Emerging trends in Maldi-Tof MS: transforming plant pathogen detection and disease management

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has emerged as a powerful tool in the rapid and accurate identification of plant pathogens, revolutionizing plant disease diagnostics and management. This technology enables the precise detection of a broad range of pathogens, including bacteria, fungi, and viruses, through the generation of unique mass spectral fingerprints. The speed and reliability of MALDI-TOF MS make it a promising alternative to traditional molecular and biochemical methods, which are often time-consuming and Labor intensive. Recent advances in MALDI-TOF MS, including improved sample preparation techniques, enhanced spectral databases, and automation, have further increased its applicability in plant pathology. Integrating MALDI-TOF MS into plant disease management frameworks can significantly improve decision-making processes, allowing for timely interventions and reducing the spread of infectious diseases. This review discusses the emerging trends in MALDI-TOF MS, its advantages over conventional methods, and its potential to transform plant pathogen detection and disease management, ultimately contributing to sustainable agricultural practices. Future directions include expanding spectral libraries, integrating MALDI-TOF MS with other diagnostic tools, and increasing accessibility to this technology in various agricultural settings.

Plant diseases caused by plant pathogens substantially reduce crop production every year, resulting in massive economic losses throughout the world. Accurate detection and identification of plant pathogens is fundamental to plant pathogen diagnostics and, thus, plant disease management. Diagnostics and disease-management strategies require techniques to enable simultaneous detection and quantification of a wide range of pathogenic and non-pathogenic microorganisms. Over the past decade, rapid development of matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques for characterization of microorganisms has enabled substantially improved detection and identification of microorganisms. In the biological sciences, MALDI-TOF MS is used to analyze specific peptides or proteins directly desorbed from intact bacteria, fungal spores, nematodes, and other microorganisms. The ability to record biomarker ions, in a broad m/z range, which are unique to and representative of individual microorganisms, forms the basis of taxonomic identification of microorganisms by MALDI-TOF MS. Recent advances in mass spectrometry have initiated new research, i.e. analysis of more complex microbial communities. Such studies are just beginning but have great potential for elucidation not only of the interactions between microorganisms and their host plants but also those among different microbial taxa living in association with plants. There has been a recent effort by the mass spectrometry community to make data from large scale mass spectrometry experiments publicly available in the form of a centralized repository. Such a resource could enable the use of MALDI-TOF MS as a universal technique for detection of plant pathogens and non-pathogens. The effects of experimental conditions are sufficiently understood, reproducible spectra can be obtained from computational database search, and microorganisms can be rapidly characterized by genus, species, or strain.

Stinging nettle (Urtica simensis) has garnered increasing attention in the realm of plant pathology for its multifaceted role in disease management. This review aims to elucidate the diverse mechanisms by which stinging nettle influences plant pathology and contributes to disease management strategies. Stinging nettle possesses notable allelopathic properties, exerting inhibitory effects on various plant pathogens through the release of allelochemicals. Furthermore, its rich phytochemical composition, including phenolics, flavonoids, and terpenoids, contributes to its antimicrobial activity against a spectrum of plant pathogens. Additionally, stinging nettle exhibits immunomodulatory effects on host plants, enhancing their resistance to pathogen invasion. Moreover, the incorporation of stinging nettle extracts or formulations into integrated disease management approaches has shown promising results in reducing disease incidence and severity in various crops. However, further research is warranted to elucidate the specific mechanisms underlying stinging nettle's efficacy in plant disease management and optimize its utilization in agricultural systems. This review underscores the potential of stinging nettle as a valuable tool in sustainable plant disease management strategies, providing insights for researchers and practitioners alike.

The indiscriminate use of chemical fungicides led to pesticide residues in food products, risk of development of new pathotypes and pollution of soil and water ecosystem. This resulted in several ill effects on human beings, flora and fauna. To overcome the ill effects of chemical pesticides, attention had been paid to explore into products of higher plants for developing novel biopesticides in plant disease management. Our ancestors had been using these botanicals for the management of plant diseases, before the era of conventional fungicides. But the popularity of pesticides of plant origin has again been increasing due to its potential fungicidal action against several plant pathogens without any deleterious effect to the crop plants as well as environment. Several plants have been identified for antimicrobial properties which can suppress the growth and multiplication of plant pathogens, reduction in storage decay and spoilage of food products. The potential plant origin pesticides, viz. neem (Azadirachta indica), garlic bulb (Allium sativum), eucalyptus (Eucalyptus globulus), turmeric (Curcuma longa), tobacco (Nicotiana tabacum), ginger (Zingiber officinale), etc., have been successfully used for the management of several plant diseases. Moreover, seed treatment + foliar spray of freshly prepared garlic bulb extract has resulted into the reduction of Alternaria blight (35.6 %), white rust (50.4 %), powdery mildew (67.7 %) and Sclerotinia rot (80.3 %) in mustard with 27.3 % increase in yield over untreated control. These pesticides can suitably fit in any integrated pest management framework as well as in organic farming system which is a necessity in the current situation. Keeping in view the ever-increasing demand for safe food, pesticides of plant origin have a pivotal role to play in the management of plant diseases in comparison to the conventional chemical pesticides. These pesticides are not only useful to the developing countries due to their easy availability, being relatively cheap, easy sustenance in any crop protection programme and having direct relevance to the developed countries for healthy and quality produce of foodstuffs.

Nanomaterials have substantial application in plant disease diagnosis and management. The nanoparticles and nanosensors have wide application in the detection of microbial infections and diagnosis of plant diseases. Enzyme-based biosensors coated with Au, Ag, Cu, or Ti-NPs may greatly enhance the sensitivity of diagnostic probes for plant infection detection. The nanomaterials may be used in plant disease management through two ways, i.e., direct application of the nanoparticles of a suitable antimicrobial chemical or by encapsulating an antimicrobial chemical by a nanomaterial. Direct application of nanoparticles has been found to suppress a number of plant pathogenic fungi and some bacteria. Nanomaterials, nanotubes, and nanocapsules can efficiently carry higher concentration of active ingredients of pesticides, etc. and may also regulate the release of the chemical. We present here a critical review on the use of nanomaterials in plant disease diagnosis and management and have discussed in detail various relevant aspects, including the commercial use of this technology.

Direct identification of fungi associated with indoor and outdoor ornamental plants by utilizing PCR assay

Surfactants in plant disease management: A brief review and case studies

Plant diseases can be traced back almost as far as recorded history. Numerous ancient writings describe plagues and blasts destroying crops and modern civilization still faces many plant disease challenges. Plant pathology has its roots in botany and notable scientists such as Tillet, Prevost, and deBary already had concluded microscopic organisms could cause plant diseases before Robert Koch established the rules of proof of pathogenicity with sheep anthrax. Plant pathologists can be credited with helping improve crop yields and food production throughout the world. However, at a time when there are increasing challenges to crop production, some that potentially may increase the severity or distribution of plant diseases, the training of future plant pathologists appears to be declining, at least in the United States. The ability of the U.S. Land Grant University (USLGU) system to attract and train future generations of plant pathologists may be at risk. Recent data from university plant pathology departments collected by The American Phytopathological Society (APS) documents a decline in the number of students completing advanced degrees in plant pathology, departments with fewer faculty with a diverse expertise in applied plant pathology, fewer stand-alone, single discipline departments of plant pathology, a reduced ability of many departments to offer specific curricular aspects of plant pathology, and a demographic profile that casts an ominous prediction for an unusually large number of faculty retirements over the next decade. The impact of these factors could be a shortage of highly skilled, applied plant pathologists in the U.S. in coming years. The affect also may be felt globally as fewer international students may receive pre-doctoral and post-doctoral training in plant pathology in the U.S. as faculty retire and are not replaced. On the other hand, this likely will create greater opportunities for universities around the world to take leadership in many aspects of plant pathology education. While a decline in students and young faculty trained in applied and field-level specialties of plant pathology (mycology, bacteriology, plant nematology, forest pathology, epidemiology, etc.) is occurring, those trained in the cellular and molecular host-pathogen interactions specialties appear to be increasing. Many plant pathology faculty hired at USLGUs in the last decade are trained in molecular biology and received their Ph.D. degree in a field other than plant pathology. They are now applying those skills to research numerous aspects of host-pathogen interactions of model pathosystems. A shift to a greater research emphasis on molecular host-pathogen interactions over the last decade is evidenced by the number of research articles published in the three APS journals; Plant Disease, Phytopathology and Molecular Plant-Microbe Interactions (MPMI). From 1985 to 2007, there has been a decline in the number of articles published in Plant Disease (-29%) and Phytopathology (-36%) and a steady increase in those published in MPMI since its inception in 1990 (+111%). With new research tools come new research questions. The tools of molecular biology have allowed us to look deeper into questions than ever before and provided us with a perspective not before seen. As we dissect a

Plant diseases are major limiting factors in agricultural production. The control of plant diseases using pesticides although quite easy and effective is being objected due to the rising concerns for food safety, environmental quality, and development of pesticide resistance in pathogens, pressing for alternative pest management practises. The plant nutrients may be important factors in changing the levels of disease tolerance or resistance in plants. However, the effect of nutrients on plant diseases and the many factors that influence this response is not properly studied. This chapter summarizes the information related to the effect of nutrients, N, K, P, S, Mn, Mg, B, Zn, Cl, Fe, Cu, and Si, on host resistance and management of plant diseases with particular reference to wheat diseases. In most of the cases of obligate plant pathogens, high N level increases the severity of the infection. In the case of facultative pathogens, higher rates of N application decreases the incidence of diseases. Potash (K) in most cases is helpful in enhancing plant resistance to pathogens. The effect of P in plant resistance to diseases, however, appears to be inconsistent. Among the micronutrients, Mn application is helpful in disease management since it plays an important role in lignin and phenol biosynthesis to limit the spread of pathogens and also in the photosynthesis of plants. Boron reduces the severity of many diseases and plays a role in cell wall structure, plant membranes, and plant metabolism. Chlorine also enhances the resistance level in host plants to diseases. Silicon helps in the control of diseases in rice. Zinc may have negative, positive, or no effect in the management of diseases. The nutrients may have synergetic effect but in some cases may affect the effect of one nutrient in reducing the severity of diseases. The incidence of diseases of wheat like leaf blotch, powdery mildew root rot, tan spots, bunt, take-all, smuts, and stem, leaf, and stripe rusts is decreased by the application of K. Nutrients may, therefore, become an important part of integrated disease management in wheat and other crop plants.

Climate change and plant diseases

Since the dawn of agriculture, plant pathogens and pests have been a scourge of humanity. Yet we have come a long way since the Romans attempted to mitigate the effects of plant disease by worshipping and honoring the god Robigus [1]. Books in the Middle Ages by Islamic and European scholars described various plant diseases and even proposed particular disease management strategies [1]. Surprisingly, the causes of plant diseases remained a matter of debate over a long period. It took Henri-Louis Duhamel du Monceau's elegant demonstration in his 1728 “Explication Physique” paper that a “contagious” fungus was responsible for a saffron crocus disease to usher in an era of documented scientific inquiry [2]. Confusion and debate about the exact nature of the causal agents of plant diseases continued until the 19th century, which not only saw the first detailed analyses of plant pathogens but also provided much-needed insight into the mechanisms of plant disease. An example of this is Anton de Bary's demonstration that a “fungus” is a cause, not a consequence, of plant disease [3]. This coming of age of plant pathology was timely. In the 19th century, severe plant disease epidemics hit Europe and caused economic and social upheaval. These epidemics were not only widely covered in the press but also recognized as serious political issues by governments [1], [4]–[6]. Many of the diseases, including late blight of potato, powdery and downy mildew of grapevine, as well as phylloxera, were due to exotic introductions from the Americas and elsewhere. These and subsequent epidemics motivated scientific investigations into crop breeding and plant disease management that developed into modern plant pathology science over the 20th century. Nowadays, our understanding of plant pathogens and the diseases they cause greatly benefits from molecular genetics and genomics. All aspects of plant pathology, from population biology and epidemiology to mechanistic research, are impacted. The polymerase chain reaction (PCR) first enabled access to plant pathogen DNA sequences from historical specimens deposited in herbaria [7]–[9]. Historical records in combination with herbarium specimens have turned out to provide powerful tools for understanding the course of past plant epidemics. Recently, thanks to new developments in DNA sequencing technology, it has become possible to reconstruct the genomes of plant pathogens in herbaria [10], [11]. In this article, we first summarize how whole genome analysis of ancient DNA has been recently used to reconstruct the 19th-century potato-blight epidemic that rapidly spread throughout Europe and triggered the Irish potato famine. We then discuss the exciting prospects offered by the emergence of the discipline of ancient plant pathogen genomics.

The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.

IntroductionSouthern blight, caused by Sclerotium rolfsii, poses a serious threat to the cultivation of Coptis chinensis, a plant with significant medicinal value. The overreliance on fungicides for controlling this pathogen has led to environmental concerns and resistance issues. There is an urgent need for alternative, sustainable disease management strategies.MethodsIn this study, Bacillus velezensis LT1 was isolated from the rhizosphere soil of diseased C. chinensis plants. Its biocontrol efficacy against S. rolfsii LC1 was evaluated through a confrontation assay. The antimicrobial lipopeptides in the fermentation liquid of B. velezensis LT1 were identified using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS). The effects of B. velezensis LT1 on the mycelial morphology of S. rolfsii LC1 were examined using scanning electron microscopy (SEM) and transmission electron microscopy (TEM).ResultsThe confrontation assay indicated that B. velezensis LT1 significantly inhibited the growth of S. rolfsii LC1, with an inhibition efficiency of 78.41%. MALDI-TOF-MS analysis detected the presence of bacillomycin, surfactin, iturin, and fengycin in the fermentation liquid, all known for their antifungal properties. SEM and TEM observations revealed that the mycelial and cellular structures of S. rolfsii LC1 were markedly distorted when exposed to B. velezensis LT1.DiscussionThe findings demonstrate that B. velezensis LT1 has considerable potential as a biocontrol agent against S. rolfsii LC1. The identified lipopeptides likely contribute to the antifungal activity, and the morphological damage to S. rolfsii LC1 suggests a mechanism of action. This study underscores the importance of exploring microbial biocontrol agents as a sustainable alternative to chemical fungicides in the management of plant diseases. Further research into the genetic and functional aspects of B. velezensis LT1 could provide deeper insights into its biocontrol mechanisms and facilitate its application in agriculture.

Potential of metal and metal oxide nanoparticles in plant disease diagnostics and management: Recent advances and challenges

Soilborne pathogenic fungi are the most serious group of plant pathogens which cause huge yield losses to crop plants. Because of the complexity in the soil environment and plant disease development, management of plant diseases caused by soilborne pathogenic fungi appears a great challenge for all times. Plant growth-promoting rhizobacteria are important soil microbial communities which are for the past few decades successfully used for the promotion of plant growth and management of plant diseases. Though there are many options available for the management of soilborne pathogens such as agronomic practices, chemical control, and varietal resistance, the biological control using either PGPR or their metabolites offers promising prospects. Agrobacterium, Arthrobacter, Azotobacter, Azospirillum, Bacillus, Burkholderia, Caulobacter, Chromobacterium, Erwinia, Flavobacterium, Micrococcus, Pseudomonas, and Serratia are some of rhizobacteria found associated in the rhizosphere of many plants, while bacteria such as Allorhizobium, Azorhizobium, Bradyrhizobium, Mesorhizobium, and Rhizobium of the family Rhizobiaceae that are found inside the roots together contribute to the collective group of PGPR. Bacillus and Pseudomonas are the two most extensively characterized PGPR genera for their metabolites against plant pathogenic microorganisms including soilborne pathogenic fungi. The metabolites of PGPR contribute to their antagonistic potential by exerting mechanisms such as antibiosis, competition, and induced systemic resistance. Antibiotic metabolites of PGPR such phenazines, pyrrolnitrin, 2,4-diacetylphloroglucinol, pyoluteorin, viscosinamide, tensin, and iturins and volatile metabolites such as hydrogen cyanide and ammonia are having direct antagonistic activity against soilborne pathogenic fungi. Both bioprocess-mediated and genetic engineering-mediated optimization of metabolite production by PGPR have been approached for the production of bioactive metabolites. The metabolites of PGPR could be the potential choice for the effective management of plant diseases caused by soilborne pathogenic fungi because of their advantages such as easy formulation, targeted delivery, and curative effect on plant diseases.