Ectopic Expression of Xylella fastidiosa rpfF Conferring Production of Diffusible Signal Factor in Transgenic Tobacco and Citrus Alters Pathogen Behavior and Reduces Disease Severity

The Exometabolome of Xylella fastidiosa in Contact with Paraburkholderia phytofirmans Supernatant Reveals Changes in Nicotinamide, Amino Acids, Biotin, and Plant Hormones

Microbial competition within plant tissues affects invading pathogens' fitness. Metabolomics is a great tool for studying their biochemical interactions by identifying accumulated metabolites. Xylella fastidiosa, a Gram-negative bacterium causing Pierce's disease (PD) in grapevines, secretes various virulence factors including cell wall-degrading enzymes, adhesion proteins, and quorum-sensing molecules. These factors, along with outer membrane vesicles, contribute to its pathogenicity. Previous studies demonstrated that co-inoculating X. fastidiosa with the Paraburkholderia phytofirmans strain PsJN suppressed PD symptoms. Here, we further investigated the interaction between the phytopathogen and the endophyte by analyzing the exometabolome of wild-type X. fastidiosa and a diffusible signaling factor (DSF) mutant lacking quorum sensing, cultivated with 20% P. phytofirmans spent media. Liquid chromatography-mass spectrometry (LC-MS) and the Method for Metabolite Annotation and Gene Integration (MAGI) were used to detect and map metabolites to genomes, revealing a total of 121 metabolites, of which 25 were further investigated. These metabolites potentially relate to host adaptation, virulence, and pathogenicity. Notably, this study presents the first comprehensive profile of X. fastidiosa in the presence of a P. phytofirmans spent media. The results highlight that P. phytofirmans and the absence of functional quorum sensing affect the ratios of glutamine to glutamate (Gln:Glu) in X. fastidiosa. Additionally, two compounds with plant metabolism and growth properties, 2-aminoisobutyric acid and gibberellic acid, were downregulated when X. fastidiosa interacted with P. phytofirmans. These findings suggest that P. phytofirmans-mediated disease suppression involves modulation of the exometabolome of X. fastidiosa, impacting plant immunity.

DSF-family quorum sensing signal-mediated intraspecies, interspecies, and inter-kingdom communication

While most bacteria are unicellular microbes they communicate with each other and with their environments to adapt their behaviors. Quorum sensing (QS) is one of the best-studied cell-cell communication modes. QS signaling is not restricted to bacterial cell-to-cell communication - it also allows communication between bacteria and their eukaryotic hosts. The diffusible signal factor (DSF) family represents an intriguing type of QS signal with multiple roles found in diverse Gram-negative bacteria. Over the last decade, extensive progress has been made in understanding DSF-mediated communication among bacteria, fungi, insects, plants, and zebrafish. This review provides an update on these new developments with the aim of building a more comprehensive picture of DSF-mediated intraspecies, interspecies, and inter-kingdom communication.

Future of Bacterial Disease Management in Crop Production

Bacterial diseases are a constant threat to crop production globally. Current management strategies rely on an array of tactics, including improved cultural practices; application of bactericides, plant activators, and biocontrol agents; and use of resistant varieties when available. However, effective management remains a challenge, as the longevity of deployed tactics is threatened by constantly changing bacterial populations. Increased scrutiny of the impact of pesticides on human and environmental health underscores the need for alternative solutions that are durable, sustainable, accessible to farmers, and environmentally friendly. In this review, we discuss the strengths and shortcomings of existing practices and dissect recent advances that may shape the future of bacterial disease management. We conclude that disease resistance through genome modification may be the most effective arsenal against bacterial diseases. Nonetheless, more research is necessary for developing novel bacterial disease management tactics to meet the food demand of a growing global population.

MqsR toxin as a biotechnological tool for plant pathogen bacterial control

Type II toxin-antitoxin (TA) systems are widespread in bacteria and are involved in important cell features, such as cell growth inhibition and antimicrobial tolerance, through the induction of persister cells. Overall, these characteristics are associated with bacterial survival under stress conditions and represent a significant genetic mechanism to be explored for antibacterial molecules. We verified that even though Xylella fastidiosa and Xanthomonas citri subsp. citri share closely related genomes, they have different Type II TA system contents. One important difference is the absence of mqsRA in X. citri. The toxin component of this TA system has been shown to inhibit the growth of X. fastidiosa. Thus, the absence of mqsRA in X. citri led us to explore the possibility of using the MqsR toxin to impair X. citri growth. We purified MqsR and confirmed that the toxin was able to inhibit X. citri. Subsequently, transgenic citrus plants producing MqsR showed a significant reduction in citrus canker and citrus variegated chlorosis symptoms caused, respectively, by X. citri and X. fastidiosa. This study demonstrates that the use of toxins from TA systems is a promising strategy to be explored aiming bacterial control.

Xylella fastidiosa in Olive: A Review of Control Attempts and Current Management

Since 2013, Xylella fastidiosa Wells et al. has been reported to infect several hosts and to be present in different areas of Europe. The main damage has been inflicted on the olive orchards of southern Apulia (Italy), where a severe disease associated with X. fastidiosa subspecies pauca strain De Donno has led to the death of millions of trees. This dramatic and continuously evolving situation has led to European and national (Italian and Spanish) measures being implemented to reduce the spread of the pathogen and the associated olive quick decline syndrome (OQDS). Research has been also carried out to find solutions to better and directly fight the bacterium and its main insect vector, Philaenus spumarius L. In the course of this frantic effort, several treatments based on chemical or biological substances have been tested, in addition to plant breeding techniques and integrated pest management approaches. This review aims to summarize the attempts made so far and describe the prospects for better management of this serious threat, which poses alarming questions for the future of olive cultivation in the Mediterranean basin and beyond.

Diseases Caused by Xylella fastidiosa in Prunus Genus: An Overview of the Research on an Increasingly Widespread Pathogen

Cultivated plants belonging to the genus Prunus are globally widespread and for some countries, are economically important crops; and they play a key role in the composition of a landscape. Xylella fastidiosa is a key threat to plant health, and several Prunus species are heavily stressed by this pathogen, such as almond, peach, and plum; many strain types of different subspecies can cause severe diseases. This review highlights different approaches to managing epidemic events related to X. fastidiosa in stone fruit plants. In fact, in most new European and Asian outbreaks, almond is the main and very common host and peach, plum, apricot, and cherry are widespread and profitable crops for the involved areas. Various diseases associated with stone fruit plants show different degrees of severity in relation to cultivar, although investigations are still limited. The development and selection of tolerant and resistant cultivars and the study of resistance mechanisms activated by the plant against X. fastidiosa infections seem to be the best way to find long-term solutions aimed at making affected areas recover. In addition, observations in orchards severely affected by the disease can be essential for collecting tolerant or resistant materials within the local germplasm. In areas where the bacterium is not yet present, a qualitative-quantitative study on entomofauna is also important for the timely identification of potential vectors and for developing effective control strategies.

Functionalized microchannels as xylem-mimicking environment: Quantifying X. fastidiosa cell adhesion

Microchannels can be used to simulate xylem vessels and investigate phytopathogen colonization under controlled conditions. In this work, we explore surface functionalization strategies for polydimethylsiloxane and glass microchannels to study microenvironment colonization by Xylella fastidiosa subsp. pauca cells. We closely monitored cell initial adhesion, growth, and motility inside microfluidic channels as a function of chemical environments that mimic those found in xylem vessels. Carboxymethylcellulose (CMC), a synthetic cellulose, and an adhesin that is overexpressed during early stages of X. fastidiosa biofilm formation, XadA1 protein, were immobilized on the device's internal surfaces. This latter protocol increased bacterial density as compared with CMC. We quantitatively evaluated the different X. fastidiosa attachment affinities to each type of microchannel surface using a mathematical model and experimental observations acquired under constant flow of culture medium. We thus estimate that bacterial cells present ∼4 and 82% better adhesion rates in CMC- and XadA1-functionalized channels, respectively. Furthermore, variable flow experiments show that bacterial adhesion forces against shear stresses approximately doubled in value for the XadA1-functionalized microchannel as compared with the polydimethylsiloxane and glass pristine channels. These results show the viability of functionalized microchannels to mimic xylem vessels and corroborate the important role of chemical environments, and particularly XadA1 adhesin, for early stages of X. fastidiosa biofilm formation, as well as adhesivity modulation along the pathogen life cycle.

Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions

Vector-borne plant diseases have significant ecological and economic impacts, affecting farm profitability and forest composition throughout the world. Bacterial vector-borne pathogens have evolved sophisticated strategies to interact with their hemipteran insect vectors and plant hosts. These pathogens reside in plant vascular tissue, and their study represents an excellent opportunity to uncover novel biological mechanisms regulating intracellular pathogenesis and to contribute to the control of some of the world's most invasive emerging diseases. In this perspective, we highlight recent advances and major unanswered questions in the realm of bacterial vector-borne disease, focusing on liberibacters, phytoplasmas, spiroplasmas, and Xylella fastidiosa.

Xylella fastidiosa subsp. pauca Strains Fb7 and 9a5c from Citrus Display Differential Behavior, Secretome, and Plant Virulence

Xylella fastidiosa colonizes the xylem of various cultivated and native plants worldwide. Citrus production in Brazil has been seriously affected, and major commercial varieties remain susceptible to Citrus Variegated Chlorosis (CVC). Collective cellular behaviors such as biofilm formation influence virulence and insect transmission of X. fastidiosa. The reference strain 9a5c produces a robust biofilm compared to Fb7 that remains mostly planktonic, and both were isolated from symptomatic citrus trees. This work deepens our understanding of these distinct behaviors at the molecular level, by comparing the cellular and secreted proteomes of these two CVC strains. Out of 1017 identified proteins, 128 showed differential abundance between the two strains. Different protein families were represented such as proteases, hemolysin-like proteins, and lipase/esterases, among others. Here we show that the lipase/esterase LesA is among the most abundant secreted proteins of CVC strains as well, and demonstrate its functionality by complementary activity assays. More severe symptoms were observed in Nicotiana tabacum inoculated with strain Fb7 compared to 9a5c. Our results support that systemic symptom development can be accelerated by strains that invest less in biofilm formation and more in plant colonization. This has potential application in modulating the bacterial-plant interaction and reducing disease severity.

Secondary Metabolites in Xylella fastidiosa-Plant Interaction

During their evolutionary history, plants have evolved the ability to synthesize and accumulate small molecules known as secondary metabolites. These compounds are not essential in the primary cell functions but play a significant role in the plants’ adaptation to environmental changes and in overcoming stress. Their high concentrations may contribute to the resistance of the plants to the bacterium Xylella fastidiosa, which has recently re-emerged as a plant pathogen of global importance. Although it is established in several areas globally and is considered one of the most dangerous plant pathogens, no cure has been developed due to the lack of effective bactericides and the difficulties in accessing the xylem vessels where the pathogen grows and produces cell aggregates and biofilm. This review highlights the role of secondary metabolites in the defense of the main economic hosts of X. fastidiosa and identifies how knowledge about biosynthetic pathways could improve our understanding of disease resistance. In addition, current developments in non-invasive techniques and strategies of combining molecular and physiological techniques are examined, in an attempt to identify new metabolic engineering options for plant defense.

From Nucleotides to Satellite Imagery: Approaches to Identify and Manage the Invasive Pathogen Xylella fastidiosa and Its Insect Vectors in Europe

Biological invasions represent some of the most severe threats to local communities and ecosystems. Among invasive species, the vector-borne pathogen Xylella fastidiosa is responsible for a wide variety of plant diseases and has profound environmental, social and economic impacts. Once restricted to the Americas, it has recently invaded Europe, where multiple dramatic outbreaks have highlighted critical challenges for its management. Here, we review the most recent advances on the identification, distribution and management of X. fastidiosa and its insect vectors in Europe through genetic and spatial ecology methodologies. We underline the most important theoretical and technological gaps that remain to be bridged. Challenges and future research directions are discussed in the light of improving our understanding of this invasive species, its vectors and host–pathogen interactions. We highlight the need of including different, complimentary outlooks in integrated frameworks to substantially improve our knowledge on invasive processes and optimize resources allocation. We provide an overview of genetic, spatial ecology and integrated approaches that will aid successful and sustainable management of one of the most dangerous threats to European agriculture and ecosystems.

Impact of Xylella fastidiosa subspecies pauca in European olives

Xylella fastidiosa is the causal agent of plant diseases that cause massive economic damage. In 2013, a strain of the bacterium was, for the first time, detected in the European territory (Italy), causing the Olive Quick Decline Syndrome. We simulate future spread of the disease based on climatic-suitability modeling and radial expansion of the invaded territory. An economic model is developed to compute impact based on discounted foregone profits and losses in investment. The model projects impact for Italy, Greece, and Spain, as these countries account for around 95% of the European olive oil production. Climatic suitability modeling indicates that, depending on the suitability threshold, 95.5 to 98.9%, 99.2 to 99.8%, and 84.6 to 99.1% of the national areas of production fall into suitable territory in Italy, Greece, and Spain, respectively. For Italy, across the considered rates of radial range expansion the potential economic impact over 50 y ranges from 1.9 billion to 5.2 billion Euros for the economic worst-case scenario, in which production ceases after orchards die off. If replanting with resistant varieties is feasible, the impact ranges from 0.6 billion to 1.6 billion Euros. Depending on whether replanting is feasible, between 0.5 billion and 1.3 billion Euros can be saved over the course of 50 y if disease spread is reduced from 5.18 to 1.1 km per year. The analysis stresses the necessity to strengthen the ongoing research on cultivar resistance traits and application of phytosanitary measures, including vector control and inoculum suppression, by removing host plants.

Citrus reticulata CrRAP2.2 Transcriptional Factor Shares Similar Functions to the Arabidopsis Homolog and Increases Resistance to Xylella fastidiosa

Xylella fastidiosa is a worldwide multihost pathogen that causes diseases in different crops. It is considered a new global threat and substantial efforts have been made in order to identify sources of resistance. Indeed, many genes have been associated with resistance to X. fastidiosa, but without functional validation. Here, we describe a C. reticulata gene homologous to the transcriptional factor RAP2.2 from Arabidopsis thaliana that increases resistance to citrus variegated chlorosis (CVC). This gene was previously detected in C. reticulata challenged with X. fastidiosa. Bioinformatics analysis together with subcellular localization and auto-activation assays indicated that RAP2.2 from C. reticulata (CrRAP2.2) is a transcriptional factor orthologous to AtRAP2.2. Thus, we used A. thaliana as a model host to evaluate the functional role of CrRAP2.2 in X. fastidiosa resistance. The inoculation of X. fastidiosa in the A. thaliana rap2.2 mutant resulted in a larger bacterial population, which was complemented by CrRAP2.2. In addition, symptoms of anthocyanin accumulation were higher in the mutant, whose phenotype was restored by CrRAP2.2, indicating that they have conserved functions in plant defense response. We therefore transformed C. sinensis with CrRAP2.2 and verified a positive correlation between CVC resistance and gene expression in transgenic lines. This is the first study using A. thaliana as model host that characterizes the function of a gene related to X. fastidiosa defense response and its application in genetic engineering to obtain citrus resistance to CVC.

Non-Lethal Effects of N-Acetylcysteine on Xylella fastidiosa Strain De Donno Biofilm Formation and Detachment

This study investigated in-vitro the non-lethal effects of N-acetylcysteine (NAC) on Xylella fastidiosa subspecies pauca strain De Donno (Xf-DD) biofilm. This strain was isolated from the olive trees affected by the olive quick decline syndrome in southern Italy. Xf-DD was first exposed to non-lethal concentrations of NAC from 0.05 to 1000 µM. Cell surface adhesion was dramatically reduced at 500 µM NAC (-47%), hence, this concentration was selected for investigating the effects of pre-, post- and co-treatments on biofilm physiology and structural development, oxidative homeostasis, and biofilm detachment. Even though 500 µM NAC reduced bacterial attachment to surfaces, compared to the control samples, it promoted Xf-DD biofilm formation by increasing: (i) biofilm biomass by up to 78% in the co-treatment, (ii) matrix polysaccharides production by up to 72% in the pre-treatment, and (iii) reactive oxygen species levels by 3.5-fold in the co-treatment. Xf-DD biofilm detachment without and with NAC was also investigated. The NAC treatment did not increase biofilm detachment, compared to the control samples. All these findings suggested that, at 500 µM, NAC diversified the phenotypes in Xf-DD biofilm, promoting biofilm formation (hyper-biofilm-forming phenotype) and discouraging biofilm detachment (hyper-attachment phenotype), while increasing oxidative stress level in the biofilm.

Recent advances in developing disease resistance in plants

Approaches to manipulating disease resistance in plants is expanding exponentially due to advances in our understanding of plant defense mechanisms and new tools for manipulating the plant genome. The application of effective strategies is only limited now by adoption of rapid classical genetic techniques and the acceptance of genetically engineered traits for some problems. The use of genome editing and cis-genetics, where possible, may facilitate applications that otherwise require considerable time or genetic engineering, depending on settling legal definitions of the products. Nonetheless, the variety of approaches to developing disease resistance has never been greater.

Overview: biotic signalling for smart pest management

Biotic signalling refers to species or phylogenetic-clade-specific signals that elicit adaptive and acceptable responses within and among organisms. It is not only the molecular basis of the ecological relationships among different species, such as parasitism, symbiosis and predation, but also serves as ideal targets that can be used to manipulate these ecological relationships. This concept was proposed by a group of scientists from the Chinese Academy of Sciences (CAS) and actively pursued in a five-year research project in 2014 funded by the CAS ($40 million), entitled 'Decoding biotic interactions and mechanism for target management of agricultural pests'. The multi-disciplinary project aimed at a systematic investigation of the intra-species and inter-species and interactions via biotic signalling, with the ultimate goal being the development of novel methods to manage the pest insects and diseases. We hereby propose a topic 'Biotic signalling sheds light on smart pest control' as a theme issue for the Philosophical Transactions of the Royal Society B. It contains a total of 18 reviews and research articles under the topic of signalling manipulation for pest management. Unravelling these complex interactions among plants, microbial pathogens and insects holds promise for developing novel strategies to protect crop plants without compromising agricultural productivity and environmental health. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.

Xylella fastidiosa subsp. pauca and fastidiosa Colonize Arabidopsis Systemically and Induce Anthocyanin Accumulation in Infected Leaves

The bacterium Xylella fastidiosa is a multihost pathogen that affects perennial crops such as grapevine, sweet orange, and olive tree worldwide. It is inherently difficult to study these pathosystems owing to the long-term growth habit of the host plant. Thus, the availability of model plants becomes essential to accelerate discoveries with economic impact. In this study, we uncovered evidence that the model plant Arabidopsis thaliana can be colonized by two different X. fastidiosa subspecies, pauca and fastidiosa. We observed that these bacteria are able to move away from the inoculation point as high bacterial populations were found in distant tissues. In addition, confocal laser scanning microscopy analysis of bacterial movement inside the petiole revealed the ability of the bacterium to move against the net xylem flow during the time course of colonization forming biofilm. These findings provide evidence for the capacity of X. fastidiosa to colonize Arabidopsis. Furthermore, leaves inoculated with X. fastidiosa showed a significant accumulation of anthocyanin. We propose that the X. fastidiosa subsp. pauca or fastidiosa colonization pattern and anthocyanin accumulation in the Arabidopsis ecotype Col-0 can be used as marker phenotypes to facilitate further studies aimed at improving genetic components involved in X. fastidiosa-host interaction.

Money Matters: Fueling Rapid Recent Insight Into Xylella fastidiosa-An Important and Expanding Global Pathogen

Xylella fastidiosa has emerged from relative obscurity into one of the most well-studied bacterial plant pathogens. While Pierce's disease of grape caused by this pathogen has been recognized as an important disease in warmer regions of the United States for nearly 100 years, the causal pathogen, X. fastidiosa has spread throughout much of the world and now also causes serious diseases of citrus, coffee, almond, olive, and other important crop plants. Our knowledge of this pathogen has been driven by the recent substantial research support justified by the economic importance of these diseases.

Quorum sensing inhibitors as antipathogens: biotechnological applications

The mechanisms through which microbes communicate using signal molecules has inspired a great deal of research. Microbes use this exchange of information, known as quorum sensing (QS), to initiate and perpetuate infectious diseases in eukaryotic organisms, evading the eukaryotic defense system by multiplying and expressing their pathogenicity through QS regulation. The major issue to arise from such networks is increased bacterial resistance to antibiotics, resulting from QS-dependent mediation of the formation of biofilm, the induction of efflux pumps, and the production of antibiotics. QS inhibitors (QSIs) of diverse origins have been shown to act as potential antipathogens. In this review, we focus on the use of QSIs to counter diseases in humans as well as plants and animals of economic importance. We also discuss the challenges encountered in the potential applications of QSIs.