A review on endophytic bacteria of orchids: functional roles toward synthesis of bioactive metabolites for plant growth promotion and disease biocontrol.

MAIN CONCLUSION: In this review, we have discussed the untapped potential of orchid endophytic bacteria as a valuable reservoir of bioactive metabolites, offering significant contributions to plant growth promotion and disease protection in the context of sustainable agriculture. Orchidaceae is one of the broadest and most diverse flowering plant families on Earth. Although the relationship between orchids and fungi is well documented, bacterial endophytes have recently gained attention for their roles in host development, vigor, and as sources of novel bioactive compounds. These endophytes establish mutualistic relationships with orchids, influencing plant growth, mineral solubilization, nitrogen fixation, and protection from environmental stress and phytopathogens. Current research on orchid-associated bacterial endophytes is limited, presenting significant opportunities to discover new species or genetic variants that improve host fitness and stress tolerance. The potential for extracting bioactive compounds from these bacteria is considerable, and optimization strategies for their sustainable production could significantly enhance their commercial utility. This review discusses the methods used in isolating and identifying endophytic bacteria from orchids, their diversity and significance in promoting orchid growth, and the production of bioactive compounds, with an emphasis on their potential applications in sustainable agriculture and other sectors.

Evaluation of ALA-capped silver, copper, and silver-copper nanoparticles for controlling fungal plant pathogens.

Phytopathogenic fungi significantly threaten global food security, causing substantial yield and quality losses. Sustainable solutions are urgently needed to combat these agricultural pathogens. This study explored the potential of silver (Ag), copper (Cu), and combined Ag/Cu nanoparticles capped with aminolevulinic acid (ALA) as antifungal agents. The nanoparticles (ALAAg, ALACu, and ALAAgCu) were synthesized via photoreduction and characterized using various techniques (UV-Vis, TEM, XRD, Zeta potential). Their antifungal activity against four key plant pathogens (Alternaria grandis, Colletotrichum truncatum, Corynespora cassiicola, and Fusarium oxysporum) was evaluated using poisoned food techniques. Notably, ALAAgCuNPs demonstrated superior antifungal activity compared to a conventional fungicide against two fungal strains. Even at lower concentrations, ALAAgCuNPs exhibited fungistatic effects comparable to those of the control. These promising results suggest the potential of ALAAgCu NPs as a broad-spectrum, potentially eco-friendly alternative for fungal control in plants and seeds. This approach is crucial for ensuring crop health, harvest quality, and food safety.

Characterization of rhizospheric fungi and their in vitro antagonistic potential against myco-phytopathogens invading Macrotyloma uniflorum plants.

Microorganisms have become more resistant to pesticides, which increases their ability to invade and infect crops resulting in decreased crop productivity. The rhizosphere plays a crucial role in protecting plants from harmful invaders. The purpose of the study was to investigate the antagonistic efficiency of indigenous rhizospheric fungal isolates against phytopathogens of M. uniflorum plants so that they could be further used as potent Biocontrol agents. Thirty rhizospheric fungal isolates were collected from the roots of the Macrotyloma uniflorum plant and initially described morphologically for the present study. Further, in vitro tests were conducted to evaluate the antifungal activity of these strains against four myco-phytopathogens namely Macrophamina phaseolina, Phomopsis sp. PhSFX-1, Nigrospora oryzae, and Boeremia exigua. These pathogens are known to infect the same crop plant, M. uniflorum, and cause declines in crop productivity. Fifteen fungal strains out of the thirty fungal isolates showed some partial antagonistic activity against the myco-phytopathogens. The potent fungal isolates were further identified using molecular techniques, specifically based on the internal transcribed spacer (ITS) region sequencing. Penicillium mallochii, Cladosporium pseudocladosporioides, Aspergillus chevalieri, Epicoccum nigrum, Metarhizium anisopliae, and Mucor irregularis were among the strains that were identified. These potent fungal strains showed effective antagonistic activity against harmful phytopathogens. Current findings suggest that these strains may be taken into consideration as synthetic fungicides which are frequently employed to manage plant diseases alternatives.

Bacillus velezensis: a versatile ally in the battle against phytopathogens-insights and prospects.

The escalating interest in Bacillus velezensis as a biocontrol agent arises from its demonstrated efficacy in inhibiting both phytopathogenic fungi and bacteria, positioning it as a promising candidate for biotechnological applications. This mini review aims to offer a comprehensive exploration of the multifaceted properties of B. velezensis, with particular focus on its beneficial interactions with plants and its potential for controlling phytopathogenic fungi. The molecular dialogues involving B. velezensis, plants, and phytopathogens are scrutinized to underscore the intricate mechanisms orchestrating these interactions. Additionally, the review elucidates the mode of action of B. velezensis, particularly through cyclic lipopeptides, highlighting their importance in biocontrol and promoting plant growth. The agricultural applications of B. velezensis are detailed, showcasing its role in enhancing crop health and productivity while reducing reliance on chemical pesticides. Furthermore, the review extends its purview in the industrial and environmental arenas, highlighting its versatility across various sectors. By addressing challenges such as formulation optimization and regulatory frameworks, the review aims to chart a course for the effective utilization of B. velezensis. KEY POINTS: • B. velezensis fights phytopathogens, boosting biotech potential • B. velezensis shapes agri-biotech future, offers sustainable solutions • Explores plant-B. velezensis dialogue, lipopeptide potential showcased.

"Delaying Rot Emergence in Persian Lime (Citrus×latifolia) Through Antifungal Hybrid Films Containing Litsea glaucescens Essential Oil".

Herein we describe the in situ inhibitory activity of three hybrid films (FL1, FL2, and FL3) against two wild strains of Colletotrichum gloeosporioides and Penicillium digitatum as causal agents of rot in Persian limes. The films FL2 and FL3 contained 1.0 and 1.3 % weight/volume Litsea glaucescens essential oil (LgEO) and significantly (p<0.05) delayed rot emergence in Persian limes caused by both pathogens up to 10 days. The physicochemical properties of LgEO and hybrid films were obtained, whereas detailed HPLC profiling revealed that fruit covered with these films significantly (p<0.01) preserved reducing sugars (sucrose, fructose, and glucose), organic acids (citric acid, ascorbic acid, malic acid, and oxalic acid), and flavonoids with nutraceutical activity (hesperidin, eriocitrin, naruritin, neohesperidin, diosmin, vitexin, rutin, and quercetin). This evidence sustains that the composites generated in this investigation improve the shelf life of Persian limes and conserve their nutraceutical content.

Synthesis, Characterization and Evaluation of the Antimicrobial and Herbicidal Activities of Some Transition Metal Ions Complexes with the Tranexamic Acid.

New tranexamic acid (TXA) complexes of ferric(III), cobalt(II), nickel(II), copper(II) and zirconium(IV) were synthesized and characterized by elemental analysis (CHN), conductimetric (Λ), magnetic susceptibility investigations (µeff), Fourier transform infrared (FT-IR), proton nuclear magnetic resonance (1H-NMR), ultraviolet visible (UV-vis.), optical band gap energy (Eg) and thermal studies (TG/DTG and DTA). TXA complexes were established in 1 : 2 (metal: ligand) stoichiometric ratio according to CHN data. Based on FT-IR and 1H-NMR data the disappeared of the carboxylic proton supported the deprotonating of TXA and linked to metal ions via the carboxylate group's oxygen atom as a bidentate ligand. UV-visible spectra and magnetic moment demonstrated that all chelates have geometric octahedral structures. Eg values indicated that our complexes are more electro conductive. DTA revealed presence of water molecules in inner and outer spheres of the complexes. DTA results showed that endothermic and exothermic peaks were identified in the degradation mechanisms. The ligand and metal complexes were investigated for their antimicrobial and herbicidal efficacy. The Co(II) and Ni(II) complexes showed antimicrobial activity against some tested species. The obtained results showed a promising herbicidal effect of TXA ligand and its metal complexes particularly copper and zirconium against the three tested plants.

The Ecological Strategy Determines the Response of Fungi to Stress: A Study of the 2,4-diacetylphloroglucinol Activity Against Aspergillus and Fusarium Species.

Aspergillus and Fusarium are two economically important genera of fungi. They cause significant yield losses and contamination of crops with mycotoxins. In this study we aimed to evaluate the impact of 2,4-diacetylphloroglucinol (2,4-DAPG) on Aspergillus and Fusarium fungi. It is hypothesized that two fungal genera, which have different ecological strategies, react differently to stress caused by a secondary metabolite produced by rhizosphere Pseudomonas species. We found that 2,4-DAPG was able to reduce biofilm formation of Aspergillus and Fusarium, as reflected in biomass and its chemical composition. Furthermore, subinhibitory concentrations of 2,4-DAPG increased the levels of ergosterol and polysaccharides (α- and ß-glucans, chitin) in the cell membrane and cell wall of Aspergillus, while decreasing them in Fusarium. 2,4-DAPG altered the production of secondary metabolites, especially mycotoxins and extracellular proteases. The production of ochratoxin A was decreased in A. ochraceus, and T-2 toxin and zearalenone, on the contrary, were increased in F. culmorum and F. sporotrichioides, respectively. Thus, using 2,4-DAPG we demonstrated that the ecological role of fungi determines their reaction to antibiotic substances produced by the plant microbiome. Our data contributes to understanding the molecular mechanisms behind symbiotic relationships in natural communities, which are mediated by the biosynthesis of antibiotics.

Activity of Common Thyme (Thymus vulgaris L.), Greek Oregano (Origanum vulgare L. ssp. hirtum), and Common Oregano (Origanum vulgare L. ssp. vulgare) Essential Oils against Selected Phytopathogens.

The aim of this study was to determine the activity of common thyme (Thymus vulgare L.), Greek oregano (Origanum vulgare L. ssp. hirtum), and common oregano (Origanum vulgare L. ssp. vulgare) essential oils (EOs) against selected phytopathogenic microorganisms in relation to their chemical profile. The EOs were obtained from the herbs of 2-year-old plants cultivated in the organic farming system in a temperate climate in Central Europe. The EOs' composition was determined by GC/MS and GC/FID. The investigated species were represented by the following three chemotypes: 'thymol' for common thyme, 'carvacrol' for Greek oregano, and mixed 'caryophyllene oxide + ß-caryophyllene' for common oregano. The antimicrobial activity of the EOs was assessed based on minimum inhibitory concentration (MIC) and minimum bactericidal/fungicidal concentration (MBC/MFC) values. The plant pathogenic bacteria Pseudomonas syringae, Xanthomonas hortorum, Erwinia carotovora, and fungi: Fusarium culmorum, Alternaria alternata, Botrytis cinerea, Epicoccum purpurascens, Cladosporium cladosporioides, Phoma strasseri, and Pythium debaryanum were tested. The EOs revealed a stronger inhibitory effect against fungal growth in comparison to bacterial growth (MIC: 0.016-2 µL/mL for fungi and 0.125-4 µL/mL for bacteria). Common thyme and Greek oregano EOs indicated stronger antimicrobial power than common oregano EO. These results were associated with the chemical profile of the analysed EOs. The growth of examined bacteria and fungi strains (in particular, X. hortorum, F. culmorum, and P. debaryanum) were negatively correlated with the content of phenolic monoterpenes and monoterpene hydrocarbons. Among the tested strains, P. strasseri turned out to be the most sensitive (MIC 0.016 µL/mL) and E. carotovora the most resistant (MIC 0.250-4 µL/mL) to all investigated EOs.

Optimization of Antifungal Properties of Hop Cone Carbon Dioxide Extracts Based on Response Surface Methodology.

Response surface methodology (RSM) was employed to optimize the process parameters of the supercritical carbon dioxide extraction of hop cones in terms of their antifungal properties against Fusarium culmorum and Aspergillus niger. The effects of temperature (40-50 °C), pressure (200-300 bar), and CO2 consumption (25-75 kgCO2/kg) on the extraction yield, content of α- and ß-acids, as well as pathogens' growth inhibition were investigated. Both pressure and CO2 consumption had a significant effect on antifungal properties. It was observed that the best results for antifungal properties were obtained when hop cones were extracted with pure carbon dioxide at the temperature of 50 °C, under the pressure of 300 bar with CO2 consumption at the level of 75 kgCO2/kg of feed for extraction. The highest antifungal properties of hop cone supercritical carbon dioxide extracts were analyzed as 100% for Fusarium culmorum and 68% for Aspergillus niger, calculated as the growth inhibition of tested pathogens. The aim of the study was to determine the optimum values of extraction parameters to achieve the maximum response and enable us to investigate the interaction of these parameters on the antifungal properties of hop cone extracts.

RNA interference: a promising biotechnological approach to combat plant pathogens, mechanism and future prospects.

Plant pathogens and other biological pests represent significant obstacles to crop Protection worldwide. Even though there are many effective conventional methods for controlling plant diseases, new methods that are also effective, environmentally safe, and cost-effective are required. While plant breeding has traditionally been used to manipulate the plant genome to develop resistant cultivars for controlling plant diseases, the emergence of genetic engineering has introduced a completely new approach to render plants resistant to bacteria, nematodes, fungi, and viruses. The RNA interference (RNAi) approach has recently emerged as a potentially useful tool for mitigating the inherent risks associated with the development of conventional transgenics. These risks include the use of specific transgenes, gene control sequences, or marker genes. Utilizing RNAi to silence certain genes is a promising solution to this dilemma as disease-resistant transgenic plants can be generated within a legislative structure. Recent investigations have shown that using target double stranded RNAs via an effective vector system can produce significant silencing effects. Both dsRNA-containing crop sprays and transgenic plants carrying RNAi vectors have proven effective in controlling plant diseases that threaten commercially significant crop species. This article discusses the methods and applications of the most recent RNAi technology for reducing plant diseases to ensure sustainable agricultural yields.

Entomopathogenic fungi in crops protection with an emphasis on bioactive metabolites and biological activities.

Plant pathogens with their abundance are harmful and cause huge damage to different agricultural crops and economy of a country as well as lead towards the shortage of food for humans. For their management, the utilization of entomopathogenic fungi is an eco-friendly technique, sustainable to the environment, safe for humans and has promising effect over chemical-based pesticides. This process requires a biochemical mechanism, including the production of enzymes, toxins, and other metabolites that facilitate host infection and invasion. Essential enzymes such as chitinase, proteinase, and lipase play a direct role in breaking down the host cuticle, the primary barrier to EPF (Entomopathogenic Fungi) infection. Additionally, secondary metabolites such as destruxins in Metarhizium, beauvericin in Beauveria, hirsutellides in Hirsutella, isarolides in Isaria, cordyols in Cordyceps, and vertihemipterins in Verticillium, among others, act both directly and indirectly to disable the defense mechanisms of insect hosts, thereby accelerating the EPF infection process. The chemical composition of these secondary metabolites varies, ranging from simple non-peptide pigments such as oosporine to highly complex piperazine derivatives such as vertihemiptellides. The biocontrol efficacy of EPF is extensively studied, with numerous fungal strains commercially available on a large scale for managing arthropod pests. This review emphasizes the role of proteins and enzymes against crop pathogens, detailing their mode of action, and describing the metabolites from entomopathogenic fungi and their biological activities. In doing so, these findings contribute to establishing a symbiotic equilibrium between agricultural productivity and environmental conservation.

New Data on Fungal Species Composition in Spruce Trunk Canker.

The composition of canker mycobiota on spruce trunks was studied in the Lisinsky forestry (Leningrad Oblast). Small cankers or canker parts were placed in a humid chamber. Fungi were identified by morphological features. Sorocybe resinae (Fr.) Fr. and Penicillium glaucoalbidum (Desm.) Houbraken & Samson were the most common. The S. resinae occurrence was 75.9 ± 7.9%. The fungus developed in the surface layers of dried resin, but was not detected in the absence of resin production. The fungus S. resinae was therefore assumed to be a nearly ubiquitous component of the mycobiota of resinous cankers on spruce trunks in Leningrad Oblast. The fungus P. glaucoalbidum has only been observed as a saprotroph in Russia earlier. Weak pathogenic properties were detected in the species in experiments; i.e., P. glaucoalbidum grew on live bark tissues in a humid chamber. Based on its high occurrence (41.4 ± 9.1%), P. glaucoalbidum was identified as a regular component of the microbiota in spruce necrotic canker. Pure cultures of P. glaucoalbidum and Oidiodendron sp. were obtained. To test the respective species as possible causative agents of trunk canker, trunks of 20 spruce trees were inoculated with the fungal cultures in a forest stand. The cultures stimulated resin secretion without causing necrosis to spread beyond the inflicted wound. To better understand the phenomenon, a more detailed study of the biota in necrotic cankers is necessary to perform with a special focus on their nonpathogenic part, which has not received proper attention as of yet.

Lactoferrin and its role in biotechnological strategies for plant defense against pathogens.

Agricultural crops are susceptible to many diseases caused by various pathogens, such as viruses, bacteria and fungi. This paper reviews the general principles of plant protection against pathogens, as well as the role of iron and antimicrobial peptide metabolism in plant immunity. The article highlights the principles of antibacterial, fungicidal and antiviral action of lactoferrin, a mammalian secretory glycoprotein, and lactoferrin peptides, and their role in protecting plants from phytopathogens. This review offers a comprehensive analysis and shows potential prospects of using the lactoferrin gene to enhance plant resistance to various phytopathogens, as well as the advantages of this biotechnological approach over existing methods of protecting plants against various diseases.

Bacillus spp. as Bio-factories for Antifungal Secondary Metabolites: Innovation Beyond Whole Organism Formulations.

Several fungi act as parasites for crops causing huge annual crop losses at both pre- and post-harvest stages. For years, chemical fungicides were the solution; however, their wide use has caused environmental contamination and human health problems. For this reason, the use of biofungicides has been in practice as a green solution against fungal phytopathogens. In the context of a more sustainable agriculture, microbial biofungicides have the largest share among the commercial biocontrol products that are available in the market. Precisely, the genus Bacillus has been largely studied for the management of plant pathogenic fungi because they offer a chemically diverse arsenal of antifungal secondary metabolites, which have spawned a heightened industrial engrossment of it as a biopesticide. In this sense, it is indispensable to know the wide arsenal that Bacillus genus has to apply these products for sustainable agriculture. Having this idea in our minds, in this review, secondary metabolites from Bacillus having antifungal activity are chemically and structurally described giving details of their action against several phytopathogens. Knowing the current status of Bacillus secreted antifungals is the base for the goal to apply these in agriculture and it is addressed in depth in the second part of this review.

SCAR marker: A potential tool for authentication of agriculturally important microorganisms.

Microbial inoculants are globally recommended for plant growth promotion and control of plant pathogens. These inoculants require stringent quality checks for sustainable field efficacy. Questionable regulatory frameworks constantly deteriorate the reliability of bio-inoculant technology. Existing global regulations do not involve any rapid molecular technique for the routine inspection of microbial preparations. Sequence characterized amplified region (SCAR) marker offers rapid and precise strain-level authentication of target microbes. Such advanced molecular techniques must be exploited to accurately validate the microbial formulations. Besides, the global dissemination of plant pathogenic microbes has always been an alarming threat to food security. SCAR markers could be used at the plant quarantine centers to rapidly detect catastrophic pathogens, thereby circumventing the import and export of contagious plant materials. The current review is focused on promoting the SCAR marker technology to validate commercial bio-inoculants and predict plant pandemics.

Molecular Mechanisms Determining the Role of Bacteria from the Genus Azospirillum in Plant Adaptation to Damaging Environmental Factors.

Agricultural plants are continuously exposed to environmental stressors, which can lead to a significant reduction in yield and even the death of plants. One of the ways to mitigate stress impacts is the inoculation of plant growth-promoting rhizobacteria (PGPR), including bacteria from the genus Azospirillum, into the rhizosphere of plants. Different representatives of this genus have different sensitivities or resistances to osmotic stress, pesticides, heavy metals, hydrocarbons, and perchlorate and also have the ability to mitigate the consequences of such stresses for plants. Bacteria from the genus Azospirillum contribute to the bioremediation of polluted soils and induce systemic resistance and have a positive effect on plants under stress by synthesizing siderophores and polysaccharides and modulating the levels of phytohormones, osmolytes, and volatile organic compounds in plants, as well as altering the efficiency of photosynthesis and the antioxidant defense system. In this review, we focus on molecular genetic features that provide bacterial resistance to various stress factors as well as on Azospirillum-related pathways for increasing plant resistance to unfavorable anthropogenic and natural factors.

Five Different Artemisia L. Species Ethanol Extracts' Phytochemical Composition and Their Antimicrobial and Nematocide Activity.

Among the plants that exhibit significant or established pharmacological activity, the genus Artemisia L. deserves special attention. This genus comprises over 500 species belonging to the largest Asteraceae family. Our study aimed at providing a comprehensive evaluation of the phytochemical composition of the ethanol extracts of five different Artemisia L. species (collected from the southwest of the Russian Federation) and their antimicrobial and nematocide activity as follows: A. annua cv. Novichok., A. dracunculus cv. Smaragd, A. santonica cv. Citral, A. abrotanum cv. Euxin, and A. scoparia cv. Tavrida. The study of the ethanol extracts of the five different Artemisia L. species using the methods of gas chromatography-mass spectrometry (GC-MS) and high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-MS/MS) allowed establishing their phytochemical profile. The obtained data on the of five different Artemisia L. species ethanol extracts' phytochemical composition were used to predict the antibacterial and antifungal activity against phytopathogenic microorganisms and nematocidal activity against the free-living soil nematode Caenorhabditis elegans. The major compounds found in the composition of the Artemisia L. ethanol extracts were monoterpenes, sesquiterpenes, flavonoids, flavonoid glycosides, coumarins, and phenolic acids. The antibacterial and antifungal activity of the extracts began to manifest at a concentration of 150 µg/mL. The A. dracunculus cv. Smaragd extract had a selective effect against Gram-positive R. iranicus and B. subtilis bacteria, whereas the A. scoparia cv. Tavrida extract had a selective effect against Gram-negative A. tumefaciens and X. arboricola bacteria and A. solani, R. solani and F. graminearum fungi. The A. annua cv. Novichok, A. dracunculus cv. Smaragd, and A. santonica cv. Citral extracts in the concentration range of 31.3-1000 µg/mL caused the death of nematodes. It was established that A. annua cv. Novichok affects the UNC-63 protein, the molecular target of which is the nicotine receptor of the N-subtype.

An Extracytoplasmic Function Sigma Factor Required for Full Virulence in Xanthomonas citri pv. citri.

The genus Xanthomonas includes more than 30 phytopathogenic species that infect a wide range of plants and cause severe diseases that greatly impact crop productivity. These bacteria are highly adapted to the soil and plant environment, being found in decaying material, as epiphytes, and colonizing the plant mesophyll. Signal transduction mechanisms involved in the responses of Xanthomonas to environmental changes are still poorly characterized. Xanthomonad genomes typically encode several representatives of the extracytoplasmic function σ (σECF) factors, whose physiological roles remain elusive. In this work, we functionally characterized the Xanthomonas citri pv. citri EcfL, a σECF factor homologous to members of the iron-responsive FecI-like group. We show that EcfL is not required or induced during iron starvation, despite presenting the common features of other FecI-like σECF factors. EcfL positively regulates one operon composed of three genes that encode a TonB-dependent receptor involved in cell surface signaling, an acid phosphatase, and a lectin-domain containing protein. Furthermore, we demonstrate that EcfL is required for full virulence in citrus, and its regulon is induced inside the plant mesophyll and in response to acid stress. Together, our study suggests a role for EcfL in the adaptation of X. citri to the plant environment, in this way contributing to its ability to cause citrus canker disease. IMPORTANCE The Xanthomonas genus comprises a large number of phytopathogenic species that infect a wide variety of economically important plants worldwide. Bacterial adaptation to the plant and soil environment relies on their repertoire of signal transduction pathways, including alternative sigma factors of the extracytoplasmic function family (σECF). Here, we describe a new σECF factor found in several Xanthomonas species, demonstrating its role in Xanthomonas citri virulence to citrus plants. We show that EcfL regulates a single operon containing three genes, which are also conserved in other Xanthomonas species. This study further expands our knowledge on the functions of the widespread family of σECF factors in phytopathogenic bacteria.

A CRISPR-based lateral flow assay for plant genotyping and pathogen diagnostics.

Efficient pathogen diagnostics and genotyping methods enable effective disease management and breeding, improve crop productivity and ensure food security. However, current germplasm selection and pathogen detection techniques are laborious, time-consuming, expensive and not easy to mass-scale application in the field. Here, we optimized a field-deployable lateral flow assay, Bio-SCAN, as a highly sensitive tool to precisely identify elite germplasm and detect mutations, transgenes and phytopathogens in <1 h, starting from sample isolation to result output using lateral flow strips. As a proof of concept, we genotyped various wheat germplasms for the Lr34 and Lr67 alleles conferring broad-spectrum resistance to stripe rust, confirmed the presence of synthetically produced herbicide-resistant alleles in the rice genome and screened for the presence of transgenic elements in the genome of transgenic tobacco and rice plants with 100% specificity. We also successfully applied this new assay to the detection of phytopathogens, including viruses and bacterial pathogens in Nicotiana benthamiana, and two destructive fungal pathogens (Puccinia striiformis f. sp. tritici and Magnaporthe oryzae Triticum) in wheat. Our results illustrate the power of Bio-SCAN in crop breeding, genetic engineering and pathogen diagnostics to enhance food security. The high sensitivity, simplicity, versatility and in-field deployability make the Bio-SCAN as an attractive molecular diagnostic tool for diverse applications in agriculture.

The Maize Pathogen Ustilago maydis Secretes Glycoside Hydrolases and Carbohydrate Oxidases Directed toward Components of the Fungal Cell Wall.

Filamentous fungi are keystone microorganisms in the regulation of many processes occurring on Earth, such as plant biomass decay and pathogenesis as well as symbiotic associations. In many of these processes, fungi secrete carbohydrate-active enzymes (CAZymes) to modify and/or degrade carbohydrates. Ten years ago, while evaluating the potential of a secretome from the maize pathogen Ustilago maydis to supplement lignocellulolytic cocktails, we noticed it contained many unknown or poorly characterized CAZymes. Here, and after reannotation of this data set and detailed phylogenetic analyses, we observed that several CAZymes (including glycoside hydrolases and carbohydrate oxidases) are predicted to act on the fungal cell wall (FCW), notably on ß-1,3-glucans. We heterologously produced and biochemically characterized two new CAZymes, called UmGH16_1-A and UmAA3_2-A. We show that UmGH16_1-A displays ß-1,3-glucanase activity, with a preference for ß-1,3-glucans with short ß-1,6 substitutions, and UmAA3_2-A is a dehydrogenase catalyzing the oxidation of ß-1,3- and ß-1,6-gluco-oligosaccharides into the corresponding aldonic acids. Working on model ß-1,3-glucans, we show that the linear oligosaccharide products released by UmGH16_1-A are further oxidized by UmAA3_2-A, bringing to light a putative biocatalytic cascade. Interestingly, analysis of available transcriptomics data indicates that both UmGH16_1-A and UmAA3_2-A are coexpressed, only during early stages of U. maydis infection cycle. Altogether, our results suggest that both enzymes are connected and that additional accessory activities still need to be uncovered to fully understand the biocatalytic cascade at play and its physiological role. IMPORTANCE Filamentous fungi play a central regulatory role on Earth, notably in the global carbon cycle. Regardless of their lifestyle, filamentous fungi need to remodel their own cell wall (mostly composed of polysaccharides) to grow and proliferate. To do so, they must secrete a large arsenal of enzymes, most notably carbohydrate-active enzymes (CAZymes). However, research on fungal CAZymes over past decades has mainly focused on finding efficient plant biomass conversion processes while CAZymes directed at the fungus itself have remained little explored. In the present study, using the maize pathogen Ustilago maydis as model, we set off to evaluate the prevalence of CAZymes directed toward the fungal cell wall during growth of the fungus on plant biomass and characterized two new CAZymes active on fungal cell wall components. Our results suggest the existence of a biocatalytic cascade that remains to be fully understood.