Á., Galvez-Roldán, C., Munar-Palmer, M., Monteagudo-Cascales, E., Rodríguez-Herva, J.-J., Krell, T., López-Solanilla, E. n.d. Pseudomonas syringae pv. tomato infection of tomato plants is mediated by GABA and l-Pro chemoperception. Molecular Plant Pathology n/a. DOI: 10.1111/mpp.13238

Sanchis-López, C., Cerna-Vargas, J.P., Santamaría-Hernando, S., Ramos, C., Krell, T., Rodríguez-Palenzuela, P., López-Solanilla, E., Huerta-Cepas, J., Rodríguez-Herva, J.J. 2021. Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria. mSystems e00951-21. DOI: 10.1128/mSystems.00951-21

Santamaría‐Hernando, S., Cerna‐Vargas, J.P., Martínez‐García, P.M., Polanco, S. de F., Nebreda, S., Rodríguez‐Palenzuela, P., Rodríguez‐Herva, J.J., López‐Solanilla, E. 2020. Blue-light perception by epiphytic Pseudomonas syringae drives chemoreceptor expression, enabling efficient plant infection. Molecular Plant Pathology. DOI: 10.1111/mpp.13001

Moreno-Pérez, A., Pintado, A., Murillo, J., Caballo-Ponce, E., Tegli, S., Moretti, C., Rodríguez-Palenzuela, P., Ramos, C. 2020. Host Range Determinants of Pseudomonas savastanoi Pathovars of Woody Hosts Revealed by Comparative Genomics and Cross-Pathogenicity Tests. Frontiers in Plant Science 11, 973. DOI: 10.3389/fpls.2020.00973

Cerna-Vargas, J.P., Santamaría-Hernando, S., Matilla, M.A., Rodríguez-Herva, J.J., Daddaoua, A., Rodríguez-Palenzuela, P., Krell, T., López-Solanilla, E. 2019. Chemoperception of Specific Amino Acids Controls Phytopathogenicity in Pseudomonas syringae pv. tomato. mBio 10, e01868-19. DOI: 10.1128/mBio.01868-19

Santamaría-Hernando, S., Senovilla, M., González-Mula, A., Martínez-García, P.M., Nebreda, S., Rodríguez-Palenzuela, P., López-Solanilla, E., Rodríguez-Herva, J.J. 2019. The Pseudomonas syringae pv. tomato DC3000 PSPTO_0820 multidrug transporter is involved in resistance to plant antimicrobials and bacterial survival during tomato plant infection. PLOS ONE 14, e0218815. DOI: 10.1371/journal.pone.0218815

Santamaría-Hernando, S; Rodríguez-Herva, JJ; Martínez-García, PM; Río-Álvarez, I; González-Melendi, P; Zamorano, J; Tapia, C; Rodríguez-Palenzuela, P; López-Solanilla, E. 2018. "Pseudomonas syringae pv. tomato exploits light signals to optimize virulence and colonization of leaves". Environmental Microbiology. DOI: 10.1111/1462-2920.14331".

Castañeda-Ojeda, MP; Moreno-Pérez, A; Ramos, C; López-Solanilla, E. 2017. "Suppression of Plant Immune Responses by the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 Type III Effector Tyrosine Phosphatases HopAO1 and HopAO2". Frontiers in Plant Science. DOI: 10.3389/fpls.2017.00680".

Bardaji, L; Echeverria, M; Rodriguez-Palenzuela, P; Martinez-Garcia, PM; Murillo, J. 2017. "Four genes essential for recombination define GInts, a new type of mobile genomic island widespread in bacteria". Scientific Reports. DOI: 10.1038/srep46254".

Martínez-García, PM; López-Solanilla, E; Ramos, C; Rodríguez-Palenzuela, P. 2016. "Prediction of bacterial associations with plants using a supervised machine-learning approach". Environmental Microbiology. DOI: 10.1111/1462-2920.13389".

Castañeda-Ojeda, MP; López-Solanilla, E; Ramos, C. 2017. "Differential modulation of plant immune responses by diverse members of the Pseudomonas savastanoi pv. savastanoi HopAF type III effector family". Molecular Plant Pathology. DOI: 10.1111/mpp.12420".

Pérez-Bueno, ML; Granum, E; Pineda, M; Flors, V; Rodriguez-Palenzuela, P; López-Solanilla, E; Barón, M. 2016. "Temporal and spatial resolution of activated plant defense responses in leaves of Nicotiana benthamiana infected with Dickeya dadantii". Frontiers in Plant Science. DOI: 10.3389/fpls.2015.01209".

Arrebola, E., Carrión, V.J., Gutiérrez-Barranquero, J.A., Pérez-García, A., Rodríguez-Palenzuela, P., Cazorla, F.M., de Vicente, A. 2015. Cellulose production in Pseudomonas syringae pv. syringae: a compromise between epiphytic and pathogenic lifestyles. FEMS Microbiology Ecology 91, fiv071. DOI: 10.1093/femsec/fiv071

Martinez-Garcia, PM; Ramos, C; Rodriguez-Palenzuela, P. 2015. "T346Hunter: a novel web-based tool for the prediction of type III, type IV and type VI secretion systems in bacterial genomes". PLoS One. DOI: 10.1371/journal.pone.0119317".

Magno-Pérez, C; Martínez-García, PM; Hierrezuelo, J; Rodriquez-Palenzuela, P; Arrebola, E; Ramos, C; de Vicente, A; Pérez-García, A; Romero, DF. 2015. "Comparative genomics within the Bacillus genus reveal the singularities of two robust Bacillus amyloliquefaciens biocontrol strains". Molecular Plant-Microbe Interactions. DOI: 10.1094/MPMI-02-15-0023-R".

Río-Álvarez, I; Muñoz-Gómez, C; Navas-Vásquez, M; García-Martínez, PM; Antúnez-Lamas, M; Rodríguez-Palenzuela, P; López-Solanilla, E. 2014. "Role of Dickeya dadantii 3937 chemoreceptors in the entry to Arabidopsis leaves through wounds". Molecular Plant Pathology. DOI: 10.1111/mpp.12227".

Tellez-Rio, A; García-Marco, S; Navas, M; López-Solanilla, E; Rees, RM; Tenorio, JL; Vallejo, A. 2015. "Nitrous oxide and methane emissions from a vetch cropping season are changed by long-term tillage practices in a Mediterranean agroecosystem". Biology and Fertility of Soils. DOI: 10.1007/s00374-014-0952-5".

Martínez-García, PM; Ruano-Rosa, D; Schilirò, E; Prieto, P; Ramos, C; Rodríguez-Palenzuela, P; Mercado-Blanco, J. 2015. "Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent against Verticillium dahliae". Standards in Genomic Sciences. DOI: 10.1186/1944-3277-10-10".

Tellez-Rio, A; García-Marco, S; Navas, M; López-Solanilla, E; Tenorio, JL; Vallejo, A. 2015. "N2O and CH4 emissions from a fallow–wheat rotation with low N input in conservation and conventional tillage under a Mediterranean agroecosystem". Science of the Total Environment. DOI: 10.1016/j.scitotenv.2014.11.041".

Santander, R.D., Monte-Serrano, M., Rodríguez-Herva, J.J., López-Solanilla, E., Rodríguez-Palenzuela, P., Biosca, E.G. 2014. Exploring new roles for the rpoS gene in the survival and virulence of the fire blight pathogen Erwinia amylovora. FEMS Microbiology Ecology 90, 895–907. DOI: 10.1111/1574-6941.12444

Taurino, M; Abelenda, JA; Río-Alvarez, I; Navarro, C; Vicedo, B; Farmaki, T; Jiménez, P; García-Agustín, P; López-Solanilla, E; Prat, S; Rojo, E; Sánchez-Serrano, JJ; Sanmartín, M. 2014. "Jasmonate-dependent modifications of the pectin matrix during potato development function as a defense mechanism targeted by Dickeya dadantii virulence factors". Plant Journal. DOI: 10.1111/tpj.12393".

Río-Álvarez, I; Rodríguez-Herva, JJ; Martínez, PM; González-Melendi, P; García-Casado, G; Rodríguez-Palenzuela, P; López-Solanilla, E. 2014. "Light regulates motility, attachment and virulence in the plant pathogen Pseudomonas syringae pv tomato DC3000". Environmental Microbiology. DOI: 10.1111/1462-2920.12240".