Review: Plant microRNAs in pathogen defense: A panacea or a piece of the puzzle?

Plant microRNAs (miRNAs) control key agronomic traits that are associated with their conserved role(s) in development. However, despite a multitude of studies, the utility of miRNAs in plant-pathogen resistance remains less certain. Reviewing the literature identifies three general classes of miRNAs regarding plant pathogen defense. Firstly, a number of evolutionary dynamic 22 nucleotide miRNA families that repress large numbers of plant immunity genes, either directly, or through triggering the biogenesis of secondary siRNAs. However, understanding of their role in defense and of their manipulation to enhance pathogen resistance are still lacking. Secondly, highly conserved miRNAs that indirectly impact disease resistance through their targets that are primarily regulating development or hormone signaling. Any alteration of these miRNAs usually results in pleiotropic impacts, which may alter disease resistance in some plant species, and against some pathogens. Thirdly, are the comparatively diverse and evolutionary dynamic set of non-conserved miRNAs, some of which contribute to pathogen resistance, but whose narrow evolutionary presence will likely restrict their utility. Therefore, reflecting the diverse and evolving nature of plant-pathogen interactions, a complex interplay of plant miRNAs with pathogen responses exists. Any miRNA-based solution for pathogen resistance will likely be highly specific, rather than a general panacea.

Algal macromolecular mediated synthesis of nanoparticles for their application against citrus canker for food security

Citrus canker is a disease of economic importance and there are limited biocontrol agents available to mitigate it in an integrated manner. This study was conducted to combat citrus canker disease using biologically active nanoparticles (Ag, Cu and ZnO and 300, 900, 1200, and 1500 ppm) synthesized from macromolecules extracted from alga, Oedogonium sp. The synthesis of the nanoparticles was confirmed by UV-Vis Spectroscopy, FTIR, SEM, XRD, and DLS Zeta sizer while their efficacy was tested against Xanthomonas citri by measuring zone of inhibition. Results indicated that Ag and Cu nanoparticles at 1200 ppm exhibit the highest activity against Xanthomonas citri, followed by ZnO at 1500 ppm. The minimum inhibitory concentrations (MIC) of Ag, Cu and ZnO NPs were 1, 2 and 10 mg mL-1, respectively while minimum bactericidal concentrations (MBC) were for Ag and Cu 2, 4 mg mL-1 and for ZnO NPs more then 10 mg mL-1, were required to kill the X. citri. Bacterial growth respectively. Macromolecules extracted from algal sources can produce nanoparticles with bactericidal potential, in the order of Ag > Cu > ZnO to mitigate citrus canker disease and ensuring sustainable food production amid the growing human population.

Bioinspired silver nanoparticle-based nanocomposites for effective control of plant pathogens: A review

Plant pathogens, including bacteria, fungi, and viruses, pose significant challenges to the farming community due to their extensive diversity, the rapidly evolving phenomenon of multi-drug resistance (MDR), and the limited availability of effective control measures. Amid mounting global pressure, particularly from the World Health Organization, to limit the use of antibiotics in agriculture and livestock management, there is increasing consideration of engineered nanomaterials (ENMs) as promising alternatives for antimicrobial applications. Studies focusing on the application of ENMs in the fight against MDR pathogens are receiving increasing attention, driven by significant losses in agriculture and critical knowledge gaps in this crucial field. In this review, we explore the potential contributions of silver nanoparticles (AgNPs) and their nanocomposites in combating plant diseases, within the emerging interdisciplinary arena of nano-phytopathology. AgNPs and their nanocomposites are increasingly acknowledged as promising countermeasures against plant pathogens, owing to their unique physicochemical characteristics and inherent antimicrobial properties. This review explores recent advancements in engineered nanocomposites, highlights their diverse mechanisms for pathogen control, and draws attention to their potential in antibacterial, antifungal, and antiviral applications. In the discussion, we briefly address three crucial dimensions of combating plant pathogens: green synthesis approaches, toxicity-environmental concerns, and factors influencing antimicrobial efficacy. Finally, we outline recent advancements, existing challenges, and prospects in scholarly research to facilitate the integration of nanotechnology across interdisciplinary fields for more effective treatment and prevention of plant diseases.

Distribution and conservation of simple sequence repeats in plant pathogenic species of Zymoseptoria and development of genomic resources for its orphaned species

To better understand the structure and evolution of the genomes of four plant pathogenic species of Zymoseptoria, we analyzed the occurrence, relative abundance (RA), and density (RD) of simple sequence repeats (SSRs) in their whole genome and transcriptome sequences. In this study, SSRs are defined as repeats of more than 12 bases in length. The genome and transcriptome sequences of Zymoseptoria ardabiliae show the highest RA (201.1 and 129.9) and RD (3229.4 and 1928.2) of SSRs, while those of Zymoseptoria pseudotritici show the lowest RA (167.2 and 118.5) and RD (2482.2 and 1687.0). The majority of SSRs in the genomic and transcriptome sequences of species were trinucleotide SSRs, while dinucleotide SSRs were the least common. The most common trinucleotide motifs in the transcriptomic sequences across all species were those that encoded the amino acid arginine. As per our motif conservation study, Zymoseptoria tritici (12.4%) possessed the most unique motifs, while Z. pseudotritici (3.9%) had the fewest. Overall, only 38.1% of the motifs were found to be conserved among the species. Gene enrichment studies reveal that three of the species, Z. ardabiliae, Zymoseptoria brevis, and Z. pseudotritici, have SSRs in their genes related to cellular metabolism, while the remaining Z. tritici harbors SSRs in genes related to DNA synthesis and gene expression. In an effort to improve the genetic resources for the orphan species of pathogenic Zymoseptoria, a total of 73,134 primers were created. The genomic resources developed in this study could help with analyses of genetic relatedness within the population and the development of species-specific markers.

Characterisation of the mating-type loci in species of Elsinoe causing scab diseases

The genus Elsinoe includes many aggressive plant pathogens that infect various economically important agricultural, horticultural and forestry plants. Significant diseases include citrus scab caused by E. fawcettii and E. australis, grapevine spot anthracnose by E. ampelina, and the emerging Eucalyptus scab and shoot malformation disease caused by the recently described E. necatrix. Despite their importance as plant pathogens, little is known regarding the biology of many Elsinoe spp. To gain insights into the reproductive biology of these fungi, we characterized the mating-type loci of seven species using whole genome sequence data. Results showed that the MAT1 locus organization and its flanking genes is relatively conserved in most cases. All seven species manifested a typical heterothallic mating system characterized by having either the MAT1-1 or MAT1-2 idiomorph present in an isolate. These idiomorphs were defined by the MAT1-1-1 or the MAT1-2-1 gene, respectively. A unique MAT1-1 idiomorph containing a truncated MAT1-2-1 gene, and a MAT1-1-1 gene, was identified in E. necatrix and E. fawcettii genomes. Additionally, two idiomorph-specific proteins were found in the MAT1-1 and MAT1-2 idiomorphs of E. australis. Universal mating-type markers confirmed heterothallism across 21 Elsinoe spp., are poised to advance future studies regarding the biology of these fungi.

Genome-wide survey and evolutionary history of the pectin methylesterase (PME) gene family in the Dothideomycetes class of fungi

Once deposited in the plant cell wall, pectin undergoes demethylesterification by endogenous pectin methylesterases (PMEs), which play various roles in growth and development, including defense against pathogen attacks. Pathogen PMEs can alter pectin's methylesterification pattern, increasing its susceptibility to degradation by other fungal pectinases and thus playing a critical role as virulence factors during early infection stages. To investigate the evolutionary history of PMEs in the Dothideomycetes class of fungi, we obtained genomic data from 15 orders (79 species) and added genomic data from 61 isolates of Corynespora cassiicola. Our analyses involved maximum likelihood phylogenies, gene genealogies, and selection analyses. Additionally, we measured PME gene expression levels of C. cassiicola using soybean as a host through RT-qPCR assays. We recovered 145 putative effector PMEs and 57 putative non-effector PMEs from across the Dothideomycetes. The PME gene family exhibits a small size (up to 5 members per genome) and comprises three major clades. The evolutionary patterns of the PME1 and PME2 clades were largely shaped by duplications and recurring gene retention events, while biased gene loss characterized the small-sized PME3 clade. The presence of five members in the PME gene family of C. cassiicola suggests that the family may play a key role in the evolutionary success of C. cassiicola as a polyphagous plant pathogen. The haplogroups Cc_PME1.1 and Cc_PME1.2 exhibited an accelerated rate of evolution, whereas Cc_PME2.1, Cc_PME2.2, and Cc_PME2.3 seem to be under strong purifying selective constraints. All five PME genes were expressed during infection of soybean leaves, with the highest levels during from six to eight days post-inoculation. The highest relative expression level was measured for CC_29_g7533, a member of the Cc_PME2.3 clade, while the remaining four genes had relatively lower levels of expression.

Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen

BACKGROUND

In agricultural ecosystems, outbreaks of diseases are frequent and pose a significant threat to food security. A successful pathogen undergoes a complex and well-timed sequence of regulatory changes to avoid detection by the host immune system; hence, well-tuned gene regulation is essential for survival. However, the extent to which the regulatory polymorphisms in a pathogen population provide an adaptive advantage is poorly understood.

RESULTS

We used Zymoseptoria tritici, one of the most important pathogens of wheat, to generate a genome-wide map of regulatory polymorphism governing gene expression. We investigated genome-wide transcription levels of 146 strains grown under nutrient starvation and performed expression quantitative trait loci (eQTL) mapping. We identified cis-eQTLs for 65.3% of all genes and the majority of all eQTL loci are within 2kb upstream and downstream of the transcription start site (TSS). We also show that polymorphism in different gene elements contributes disproportionally to gene expression variation. Investigating regulatory polymorphism in gene categories, we found an enrichment of regulatory variants for genes predicted to be important for fungal pathogenesis but with comparatively low effect size, suggesting a separate layer of gene regulation involving epigenetics. We also show that previously reported trait-associated SNPs in pathogen populations are frequently cis-regulatory variants of neighboring genes with implications for the trait architecture.

CONCLUSIONS

Overall, our study provides extensive evidence that single populations segregate large-scale regulatory variation and are likely to fuel rapid adaptation to resistant hosts and environmental change.

Biogenic zinc oxide nanoparticles: A viable agricultural tool to control plant pathogenic fungi and its potential effects on soil and plants

Fungal and bacterial pathogens represent some of the greatest challenges facing crop production globally and account for about 20-40 % crop losses annually. This review highlights the use of ZnO NPs as antimicrobial agents and explores their mechanisms of actions against disease causing plant fungal pathogens. The behavior of ZnO NPs in soil and their interactions with the soil components were also highlighted. The review discusses the potential effects of ZnO NPs on plants and their mechanisms of action on plants and how these mechanisms are related to their physicochemical properties. In addition, the reduction of ZnO NPs toxicity through surface modification and coating with silica is also addressed. Soil properties play a significant role in the dispersal, aggregation, stability, bioavailability, and transport of ZnO NPs and their release into the soil. The transport of ZnO NPs into the soil might influence soil components and, as a result, plant physiology. The harmful effects of ZnO NPs on plants and fungi are caused by a variety of processes, the most important of which is the formation of reactive oxygen species, lysosomal instability, DNA damage, and the reduction of oxidative stress by direct penetration/liberation of Zn2+ ions in plant/fungal cells. Based on these highlighted areas, this review concludes that ZnO NPs exhibit its antifungal activity via generations of reactive oxygen species, coupled with the inhibition of various metabolic pathways. Despite the numerous advantages of ZnO NPs, there is need to regulate its uses to minimize the harmful effects that may arise from its applications in the soil and plants.

Genetic rearrangements in Pseudomonas amygdali pathovar aesculi shape coronatine plasmids

Plant pathogenic Pseudomonas species use multiple classes of toxins and virulence factors during host infection. The genes encoding these pathogenicity factors are often located on plasmids and other mobile genetic elements, suggesting that they are acquired through horizontal gene transfer to confer an evolutionary advantage for successful adaptation to host infection. However, the genetic rearrangements that have led to mobilization of the pathogenicity genes are not fully understood. In this study, we have sequenced and analyzed the complete genome sequences of four Pseudomonas amygdali pv. aesculi (Pae), which infect European horse chestnut trees (Aesculus hippocastanum) and belong to phylogroup 3 of the P. syringae species complex. The four investigated genomes contain six groups of plasmids that all encode pathogenicity factors. Effector genes were found to be mostly associated with insertion sequence elements, suggesting that virulence genes are generally mobilized and potentially undergo horizontal gene transfer after transfer to a conjugative plasmid. We show that the biosynthetic gene cluster encoding the phytotoxin coronatine was recently transferred from a chromosomal location to a mobilizable plasmid that subsequently formed a co-integrate with a conjugative plasmid.

Long-term fertilization suppresses rice pathogens by microbial volatile compounds

Microbial volatile organic compounds (VOCs) can suppress plant pathogens. Although fertilization strongly affects soil microbial communities, the influence of fertilization on microbial VOC-mediated suppression of pathogens has not been elucidated. Soil was sampled from a paddy field that had been subjected to the following treatments for 30 years: a no-fertilizer control, mineral fertilization (NPK), NPK combined with rice straw (NPK + S), NPK combined with chicken manure (70% NPK + 30% M). Then, within a laboratory experiment, pathogens were exposed to VOCs without physical contact to assess the impact of VOCs emitted from paddy soils on in vitro growth of the fungal rice pathogens: Pyricularia oryzae and Rhizoctonia solani. The VOCs emitted from soil reduced the mycelial biomass of P. oryzae and R. solani by 36-51% and 10-30%, respectively, compared to that of the control (no soil; no VOCs emission). Overall, the highest suppression of P. oryzae and R. solani was in the NPK and NPK + S soils, which emitted more quinones, phenols, and low alcohols than NPK + M soils. The abundances of quinones and phenols in the soil air were maximal in the NPK-fertilized soil because the low ratio of dissolved organic carbon and Olsen-P increased the population of key species such as Acidobacteriae, Anaerolineae, and Entorrhizomycetes. The abundance of alcohols was minimum in the NPK + S fertilized soil because the high SOC content decreased the population of Sordariomycetes. In conclusion, mineral fertilization affects bacterial and fungal VOC emissions, thereby suppressing the growth of R. solani and P. oryzae.

Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genus Pseudozyma (Ustilaginales)

BACKGROUND

The Ustilaginales comprise hundreds of plant-parasitic fungi with a characteristic life cycle that directly links sexual reproduction and parasitism: One of the two mating-type loci codes for a transcription factor that not only facilitates mating, but also initiates the infection process. However, several species within the Ustilaginales have no described parasitic stage and were historically assigned to the genus Pseudozyma. Molecular studies have shown that the group is polyphyletic, with members being scattered in various lineages of the Ustilaginales. Together with recent findings of conserved fungal effectors in these non-parasitic species, this raises the question if parasitism has been lost recently and in multiple independent events or if there are hitherto undescribed parasitic stages of these fungi.

RESULTS

In this study, we sequenced genomes of five Pseudozyma species together with six parasitic species from the Ustilaginales to compare their genomic capability to perform two central functions in sexual reproduction: mating and meiosis. While the loss of sexual capability is assumed in certain lineages and asexual species are common in Asco- and Basidiomycota, we were able to successfully annotate potentially functional mating and meiosis genes that are conserved throughout the whole group.

CONCLUSION

Our data suggest that at least the key functions of a sexual lifestyle are maintained in the analyzed genomes, challenging the current understanding of the so-called asexual species with respect to their evolution and ecological role.

Long-term impact of pulses crop rotation on soil fungal diversity in aerobic and wetland rice cultivation

Pulse crop rotation in rice cultivation is a widely accepted agronomic practice. Depending upon the water regime, rice cultivation has been classified into wetland and aerobic practices. However, no studies have been conducted so far to understand the impact of pulse crop rotation and rice mono-cropping on fungal diversity, particularly in aerobic soil. A targeted metagenomic study was conducted to compare the effects of crop rotations (rice-rice and rice-pulse) on fungal diversity in wetland and aerobic rice soils. Out of 445 OTUs, 41.80% was unknown and 58.20% were assigned to six phyla, namely Ascomycota (56.57%), Basidiomycota (1.32%), Zygomycota (0.22%), Chytridiomycota (0.04%), Glomeromycota (0.03%), and Blastocladiomycota (0.02%). Functional trait analysis found wetland rice-pulse rotation increased symbiotrophs (36.7%) and saprotrophs (62.1%) population, whereas higher pathotrophs were found in aerobic rice-rice (62.8%) and rice-pulse (61.4%) cropping system. Certain soil nutrients played a major role in shaping the fungal community; Ca had significant (p < 0.05) positive impact on saprotroph, symbiotroph and endophytes, whereas Cu had significant (p < 0.05) negative impact on pathotrophs. This study showed that rice-pulse crop rotation could enhance the saprophytic and symbiotic fungal diversity in wetland and reduce the population of pathogens in aerobic rice cultivation.

Comparative analysis of adenylate isopentenyl transferase genes in plant growth-promoting bacteria and plant pathogenic bacteria

Cytokinin is a major phytohormone that has been used in agriculture as a plant-growth stimulating compound since its initial discovery in the 1960s. Isopentenyl transferase (IPT) is a rate-limiting enzyme for cytokinin biosynthesis, which is produced by plants as well as bacteria including both plant pathogenic species and plant growth-promoting bacteria (PGPB). It has been hypothesized that there may be differences in IPT function between plant pathogens and PGPB. However, a comprehensive comparison of IPT genes between plant pathogenic and PGPB species has not been performed. Here, we performed a global comparison of IPT genes across bacteria, analyzing their DNA sequences, codon usage, phyletic distribution, promoter structure and genomic context. We found that adenylate type IPT genes are highly specific to plant-associated bacteria and subdivide into two major clades: clade A, largely composed of proteobacterial plant pathogens; and clade B, largely composed of actinomycete PGPB species. Besides these phylogenetic differences, we identified several genomic features that suggest differences in IPT regulation between pathogens and PGPB. Pathogen-associated IPTs tended to occur in predicted virulence loci, whereas PGPB-associated IPTs tended to co-occur with other genes involved in cytokinin metabolism and degradation. Pathogen-associated IPTs also showed elevated gene copy numbers, significant deviation in codon usage patterns, and extended promoters, suggesting differences in regulation and activity levels. Our results are consistent with the hypothesis that differences in IPT regulation and activity exist between plant pathogens and PGPB, which determine their effect on plant host phenotypes through the control of cytokinin levels.

Fatal attraction: How Phytophthora zoospores find their host

Oomycete plant pathogens, such as Phytophthora and Pythium species produce motile dispersal agents called zoospores that actively target host plants. Zoospores are exceptional in their ability to display taxis to chemical, electrical and physical cues to navigate the phyllosphere and reach stomata, wound sites and roots. Many components of root exudates have been shown attractive or repulsive to zoospores. Although some components possess very strong attractiveness, it seems that especially the mix of components exuded by the primary host is most attractive to zoospores. Zoospores actively approach attractants with swimming behaviour reminiscent of other microswimmers. To achieve a unified description of zoospore behaviour when sensing an attractant, we propose the following terms for the successive stages of the homing response: reorientation, approaching, retention and settling. How zoospores sense and process attractants is poorly understood but likely involves signal perception via cell surface receptors. Since zoospores are important for infection, undermining their activity by luring attractants or blocking receptors seem promising strategies for disease control.

FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species

Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and Fun^Fun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.

Genome sequencing and annotation of Cercospora sesami, a fungal pathogen causing leaf spot to Sesamum indicum

Cercospora sesami is a plant pathogen that causes leaf spot disease in sesame plants worldwide. In this study, genome sequence assembly of C. sesami isolate Cers 52-10 (MCC 9069) was generated using native paired-end and mate-pair DNA sequencing based on the Illumina HiSeq 2500 platform. The genome assembly of C. sesami is 34.3 Mb in size with an N50 of 26,222 bp and an average GC content of 53.02%. A total number of 10,872 genes were predicted in this study, out of which 9,712 genes were functionally annotated. Genes assigned to carbohydrate-active enzyme classes were also identified during the study. A total of 80 putative effector candidates were predicted and functionally annotated. The C. sesami genome sequence is available at DDBJ/ENA/GenBank, and other associated information is submitted to Mendeley's data.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03468-4.

Bacillus sp. extract used to fabricate ZnO nanoparticles for their antagonist effect against phytopathogens

In order to achieve the food demand of a growing population, agricultural productivity needs to be increased by employing safe strategies. In the present study we have evaluated ZnONPs that were synthesized from the culture supernatant of Bacillus subtilis. Bio mimetically synthesized ZnONPs showed a surface resonance peak of 355 nm corresponding to NPs formation. Further, NPs were examined for their size, shape and element confirmation by DLS, AFM, SEM, TEM and EDAX, which confirmed the synthesized NPs were nearly spherical in size with average diameter of 32 nm by TEM. Surface charge of + 34.3 mV was observed for NPs with a low poly-dispersity index of 0.21. In vitro efficacy studies against fungi Colletotrichum capsici, Sclerotium rolfsii, Alternaria solani and Fusarium oxysporum f. sp. cicero showed up to 99% mycelial growth inhibition at 0.125% ZnONPs. Further, in-vitro disk-diffusion assay showed inhibition zones of 23 ± 0.4 mm and 12.67 ± 0.24 mm for Xanthomonas axonopodis pv. punicae (Xap) and Xanthomonas oryzae pv. oryzae (Xoo) bacterial cultures. Plant toxicity study was observed that ≤ 0.14% NPs concentration was safe under greenhouse conditions. Overall, the present study emphasizes the potential effect of ZnONPs against agricultural pathogens which play an important role in agriculture production.

Molecular sensors reveal the mechano-chemical response of Phytophthora infestans walls and membranes to mechanical and chemical stress

Phytophthora infestans, causal agent of late blight in potato and tomato, remains challenging to control. Unravelling its biomechanics of host invasion, and its response to mechanical and chemical stress, could provide new handles to combat this devastating pathogen. Here we introduce two fluorescent molecular sensors, CWP-BDP and NR12S, that reveal the micromechanical response of the cell wall-plasma membrane continuum in P. infestans during invasive growth and upon chemical treatment. When visualized by live-cell imaging, CWP-BDP reports changes in cell wall (CW) porosity while NR12S reports variations in chemical polarity and lipid order in the plasma membrane (PM). During invasive growth, mechanical interactions between the pathogen and a surface reveal clear and localized changes in the structure of the CW. Moreover, the molecular sensors can reveal the effect of chemical treatment to CW and/or PM, thereby revealing the site-of-action of crop protection agents. This mechano-chemical imaging strategy resolves, non-invasively and with high spatio-temporal resolution, how the CW-PM continuum adapts and responds to abiotic stress, and provides information on the dynamics and location of cellular stress responses for which, to date, no other methods are available.

Pre-invasion assessment on African invasive grasses revealed five new species of ergot fungi, Claviceps section Pusillae

Ergot, the genus Claviceps comprises several deeply diverged lineages, recently classified as sections. Among them, the section Pusillae, is the most speciose, with a centre of distribution in Africa but occurring worldwide, often as a consequence of its invasive potential. This section includes the most severe plant pathogens such as Claviceps africana and C. gigantea, responsible for toxicoses and a significant reduction in the seed yields of Sorghum and Zea. In this study we surveyed ergot diversity in South Africa, focusing on grasses native to this region, but known for their high potential of invasiveness. The revision based on molecular and phenotypic markers revealed 16 species, with a high proportion of undescribed diversity, confirming Africa as a hot spot for this section. Five new species, Claviceps tulasnei, Claviceps eulaliae, Claviceps hypertheliae, Claviceps fredericksoniae and Claviceps arundinellae were described from Setaria, Eulalia, Hyperthelia, Miscanthus and Arundinella respectively. Claviceps texensis infecting Cenchrus, previously only identified from the same host in Texas, USA, was confirmed to be present in Africa, which is assumed to be its primary area of distribution. In addition, the host grass genus Anthephora is newly reported as a host of Claviceps digitariae. The most of the taxa were negligible concerning alkaloid production, with the exception of C. fredericksoniae, which is a sister of potent alkaloid producer C. africana, and produces mainly DH-ergosine, together with traces of DH-ergocornine. The host/parasite associations within Pusillae section is very narrow, suggesting that co-speciation is the major speciation driver in this group. Host grasses of the described species are already recognised invasive species and their ovarial parasites need to be monitored. This is highlighted by the fact that all Pusillae produced air-borne secondary conidia, which is autapomorphy of this section and considered to be important for their invasive abilities.

Microorganisms in biological control strategies to manage microbial plant pathogens: a review

Chemical fertilizers and pesticides are an integral part of modern agriculture and are often associated with numerous environmental problems. Biological agents such as microorganisms can largely replace chemical fertilizers and pesticides. The proper use of selected microorganisms such as bacteria, fungi and viruses have several benefits for agriculture. These include a healthy soil microbiota, biological production of important compounds that promote plant health, and to be used as biocontrol agents (BCAs) that provide protection from plant pathogenic microorganisms. Scientists have found that several bacterial genera including Bacillus and Pseudomonas have antimicrobial activity against numerous pathogenic bacterial and fungal plant pathogens. Trichoderma, Aspergillus, and Penicillium are among the most common fungal genera used as BCAs against both bacterial and fungal plant pathogens. Several bacteriophages and mycoviruses are also found effective as BCAs against selective plant pathogens. Fusarium oxysporum is a commonly found microbial plant pathogen causing wilts and rots in plants. Overall, it can be concluded that the use of microbial BCAs is an effective practice against microbial plant pathogens.

Scaling-up to understand tree-pathogen interactions: A steep, tough climb or a walk in the park?

Plants have proficient tools that allow them to survive interactions with pathogens. Upon attack, they respond with specific countermeasures, which are controlled by the immune system. However, defences can fail and this failure exposes plants to fast-spreading devastation. Trees face similar challenges to other plants and their immune system allows them to mount defences against pathogens. However, their slow growth, longevity, woodiness, and size can make trees a challenging system to study. Here, we review scientific successes in plant systems, highlight the key challenges and describe the enormous opportunities for pathology research in trees. We discuss the benefits that scaling-up our understanding on tree-pathogen interactions can provide in the fight against plant pathogenic threats.

Secondary metabolites of the genus Nigrospora from terrestrial and marine habitats: Chemical diversity and biological activity

Secondary metabolites produced by the ascomycetes have attracted wide attention from researchers. Their diverse chemical structures and rich biological activities are essential in medicine, food, and agriculture. The monophyletic Nigrospora genus belongs to the Apiosporaceae family and is a rich source of novel and diverse bioactive metabolites. It occurs as a common plant pathogen, endophyte, and saprobe distributed in many ecosystems worldwide. Researchers have focused on discovering new species and secondary metabolites in the past ten years. The host diseases caused by Nigrospora species are also investigated. This review describes 50 references from Web of Science, CNKI, Google Scholar and PubMed related to the secondary metabolites from Nigrospora. Here, a total of 231 compounds isolated from five known species and 21 unidentified species of Nigrospora from January 1991 to June 2022 are summarized. Their structures are attributed to polyketides, terpenoids, steroids, N-containing compounds, and fatty acids. Meanwhile, 77 metabolites exhibited various biological activities like cytotoxic, antifungal, antibacterial, antiviral, antioxidant, anti-inflammatory, antileukemic, antimalarial, phytotoxic, enzyme inhibitory, etc. Notably, this review presents a comprehensive literature survey focusing on the chemistry and bioactivity of secondary metabolites from Nigrospora.

Zinc nanoparticles: Mode of action and efficacy against boscalid-resistant Alternaria alternata isolates

The antifungal potential of ZnO-NPs against Alternaria alternata isolates with reduced sensitivity to the succinate dehydrogenase inhibitor (SDHI) boscalid, resulting from target site modifications, was evaluated in vitro and in vivo. ZnO-NPs could effectively inhibit mycelial growth in a dose-dependent way in both boscalid (BOSC) sensitive (BOSC-S) and resistant (BOSC-R) isolates. The fungitoxic effect of ZnO-NPs against the pathogen was significantly enhanced when combined with boscalid compared to the individual treatments in all phenotype cases (BOSC-S/R) both in vitro and in vivo. Fungitoxic effect of ZnO-NPs could be, at least partly, attributed to zinc ion release as indicated by the positive correlation between sensitivities to the nanoparticles and their ionic counterpart ZnSO₄ and the alleviation of the ZnO-NPs fungitoxic action in the presence of the strong chelating agent EDTA. The superior effectiveness of ZnO-NPs against A. alternata, compared to ZnSO_4, could be due to nanoparticle properties interfering with cellular ion homeostasis mechanisms. The observed additive action of the oxidative phosphorylation-uncoupler fluazinam (FM) against all phenotypes indicates a possible role of ATP-dependent ion efflux mechanism in the mode of action of ZnO-NPs. A potential role of ROS production in the fungitoxic action of ZnO-NPs was evident by the additive/synergistic action of salicylhydroxamate (SHAM), which blocks the alternative oxidase antioxidant action. Mixture of ZnO-NPs and boscalid, resulting in a "capping" effect for the nanoparticles and significantly reducing their mean size, probably accounted for the synergistic effect of the mixture against both sensitive and resistant A. alternata isolates. Summarizing, results indicated that ZnO-NPs can be effectively used against A. alternata both alone or in combination with boscalid, providing an effective tool for combating SDHI-resistance and reducing the environmental fingerprint of synthetic fungicides.

Interactive effects of tropospheric ozone and blast disease (Magnaporthe oryzae) on different rice genotypes

Rising tropospheric ozone concentrations can cause rice yield losses and necessitate the breeding of ozone-tolerant rice varieties. However, ozone tolerance should not compromise the resistance to important biotic stresses such as the rice blast disease. Therefore, we investigated the interactive effects of ozone and rice blast disease on nine different rice varieties in an experiment testing an ozone treatment, blast inoculation, and their interaction. Plants were exposed to an ozone concentration of 100 ppb for 7 h per day or ambient air throughout the growth period. Half of the plants were simultaneously infected with rice blast inoculum. Grain yield was significantly reduced in the blast treatment (17%) and ozone treatment (37%), while the combination of both stresses did not further decrease grain yields compared to ozone alone. Similar trends occurred for physiological traits such as vegetation indices, normalized difference vegetation index (NDVI), photochemical reflectance index (PRI), Lichtenthaler index 2 (Lic2), and anthocyanin reflectance index 1 (ARI1), as well as stomatal conductance and lipid peroxidation. Ozone exposure mitigated the formation of visible blast symptoms, while blast inoculation did not significantly affect visible ozone symptoms. Although different genotypes showed contrasting responses to the two types of stresses, no systematic pattern was observed regarding synergies or trade-offs under the two types of stresses. Therefore, we conclude that despite the similarities in physiological stress responses to ozone and blast, the tolerance to these stresses does not appear to be genetically linked in rice.

Understanding enemy's weapons to an effective prevention: common virulence effects across microbial phytopathogens kingdoms

Plant-pathogens interaction is an ongoing confrontation leading to the emergence of new diseases. The majority of the invading microorganisms inject effector proteins into the host cell, to bypass the sophisticated defense system of the host. However, the effectors could also have other specialized functions, which can disrupt various biological pathways of the host cell. Pathogens can enrich their effectors arsenal to increase infection success or expand their host range. This usually is accomplished by the horizontal gene transfer. Nowadays, the development of specialized software that can predict proteins structure, has changed the experimental designing in effectors' function research. Different effectors of distinct plant pathogens tend to fold alike and have the same function and focussed structural studies on microbial effectors can help to uncover their catalytic/functional activities, while the structural similarity can enable cataloguing the great number of pathogens' effectors. In this review, we collectively present phytopathogens' effectors with known enzymatic functions and proteins structure, originated from all the kingdoms of microbial plant pathogens. Presentation of their common domains and motifs is also included. We believe that the in-depth understanding of the enemy's weapons will help the development of new strategies to prevent newly emerging or re-emerging plant pathogens.

Insights into the beneficial roles of dark septate endophytes in plants under challenging environment: resilience to biotic and abiotic stresses

Dark septate endophytes (DSE) exert a plethora of effects in regulating plant growth, signalling and stress tolerance. The advent of metagenomics has led to the identification of various species of DSE to be associated with plant organs. They are known to modulate growth, nutrient uptake, phytohormone biosynthesis and production of active bioconstituents in several plants. The interactions between the DSE and host plants are mostly mutualistic but they can also be neutral or exhibit negative interactions. The DSE has beneficial role in removal/sequestration of toxic heavy metals from various environmental sites. Here, we discuss the beneficial role of DSE in enhancing plant tolerance to heavy metal stress, drought conditions, high salinity and protection from various plant pathogens. Furthermore, the underlying mechanism of stress resilience facilitated by DSE-plant interaction has also been discussed. The article also provides insights to some important future perspectives associated with DSE-mediated phytoremediation and reclamation of polluted land worldwide thus facilitating sustainable agriculture.

First report of Cercospora cf. malloti causing brown eyespot on strawberry in Brazil

Strawberry (Fragaria x ananassa Duch.) is one of the most consumed fruits from the Rosaceae family in Brazil. It is cultivated on ~4,500 ha in all regions of the country, with a wide range of fungi causing leaf diseases. Strawberry leaves (cv. San Andreas) with symptoms of eyespot usually related to Mycosphaerella fragariae (Ramularia tulasnei) (Mazaro et al. 2006) were observed in April 2019, in a field located in Santa Maria, Rio Grande do Sul state, Brazil (29°43'19.6"S / 53°43'04.6"W). However, the symptoms slightly differed from Mycospherella blight as well as the fungi structures observed under an optical microscope. The symptomatic leaves had small circular spots, initially reddish-purple to dark brown color, which later increased in size. The center of the lesion was grayish pale, where dark brown conidiophores were found over it. The symptom occurred in 50% of the leaves of all plants during the crop season. To identify the causal agent, symptomatic leaves were collected and superficially disinfected with 70% ethanol for 30 s followed by 0.5% bleach for 30 s and then washed in sterile water. The leaves were placed in germination boxes with a moistened paper filter and incubated at 25 ºC and 12 h photoperiod for four days. After the formation of the fungal structures, the fungi was isolated in potato dextrose agar (PDA) medium and kept for 20 days at 25 ºC. Colonies were dark brown with pale pink aerial mycelium. The conidia were hyaline, single- to multi-septated with a filiform shape, straight or slightly curved. The fasciculate conidiophores on the stroma measured 20 to 70 x 2.5 to 3.5 µm. Conidia average measurement was 10.2 to 82.4 x 4. to 8.8 µm, similar to morphological characteristics of the genus Cercospora. The isolate named M6 was deposited in the Brazilian National System of Genetic Registration (SISGEN) no A57AE19. The DNA was extracted from a monosporic culture of M6 in PDA plates, which presented all typical aspects previously described. To confirm the identity, the PCR amplification was carried out for internal transcribed spacer (ITS) region ITS 1-5.8S - ITS 2 and Calmodulin region (CAL) genes (Acqua et al, 2011). The ITS (No. MZ713249) and CAL (No. MZ713254) sequences were deposited in the Genbank database. BLASTn analysis revealed the isolate was 99% similar to Cercospora cf. malloti which access codes in GenBank are KT 193689 and KT 193738 (Nguanhom et al. 2015). A pathogenicity test was performed to fulfill Koch's postulates. Strawberry plants with healthy leaves (60 days old), were inoculated by spraying a conidial suspension (1 × 105 conidia/ml). Control plants were sprayed with sterile water. The plants were incubated in a greenhouse at 28 ºC for 12 h photoperiod at 80% relative humidity under drip irrigation keeping at least 60% of field capacity. Six plants were used as replicates. Twenty days after inoculation, small circular reddish-purple spots were found, which later increased in size. Ten days later, the spots presented dark brown conidiophores over the center of the lesion. The symptoms described above were observed in all inoculated leaves. The control plants remained symptom-free. The pathogen was then re-isolated from the lesions and identified as C. cf. malloti based on the morphological aspects described above on PDA. In Thailand C. cf. malloti is reported on crops like Brassica alboglabra (cabbage) (Nguanhom et al. 2015), but not in strawberries. To our knowledge, this is the first report of C. cf. malloti pathogenic to strawberries in Brazil.

Invasive Alien Plant Pathogens: The Need of New Detection Methods

Invasive alien species are a major threat to natural and anthropogenic ecosystems and to the economy. Many invasive fungal species have severely impacted ecology and human lifestyle in the past. Most of them express a pathogenic lifestyle following introduction into a new region and hosts. They are usually cryptic during the introduction phase and hard to be identified, classified, and monitored.The increasing number of new alien pests coincide with the rapid increase in the volume and diversity of intercontinental trade in plants for planting, underlying the need to reduce the risk of their introduction with the development of molecular-based, inexpensive, rapid, accurate, and reliable methods that can identify and intercept plant pathogens even before symptoms occur in the new environment of diffusion. Applicative aerobiology, for instance, represents a challenging research line for the implementation of pest detection protocols during the early stage of fungal introduction, being capable to target aerial dispersed propagules.In addition to this, new metabarcoding protocols based on an innovative multigene approach, although not yet tested on fungi, are able to provide an output with very high taxonomic resolution and are likely to be considered in the next-future biosurveillance of invasive fungal pathogens.

DNA Extraction Methods to Obtain High DNA Quality from Different Plant Tissues

DNA extraction from plant samples is very important for a good performance of diagnostic molecular assays in phytopathology. The variety of matrices (such as leaves, roots, and twigs) requires a differentiated approach to DNA extraction. Here we describe three categories of matrices: (a) symptomatic bark/wood tissue; (b) residues of frass resulting from insect woody trophic activities, portions of the galleries produced in the wood, and tissues surrounding exit holes; and (c) leaves of different plant species. To improve the performances of diagnostic assays, we here describe DNA extraction procedures that have been optimized for each matrix type.

Evaluation of Tarsonemus bilobatus and Podosphaera xanthii as suitable resources for Proprioseiopsis mexicanus in cucurbit systems in the Southeast USA

Tritrophic relationships involving tarsonemids and predatory phytoseiids are common in a variety of agroecosystems, but due to the wide range of diets in both families, it is necessary to understand what food resources they are consuming to determine potential impact on crops. We investigated a frequent association of cucurbit powdery mildew (Podosphaera xanthii), Tarsonemus bilobatus, and Proprioseiopsis mexicanus in watermelon and pumpkin fields to determine whether P. mexicanus is consuming either or both of the other organisms. We also examined developmental and reproductive capability of P. mexicanus on these diets. If P. mexicanus is an effective predator of T. bilobatus, it may also be useful in controlling pest tarsonemids, such as broad mites. Proprioseiopsis mexicanus either starved or escaped from arenas rather than consume P. xanthii. When consuming T. bilobatus, P. mexicanus females developed from larva to adult in ca. 3 days. On this diet, the preoviposition period was ca. 2 days and P. mexicanus laid 1.7 eggs/day. These results are comparable to some of the higher-quality non-prey resources investigated in the literature. Starved female P. mexicanus consumed 6.5 T. bilobatus of mixed stages in 1 h. This study provides support for further research into the importance of non-pest tarsonemids as a resource to maintain the presence of generalist predatory mites as an early-intervention natural enemy. Further work should examine the efficacy of P. mexicanus as a natural enemy of economically important pest tarsonemids.

A playbook for developing disease-resistant crops through immune receptor identification and transfer

Plants are resistant to most pathogens because of an immune system that perceives invading microbes and activates defense. A large repertoire of innate immune receptors mediates specific direct or indirect recognition of pathogen-derived molecules. Disease is often a consequence of insufficient immune surveillance, and the transfer of immune receptor genes from resistant plants to susceptible crop varieties is an effective strategy for combating disease outbreaks. We discuss approaches for identifying intracellular and cell surface immune receptors, with particular focus on recently developed and emerging methodologies. We also review considerations for the transfer of immune receptor genes into crop species, including additional host factors that may be required for immune receptor function. Together, these concepts lay out a broadly applicable playbook for developing crop varieties with durable disease resistance.

Molecular targets for antifungals in amino acid and protein biosynthetic pathways

Fungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems caused by fungal pathogens. There is a growing need for improvement of the availability of antifungal drugs, decreasing their prices and reducing side effects. Searching for novel approaches in this respect, amino acid and protein biosynthesis pathways appear to be competitive. The route that leads from amino acid biosynthesis to protein folding and its activation is rich in enzymes that are descriptive of fungi. Blocking the action of those enzymes often leads to avirulence or growth inhibition. In this review, we want to trace the principal processes of fungi vitality. We present the data of genes encoding enzymes involved in amino acid and protein biosynthesis, potential molecular targets in antifungal chemotherapy, and describe the impact of inhibitors on fungal organisms.

Trichoderma as biological control agent: scope and prospects to improve efficacy

A major current challenge is to increase the food production while preserving natural resources. Agricultural practices that enhance the productivity and progressively improve the soil quality are relevant to face this challenge. Trichoderma species are widely used in agriculture to stimulate the plant growth and to control different pathogens affecting crops, representing useful tools for sustainable food production. This mini-review summarizes applications of Trichoderma strains in agriculture to control fungal pathogens, nematodes and insects, the involved biocontrol mechanisms, efficacy and inoculation forms in greenhouse, field and post-harvest conditions. Aspects of Trichoderma handling that influence on biocontrol efficacy such as preventive treatments, frequency of applications and delivery methods are discussed. Strategies useful to improve the antagonistic performance such as the use of native strains, protoplast fusion, formulation, growth on pathogen cell wall medium and combination with other antagonists in integrated treatments are discussed. This mini-review provides practical knowledge to design safe and optimal biocontrol strategies based on Trichoderma and pose challenges to expand its antagonist performance.

Selection and characterization of two monoclonal antibodies specific for the Aspergillus flavus major antigenic cell wall protein Aflmp1

Aspergillus flavus is a major fungal pathogen of plants and an opportunistic pathogen of humans. In addition to the direct impact of infection, it produces immunosuppressive and carcinogenic aflatoxins. The early detection of A. flavus is therefore necessary to diagnose and monitor fungal infection, to prevent aflatoxin contamination of food and feed, and for effective antifungal therapy. Aspergillus-specific monoclonal antibodies (mAbs) are promising as diagnostic and therapeutic reagents for the tracking and treatment of Aspergillus infections, respectively. However, A. flavus has a complex cell wall composition and dynamic morphology, hindering the discovery of mAbs with well-characterized targets. Here we describe the generation and detailed characterization of mAb5.52 (IgG2aκ) and mAb17.15 (IgG1κ), which bind specifically to the highly immunogenic cell wall antigen A. flavus mannoprotein 1 (Aflmp1). Both mAbs were generated using hybridoma technology following the immunization of mice with a recombinant truncated version of Aflmp1 (ExD, including the homologous CR4 domain) produced in bacteria. We show that mAb5.52 and mAb17.15 bind specifically to A. flavus and A. parasiticus cell wall fragments (CWFs), with no cross-reaction to CWFs from other fungal pathogens. Immunofluorescence microscopy revealed that both mAbs bind to the surface of Aspergillus hyphae and that mAb17.15 also binds to spores. The epitope for both mAbs is localized within the CR4 region of the Aflmp1 protein. These Aspergillus-specific mAbs may be useful for the early detection of fungal infection in food/feed crops, for serodiagnosis in patients with invasive aspergillosis caused by A. flavus infection and for the development of antibody-expressing disease-resistant crops.

Plant-produced bacteriocins inhibit plant pathogens and confer disease resistance in tomato

Bacteriocins are a diverse group of bacterial antimicrobial peptides (AMPs) that represent potential replacements for current antibiotics due to their novel modes of action. At present, production costs are a key constraint to the use of bacteriocins and other AMPs. Here, we report the production of bacteriocins in planta - a potentially scalable and cost-effective approach for AMP production. Nine bacteriocin genes with three different modes of action and minimal or no post-translational modifications were synthesized, cloned and used to transform Arabidopsis thaliana. To confirm bacteriocin functionality and the potential to use these plants as biofactories, Arabidopsis T₃ crude leaf extracts were subjected to inhibition assays against the bacterial pathogens Clavibacter michiganensis subsp. michiganensis (Cmm) and Pseudomonas syringae pv. tomato DC3000 (Pst). Six and seven of nine extracts significantly inhibited Cmm and Pst, respectively. Three bacteriocin genes (plantaricin, enteriocin, and leucocin) were then selected for over-expression in tomato (Solanum lycopersicum). In vitro plant pathogen inhibition assays of T₀, T₁ and T₂ transgenic tomato leaf extracts confirmed antimicrobial activity against both pathogens for all three generations of plants, indicating their potential use as stable biopesticide biofactories. Plantaricin and leucocin-expressing T₂ tomato plants were resistant to Cmm, and leucocin-expressing T₂ plants were resistant to Pst. This study highlights that plants can be used as biofactories for AMP production and that the expression of bacteriocins in planta may offer new opportunities for disease control in agriculture.

Current trends and challenges in the synthesis and applications of chitosan-based nanocomposites for plants: A review

Chitosan, a low-cost and multipurpose polymer with numerous desired physicochemical and biological properties has been tested for various applications in agriculture, pharmacy, and biomedicine industries. The availability of functional groups along the backbone makes chitosan readily available for other polymers and metal ions to form bio-nanocomposites. Different types of chitosan-based nanocomposites have been designed and tested for the enhancement of chitosan efficiency and ultimately widening the application areas of chitosan in plants. These nanocomposites serve different purposes such as eliciting plant's defence systems against different threats (pathogen attack), antimicrobial agent against bacteria, fungi and viruses, enhancement of nutrient uptake by plants, control release of micro/macronutrients, fungicides and herbicides. In this review, an extensive outlook has been provided (mainly in the last five years) to recent trends and advances in the fabrication and application of chitosan-based composites. Finally, current challenges and future development opportunities of chitosan-based nanocomposites for plants are discussed.

Copper nanoparticles against benzimidazole-resistant Monilinia fructicola field isolates

Nano-fungicides are expected to play an important role in future plant disease management. Their unique properties include a broad antimicrobial action, increased effectiveness in lower doses, slower a.i. release and/or enhanced drug delivery and an ability to control drug-resistant pathogens, which makes them appealing candidates for use as eco-friendly antifungal alternatives to counter fungicides resistance. Copper nanoparticles (Cu-NPs) could suppress mycelial growth in both sensitive (BENS) and resistant (BEN-R) Monilinia fructicola isolates harboring the E198A benzimidazole resistance mutation, more effectively than copper oxide NPs (CuO-NPs) and Cu(OH)₂. A significant synergy of Cu-NPs with thiophanate methyl (TM) was observed against BEN-S isolates both in vitro and when applied on plum fruit suggesting enhanced availability or nanoparticle induced transformation of TM to carbendazim. ATP-dependent metabolism is probably involved in the mode of fungitoxic action of Cu-NPs as indicated by the synergy observed between Cu-NPs and the oxidative phosphorylation-uncoupler fluazinam (FM). Copper ion release contributed in the toxic action of Cu-NPs against M. fructicola, as indicated by synergism experiments with ethylenediaminetetraacetic acid (EDTA), although the lack of correlation between nano and bulk/ionic copper forms indicate an additional nano-property mediated mechanism of fungitoxic action. Results suggested that Cu-NPs can be effectively used in future plant disease management as eco-friendly antifungal alternatives to counter fungicides resistance and reduce the environmental footprint of synthetic fungicides.

Antimicrobial activity of Streptomyces spp. isolated from Apis dorsata combs against some phytopathogenic bacteria

The aim of this study was to investigate the antimicrobial potential of actinomycetes isolated from combs of the giant honey bee, Apis dorsata. In total, 25 isolates were obtained from three different media and were screened for antimicrobial activity against four plant pathogenic bacteria (Ralstonia solanacearum, Xanthomonas campestris pv. campestris, Xanthomonas oryzae pv. oryzae and Pectobacterium carotovorum). Following screening using a cross-streaking method, three isolates showed the potential to inhibit the growth of plant pathogenic bacteria. Based on a 96-well microtiter assay, the crude extract of DSC3-6 had minimum inhibitory concentration (MIC) values against X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum of 16, 32, 32 and 64 mg L^-1, respectively. The crude extract of DGA3-20 had MIC values against X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum of 32, 32, 32 and 64 mg L^-1, respectively. The crude extract of DGA8-3 at 32 mgL^-1 inhibited the growth of X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum. Based on their 16S rRNA gene sequences, all isolates were identified as members of the genus Streptomyces. The analysis of 16S rRNA gene sequence similarity and of the phylogenetic tree based on the maximum likelihood algorithm showed that isolates DSC3-6, DGA3-20 and DGA8-3 were closely related to Streptomyces ramulosus (99.42%), Streptomyces axinellae (99.70%) and Streptomyces drozdowiczii (99.71%), respectively. This was the first report on antibacterial activity against phytopathogenic bacteria from actinomycetes isolated from the giant honey bee.

Fungal Extracellular Vesicles in Pathophysiology

Fungal pathogens are a concern in medicine and agriculture that has been exacerbated by the emergence of antifungal-resistant varieties that severely threaten human and animal health, as well as food security. This had led to the search for new and sustainable treatments for fungal diseases. Innovative solutions require a deeper understanding of the interactions between fungal pathogens and their hosts, and the key determinants of fungal virulence. Recently, a link has emerged between the release of extracellular vesicles (EVs) and fungal virulence that may contribute to finding new methods for fungal control. Fungal EVs carry pigments, carbohydrates, protein, nucleic acids and other macromolecules with similar functions as those found in EVs from other organisms, however certain fungal features, such as the fungal cell wall, impact EV release and cargo. Fungal EVs modulate immune responses in the host, have a role in cell-cell communication and transport molecules that function in virulence. Understanding the function of fungal EVs will expand our knowledge of host-pathogen interactions and may provide new and specific targets for antifungal drugs and agrichemicals.

Tackling microbial threats in agriculture with integrative imaging and computational approaches

Pathogens and pests are one of the major threats to agricultural productivity worldwide. For decades, targeted resistance breeding was used to create crop cultivars that resist pathogens and environmental stress while retaining yields. The often decade-long process of crossing, selection, and field trials to create a new cultivar is challenged by the rapid rise of pathogens overcoming resistance. Similarly, antimicrobial compounds can rapidly lose efficacy due to resistance evolution. Here, we review three major areas where computational, imaging and experimental approaches are revolutionizing the management of pathogen damage on crops. Recognizing and scoring plant diseases have dramatically improved through high-throughput imaging techniques applicable both under well-controlled greenhouse conditions and directly in the field. However, computer vision of complex disease phenotypes will require significant improvements. In parallel, experimental setups similar to high-throughput drug discovery screens make it possible to screen thousands of pathogen strains for variation in resistance and other relevant phenotypic traits. Confocal microscopy and fluorescence can capture rich phenotypic information across pathogen genotypes. Through genome-wide association mapping approaches, phenotypic data helps to unravel the genetic architecture of stress- and virulence-related traits accelerating resistance breeding. Finally, joint, large-scale screenings of trait variation in crops and pathogens can yield fundamental insights into how pathogens face trade-offs in the adaptation to resistant crop varieties. We discuss how future implementations of such innovative approaches in breeding and pathogen screening can lead to more durable disease control.

Use of silver nanoparticles to counter fungicide-resistance in Monilinia fructicola

The potential of Ag-NPs to suppress Monilia fructicola isolates and to broaden the effectiveness of fungicides to overcome resistance was tested in vitro and in vivo. Twenty-three M. fructicola isolates were subjected to fungitoxicity screening with a number of fungicides in vitro, which resulted in the detection of 18 isolates resistant to benzimidazoles (BEN-R) thiophanare methyl (TM) and carbendazim (CARB). DNA sequencing revealed the E198A resistance mutation in the β-tubulin gene, target site of the benzimidazole fungicides in all resistant isolates. Ag-NPs effectively suppressed mycelial growth in both sensitive (BENS) and resistant isolates. The combination of Ag-NPs with TM led to a significantly enhanced fungitoxic effect compared to the individual treatments regardless resistant phenotype (BEN-R/S) both in vitro and when applied on apple fruit. The above observed additive/synergistic action is probably associated with an enhanced Ag-NPs activity/availability as indicated by the positive correlation between Ag-NPs and TM + Ag-NPs treatments. No correlation was found between AgNO₃ and Ag-NPs suggesting that difference(s) exist in the fungitoxic mechanism of action between nanoparticles and their ionic counterparts. Synergy observed between Ag-NPs and the oxidative phosphorylation-uncoupler fluazinam (FM) against both resistance phenotypes indicates a possible role of energy (ATP) metabolism in the mode of action of Ag-NPs. Additionally, the role of released silver ions on the fungitoxic action of Ag-NPs against M. fructicola was found to be limited because the combination with NaCl revealed a synergistic rather than the antagonistic effect that would be expected from silver ion binding with chlorine ions. The results of this study suggested that Ag-NPs can be effectively used against M. fructicola and when used in combination with conventional fungicides they could provide the means for countering benzimidazole resistance and at the same time reduce the environmental impact of synthetic fungicides by reducing doses needed for the control of the pathogen.

Nest substrate, more than ant activity, drives fungal pathogen community dissimilarity in seed-dispersing ant nests

Myrmecochory is a widespread mutualism in which plants benefit from seed dispersal services by ants. Ants might also be providing seeds with an additional byproduct benefit via reduced plant pathogen loads in the ant nest environment through their antimicrobial glandular secretions. We investigate this byproduct benefit by identifying fungal communities in ant nests and surrounding environments and quantifying fungal community change (1) through time, (2) between different nest substrates, and (3) as a function of average ant activity levels within nests (based on observed ant activity at nest entrances throughout the summer). We split fungal communities by functional guild to determine seed-dispersing ant-induced changes in the overall fungal community, the animal pathogen fungal community, the plant pathogen fungal community, and the myrmecochore pathogen fungal community. Nest substrate (soil or log) explained much of the variation in fungal community dissimilarity, while substrate occupation (ant nest or control sample) and time had no influence on fungal community composition. Average ant activity had no effect on the community turnover in fungal communities except for the myrmecochore pathogenic fungal community. In this community, higher ant activity throughout the summer resulted in more fluctuation in the pathogenic community in the ant nest. Our results are not consistent with a byproduct benefit framework in myrmecochory, but suggest that nest substrate drives dissimilarity in fungal communities. The influence of nest substrate on fungal communities has important implications for seeds taken into ant nests, as well as ant nest location choice by queens and during nest relocation.

Nutraceutical and antimicrobial potentials of Bambara groundnut (Vigna subterranean): A review

Bambara groundnut (Vigna subterranea (L.) Verdc.) [BGN] is an easy-to-cultivate vegetable crop neglected over the past years. It is a drought-tolerant crop with nutritional and medicinal values and as a result, the crop is referred to as nutraceuticals. Based on this, there exist a need to review the beneficial potential (nutraceutical value) of this neglected and underutilized crop to protect and promote its cultivation for food (source of nutrients) and medicines especially among rural poor communities in sub-Saharan Africa. This review systematically examines the background information and uses of BGN. The antimicrobial properties of BGN were also considered and examined to ascertain its nutraceutical importance. BGN has been reported as a crop possessing antioxidant and antimicrobial properties. Clinically, the extracts of BGN have been reported to exhibit antimicrobial activities against bacteria such as Klebsiella pneumoniae subsp. pneumoniae ATCC 700603, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus subsp. aureus ATCC 33591, Escherichia coli, Bacillus cereus, yeast (Candida albicans) and mold (Aspergillus niger). This review outlines the uses of BGN as a functional food crop as well as its nutraceutical and antimicrobial potentials. However, there exist paucity of knowledge and literature on the crop's antimicrobial activities especially against plant pathogens of economic importance. Hence, this review proposes that more research be geared towards assessing the nutraceutical value and antimicrobial potentials of this crop against plant pathogens of economic importance and the promotion of the crop's cultivation.

Reconsideration of species boundaries and proposed DNA barcodes for Calonectria

Calonectria represents a genus of phytopathogenic ascomycetous fungi with a worldwide distribution. In recent years, there has been an increase in the number of taxonomic studies on these fungi. Currently, there are 169 described species of Calonectria based on comparisons of DNA sequence data, combined with morphological characteristics. However, for some of these species, the sequence data utilised at the time of their description were relatively limited. This has justified an urgent need to reconsider the species boundaries for Calonectria based on robust genus-wide phylogenetic analyses. In this study, we utilised 240 available isolates including the ex-types of 128 Calonectria species, and re-sequenced eight gene regions (act, cmdA, his3, ITS, LSU, rpb2, tef1 and tub2) for them. Sequences for 44 Calonectria species, for which cultures could not be obtained, were downloaded from GenBank. DNA sequence data of all the 169 Calonectria species were then used to determine their phylogenetic relationships. As a consequence, 51 species were reduced to synonymy, two new species were identified, and the name Ca. lauri was validated. This resulted in the acceptance of 120 clearly defined Calonectria spp. The overall data revealed that the genus includes 11 species complexes, distributed across the Prolate and Sphaero-Naviculate Groups known to divide Calonectria. The results also made it possible to develop a robust set of DNA barcodes for Calonectria spp. To accomplish this goal, we evaluated the outcomes of each of the eight candidate DNA barcodes for the genus, as well as for each of the 11 species complexes. No single gene region provided a clear identity for all Calonectria species. Sequences of the tef1 and tub2 genes were the most reliable markers; those for the cmdA, his3, rpb2 and act gene regions also provided a relatively effective resolution for Calonectria spp., while the ITS and LSU failed to produce useful barcodes for species discrimination. At the species complex level, results showed that the most informative barcodes were inconsistent, but that a combination of six candidate barcodes (tef1, tub2, cmdA, his3, rpb2 and act) provided stable and reliable resolution for all 11 species complexes. A six-gene combined phylogeny resolved all 120 Calonectria species, and revealed that tef1, tub2, cmdA, his3, rpb2 and act gene regions are effective DNA barcodes for Calonectria.

Smut fungi as a stratagem to characterize rust effectors: opportunities and challenges

The rust pathogens are one of the most complex fungi in the Basidiomycetes. The development of genomic resources for rust and other plant pathogens has opened the opportunities for functional genomics of fungal genes. Despite significant progress in the field of fungal genomics, functional characterization of the genome components has lacked, especially for the rust pathogens. Their obligate nature and lack of standard stable transformation protocol are the primary reasons for rusts to be one of the least explored genera despite its significance. In the recently sequenced rust genomes, a vast catalogue of predicted effectors and pathogenicity genes have been reported. However, most of these candidate genes remained unexplored due to the lack of suitable characterization methods. The heterologous expression of putative effectors in Nicotiana benthamiana and Arabidopsis thaliana has proved to be a rapid screening method for identifying the role of these effectors in virulence. However, no fungal system has been used for the functional validation of these candidate genes. The smuts, from the evolutionary point of view, are closely related to the rust pathogens. Moreover, they have been widely studied and hence could be a suitable model system for expressing rust fungal genes heterologously. The genetic manipulation methods for smuts are also well standardized. Complementation assays can be used for functional validation of the homologous genes present in rust and smut fungal pathogens, while the species-specific proteins can be expressed in the mutant strains of smut pathogens having reduced or no virulence for virulence analysis. We propose that smuts, especially Ustilago maydis, may prove to be a good model system to characterize rust effector proteins in the absence of methods to manipulate the rust genomes directly.

Screening and identification of BP100 peptide conjugates active against Xylella fastidiosa using a viability-qPCR method

Background

Xylella fastidiosa is one of the most harmful bacterial plant pathogens worldwide, causing a variety of diseases, with huge economic impact to agriculture and environment. Although it has been extensively studied, there are no therapeutic solutions to suppress disease development in infected plants. In this context, antimicrobial peptides represent promising alternatives to traditional compounds due to their activity against a wide range of plant pathogens, their low cytotoxicity, their mode of action that make resistance more difficult and their availability for being expressed in plants.

Results

Peptide conjugates derived from the lead peptide BP100 and fragments of cecropin, magainin or melittin were selected and tested against the plant pathogenic bacteria X. fastidiosa. In order to screen the activity of these antimicrobials, and due to the fastidious nature of the pathogen, a methodology consisting of a contact test coupled with the viability-quantitative PCR (v-qPCR) method was developed. The nucleic acid-binding dye PEMAX was used to selectively quantify viable cells by v-qPCR. In addition, the primer set XF16S-3 amplifying a 279 bp fragment was selected as the most suitable for v-qPCR. The performance of the method was assessed by comparing v-qPCR viable cells estimation with conventional qPCR and plate counting. When cells were treated with peptide conjugates derived from BP100, the observed differences between methods suggested that, in addition to cell death due to the lytic effect of the peptides, there was an induction of the viable but non-culturable state in cells. Notably, a contact test coupled to v-qPCR allowed fast and accurate screening of antimicrobial peptides, and led to the identification of new peptide conjugates active against X. fastidiosa.

Conclusions

Antimicrobial peptides active against X. fastidiosa have been identified using an optimized methodology that quantifies viable cells without a cultivation stage, avoiding underestimation or false negative detection of the pathogen due to the viable but non-culturable state, and overestimation of the viable population observed using qPCR. These findings provide new alternative compounds for being tested in planta for the control of X. fastidiosa, and a methodology that enables the fast screening of a large amount of antimicrobials against this plant pathogenic bacterium.

Biocontrol ability and volatile organic compounds production as a putative mode of action of yeast strains isolated from organic grapes and rye grains

The inhibiting activity of three yeast strains belonging to Pichia kudriavzevii, Pichia occidentalis, and Meyerozyma quilliermondii/Meyerozyma caribbica genera against common plant pathogens representing Mucor spp., Penicillium chrysogenum, Penicillium expansum, Aspergillus flavus, Fusarium cereals, Fusarium poae, as well as Botrytis cinerea genera was investigated. The yeast strains tested had a positive impact on growth inhibition of all target plant pathogens. The degree of inhibition was more than 50% and varied depending on both the yeast antagonist and the mold. Ethyl esters of medium-chain fatty acids, phenylethyl alcohol, and its acetate ester prevailed among the analyzed volatile organic compounds (VOCs) emitted by yeasts in the presence of the target plant pathogens. Due to the method used, assuming no contact between the antagonist and the pathogen, the antagonistic activity of the yeast strains studied resulted mainly from the production of biologically active VOCs. Moreover, the antagonistic activity was not only restricted to a single plant pathogen but effective towards molds of different genera, making the yeast strains studied very useful for potential application in biological control.

Omics applications: towards a sustainable protection of tomato

Transcriptome data and gene expression analysis have a huge potential in the study of multiple relationships involving plants, pathogens, and pests, including the interactions with beneficial microorganisms such as endophytes or other functional groups. Next-generation sequencing (NGS) and other recent long-read-based sequencing approaches (i.e., nanopore and others) provide unprecedented tools allowing the fast identification of plant information processing systems, in situ and in real time, fundamental for crop management and pest regulation. Other -omics approaches such as metagenomics and metatranscriptomics allow high-resolution insights on the rhizosphere ecology. They may highlight key factors affecting belowground biodiversity or processes, modulating the expression of stress-responsive pathways. The application of miRNAs and other small RNAs is a relatively new field of application, with enormous potential for the selective activation of defense pathways. However, limitations concerning the stability of the RNA molecules and their effective delivery must be overcome.

Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin

Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from rice plant as the reference. Re-sequencing results revealed that the genome of strain AU6208 comprised 96 contigs corresponding to a 6.1 Mbp genome of the strain AU6208, with 5322 coding sequences and 68.2 % GC content; this is much larger compared to the genome previously sequenced by us and described by Seo et al (2015), which was reported to be 4.1 Mbp comprising >1200 contigs, 4361 coding sequences, and 67.31 % GC content. Moreover, this updated genome shares >80 % identity to the 7.2 Mbp genome of BGR1, which encodes 6491 coding sequences and has 68.3 % GC content. Further computational analysis revealed that the strain AU6208 encodes several bacteriocin biosynthesis genes, antibiotic, as well as virulent genes such as toxoflavin genes, which included 425 specialty genes and 12 toxoflavin genes. Upon further characterization, 12 toxoflavins (ToxA, B, C, D, E, F, G, H, I, J, TofI, and TofR) were found in AU6208 with 70-100 % sequence, family, and domain similarity with that of BGR1. Upon comparison with BGR1, the structural characterizations of selected toxoflavin genes (ToxB, ToxC, ToxG, H, and TofI) revealed variations in 2D and 3D structures such as differences in α-helix, β-sheets, loops, physiological properties of proteins, RMSD values, etc. These variations may play significant role in different mode of action in different hosts thereby indicating that in addition to their respective hosts, toxoflavins could also contribute to exploit other hosts across the kingdom. In addition to understanding the epidemiology of strain AU6208, this updated genomics data will also unfold the pathogenicity of bacteria in diversity of various hosts and anti-virulence.