Expecting the unexpected: factors influencing the emergence of fungal and oomycete plant pathogens

Harnessing microbial communities for enhanced plant resilience against diseases

Background

Phytophthora infestans (P. infestans) and other plant infections threaten global agriculture and food security. This research incorporated Pseudomonas strains in microbial consortia to boost plant tolerance to P. infestans. The P. infestans fungus causes collapse and deterioration in many crops like potatoes by quickly spreading through their tubers and leaves in warm, damp weather.

Objective

The main goals were to identify effective Pseudomonas strains (those with high inhibitory activity), test their interactions (both inhibitory and synergistic), and determine the effect of inoculum density on disease treatment.

Methods

We used the following methodologies, from potato shoots and rhizosphere samples, Nine different strains of the antifungal bacterium Pseudomonas which were identified with preliminary antifungal activity. Bintje showed the greatest resistance to P. infestans among the three potato types that were examined. Methods utilized comprised: Quantification of bacterial density and growth, the inhibitory assays for P. infestans, experiments on leaf disc infections, Assessing the severity of an infection, Analysis of zoospore discharge. Studies on the integrated development of bacteria and valuation using statistical methods.

Results

The study revealed the complexity of microbial interactions, host-specific reactions, and cell density's impact on treatment success. The study suggests using Pseudomonas strains as biocontrol agents, advancing sustainable agriculture. Microbial consortia disease management requires advanced methodologies, according to the findings. Investigating long-term ecological impacts on soil health, microbial diversity, and crop yield sustainability; validating identified microbial consortia through field trials; evaluating scalability and economic viability; and researching genetic engineering for customized disease control are recommended.

Conclusions

Results suggest a shift from chemical pesticides to environmentally friendly plant disease control considering its ethical and regulatory implications. This study emphasizes the intricacy of microbial interactions and the need for informed biocontrol decisions. Their study also increases ecological knowledge and encourages innovative, sustainable worldwide agriculture.

Fungal communities in boreal soils are influenced by land use, agricultural soil management, and depth

Land use and agricultural soil management affect soil fungal communities that ultimately influence soil health. Subsoils harbor nutrient reservoir for plants and can play a significant role in plant growth and soil carbon sequestration. Typically, microbial analyses are restricted to topsoil (0-30 cm) leaving subsoil fungal communities underexplored. To address this knowledge gap, we analyzed fungal communities in the vertical profile of four boreal soil treatments: long-term (24 years) organic and conventional crop rotation, meadow, and forest. Internal transcribed spacer (ITS2) amplicon sequencing revealed soil-layer-specific land use or agricultural soil management effects on fungal communities down to the deepest measured soil layer (40-80 cm). Compared to other treatments, higher proportion of symbiotrophs, saprotrophs, and pathotrophs + plant pathogens were found in forest, meadow and crop rotations, respectively. The proportion of arbuscular mycorrhizal fungi was higher in deeper (>20 cm) soil than in topsoil. Forest soil below 20 cm was dominated by fungal functional groups with proposed interactions with plants or other soil biota, whether symbiotrophic or pathotrophic. Ferrous oxide was an important factor shaping fungal communities throughout the vertical profile of meadow and cropping systems. Our results emphasize the importance of including subsoil in microbial community analyses in differently managed soils.

Characterization of Hazelnut Trees in Open Field Through High-Resolution UAV-Based Imagery and Vegetation Indices

The increasing demand for hazelnut kernels is favoring an upsurge in hazelnut cultivation worldwide, but ongoing climate change threatens this crop, affecting yield decreases and subject to uncontrolled pathogen and parasite attacks. Technical advances in precision agriculture are expected to support farmers to more efficiently control the physio-pathological status of crops. Here, we report a straightforward approach to monitoring hazelnut trees in an open field, using aerial multispectral pictures taken by drones. A dataset of 4112 images, each having 2Mpixel resolution per tree and covering RGB, Red Edge, and near-infrared frequencies, was obtained from 185 hazelnut trees located in two different orchards of the Piedmont region (northern Italy). To increase accuracy, and especially to reduce false negatives, the image of each tree was divided into nine quadrants. For each quadrant, nine different vegetation indices (VIs) were computed, and in parallel, each tree quadrant was tagged as "healthy/unhealthy" by visual inspection. Three supervised binary classification algorithms were used to build models capable of predicting the status of the tree quadrant, using the VIs as predictors. Out of the nine VIs considered, only five (GNDVI, GCI, NDREI, NRI, and GI) were good predictors, while NDVI SAVI, RECI, and TCARI were not. Using them, a model accuracy of about 65%, with 13% false negatives was reached in a way that was rather independent of the algorithms, demonstrating that some VIs allow inferring the physio-pathological condition of these trees. These achievements support the use of drone-captured images for performing a rapid, non-destructive physiological characterization of hazelnut trees. This approach offers a sustainable strategy for supporting farmers in their decision-making process during agricultural practices.

Optimizing Corn Tar Spot Measurement: A Deep Learning Approach Using Red-Green-Blue Imaging and the Stromata Contour Detection Algorithm for Leaf-Level Disease Severity Analysis

Visual detection of stromata (brown-black, elevated fungal fruiting bodies) is the primary method for quantifying tar spot early in the season because these structures are definitive signs of the disease and essential for effective disease monitoring and management. Here, we present the Stromata Contour Detection Algorithm version 2 (SCDA v2), which addresses the limitations of the previously developed SCDA version 1 (SCDA v1), without the need to empirically search for optimal decision-making input parameters (DMIPs) while achieving higher and consistent accuracy in tar spot stromata detection. SCDA v2 operates in two components: (i) SCDA v1 producing tar spot-like region proposals for a given input corn leaf Red-Green-Blue (RGB) image and (ii) a pretrained convolutional neural network (CNN) classifier identifying true tar spot stromata from the region proposals. To demonstrate the enhanced performance of the SCDA v2, we used datasets of RGB images of corn leaves from field (low, middle, and upper canopies) and glasshouse conditions under variable environments, exhibiting different tar spot severities at various corn developmental stages. Various accuracy analyses (F1 score, linear regression, and Lin's concordance correlation) showed that SCDA v2 had a greater agreement with the reference data (human visual annotation) than SCDA v1. SCDA v2 achieved 73.7% mean Dice values (overall accuracy) compared with 30.8% for SCDA v1. The enhanced F1 score primarily resulted from eliminating overestimation cases using the CNN classifier. Our findings indicate the promising potential of SCDA v2 for glasshouse and field-scale applications, including tar spot phenotyping and surveillance projects.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Elsinoe species: The rise of scab diseases

The genus Elsinoe contains many aggressive pathogens of a wide range of plants, many of which are economically important. These fungal pathogens cause serious scab diseases affecting various plant parts, impacting plant vigour, yield and market value. While studies on Elsinoe species have predominantly focused on their taxonomy, there is a conspicuous gap in knowledge of these fungi from a plant pathology perspective. In this review, we draw together and critically evaluate the existing, but rather fragmented, research on the taxonomic status, phylogenetic relationships, host range, as well as the biology and epidemiology of Elsinoe species. Our aim is primarily to augment the existing understanding of the global significance of Elsinoe species, and furthermore, to shed light on the escalating prominence of scab diseases caused by species in a fungal genus that has been known for over 100 years but remains relatively poorly understood and somewhat enigmatic.

Globisporangium tabrizense sp. nov., Globisporangium mahabadense sp. nov., and Pythium bostanabadense sp. nov. (Oomycota), three new species from Iranian aquatic environments

During a survey on the biodiversity of oomycetes in aquatic environments in northwest Iran (East Azarbaijan and West Azarbaijan provinces), three Pythium and four Globisporangium isolates were recovered from agricultural water pools and irrigation canals, respectively. Through a polyphasic approach combining morphology and phylogenetic analysis using the nuclear rDNA ITS1-5.8 S-ITS2 (ITS) and partial sequences of the cytochrome c oxidase subunit I and II (COX1 and COX2), three novel species were identified namely Globisporangium tabrizense sp. nov., G. mahabadense sp. nov., and Pythium bostanabadense sp. nov. Furthermore, experiments confirmed the pathogenicity of all identified species on cucumber seedlings, suggesting a pathogenic lifestyle also in aquatic systems. Our research contributes to a better understanding of the diversity, host range and distribution of oomycetes genera Globisporangium and Pythium in northwestern Iran. Detailed morphological descriptions and illustrations are provided for all species.

The contribution of tropical long-term studies to mycology

Fungi are arguably the most diverse eukaryotic kingdom of organisms in terms of number of estimated species, trophic and life history strategies, and their functions in ecosystems. However, our knowledge of fungi is limited due to a distributional bias; the vast majority of available data on fungi have been compiled from non-tropical regions. Far less is known about fungi from tropical regions, with the bulk of these data being temporally limited surveys for fungal species diversity. Long-term studies (LTS), or repeated sampling from the same region over extended periods, are necessary to fully capture the extent of species diversity in a region, but LTS of fungi from tropical regions are almost non-existent. In this paper, we discuss the contributions of LTS of fungi in tropical regions to alpha diversity, ecological and functional diversity, biogeography, hypothesis testing, and conservation-with an emphasis on an ongoing tropical LTS in the Pakaraima Mountains of Guyana. We show how these contributions refine our understanding of Fungi. We also show that public data repositories such as NCBI, IUCN, and iNaturalist contain less information on tropical fungi compared to non-tropical fungi, and that these discrepancies are more pronounced in fungi than in plants and animals.

Roadmap to Success: How Oomycete Plant Pathogens Invade Tissues and Deliver Effectors

Filamentous plant pathogens threaten global food security and ecosystem resilience. In recent decades, significant strides have been made in deciphering the molecular basis of plant-pathogen interactions, especially the interplay between pathogens' molecular weaponry and hosts' defense machinery. Stemming from interdisciplinary investigations into the infection cell biology of filamentous plant pathogens, recent breakthrough discoveries have provided a new impetus to the field. These advances include the biophysical characterization of a novel invasion mechanism (i.e., naifu invasion) and the unraveling of novel effector secretion routes. On the plant side, progress includes the identification of components of cellular networks involved in the uptake of intracellular effectors. This exciting body of research underscores the pivotal role of logistics management by the pathogen throughout the infection cycle, encompassing the precolonization stages up to tissue invasion. More insight into these logistics opens new avenues for developing environmentally friendly crop protection strategies in an era marked by an imperative to reduce the use of agrochemicals.

Polyphasic Characterization of the Biocontrol Potential of a Novel Strain of Trichoderma atroviride Isolated from Central Mexico

This work describes the characterization of Trichoderma atroviride strain CMU-08, isolated from Michoacán, Mexico. CMU-08 demonstrated robust growth and conidiation across a temperature range from 16 to 32 °C and a pH range from 4 to 9 on potato dextrose agar (PDA) and malt extract agar (MEA) media. The strain is an efficient antagonist of six species of phytopathogenic fungi and oomycetes in PDA, MEA, and Vogel minimal medium (VMM). Antagonist mechanisms of CMU-08 included direct mycoparasitism observed in dual-culture assays, as well as antibiosis attributed to growth inhibition via both volatile and non-volatile metabolites, with the effectiveness varying depending on the test phytopathogen and culture medium. Extracellular filtrates (ECFs) recovered from liquid cultures of CMU-08 under basal and induced conditions using Botrytis cinerea cell walls significantly inhibited their growth at a concentration of 750 µg/mL. Moreover, in detached tomato leaf assays, these ECFs reduced foliar damage caused by B. cinerea by 24-34%. The volatile organic compounds (VOCs) produced by CMU-08 also exhibited substantial efficacy, reducing foliar damage by up to 50% in similar tests. Despite showing no basal extracellular chitinase enzymatic activity, CMU-08 demonstrated significant induction of this activity in cultures supplemented with B. cinerea and Fusarium sp. cell walls. Four genes encoding extracellular chitinases (chit33, chit36, ech42, and locus 217415) showed different dynamics of transcriptional regulation during the dual-culture confrontation of strain CMU-08 with B. cinerea and Fusarium sp., varying according to the phytopathogen and the interaction stage. The CMU-08 strain shows physiological versatility and employs a variety of antagonist mechanisms toward different species of phytopathogenic microorganisms, making it a good candidate for developing a biocontrol product for field application.

Monitoring the phenology of plant pathogenic fungi: why and how?

Phenology is a key adaptive trait of organisms, shaping biotic interactions in response to the environment. It has emerged as a critical topic with implications for societal and economic concerns due to the effects of climate change on species' phenological patterns. Fungi play essential roles in ecosystems, and plant pathogenic fungi have significant impacts on global food security. However, the phenology of plant pathogenic fungi, which form a huge and diverse clade of organisms, has received limited attention in the literature. This diversity may have limited the use of a common language for comparisons and the integration of phenological data for these taxonomic groups. Here, we delve into the concept of 'phenology' as applied to plant pathogenic fungi and explore the potential drivers of their phenology, including environmental factors and the host plant. We present the PhenoFun scale, a phenological scoring system suitable for use with all fungi and fungus-like plant pathogens. It offers a standardised and common tool for scientists studying the presence, absence, or predominance of a particular phase, the speed of phenological phase succession, and the synchronism shift between pathogenic fungi and their host plants, across a wide range of environments and ecosystems. The application of the concept of 'phenology' to plant pathogenic fungi and the use of a phenological scoring system involves focusing on the interacting processes between the pathogenic fungi, their hosts, and their biological, physical, and chemical environment, occurring during the life cycle of the pathogen. The goal is to deconstruct the processes involved according to a pattern orchestrated by the fungus's phenology. Such an approach will improve our understanding of the ecology and evolution of such organisms, help to understand and anticipate plant disease epidemics and their future evolution, and make it possible to optimise management models, and to encourage the adoption of cropping practices designed from this phenological perspective.

Fungal Diseases in Yerba Mate: Status and Management Strategies

Yerba mate (Ilex paraguariensis St. Hil.), with its health benefits and socioeconomic significance, plays a crucial role in Argentina and other South American countries like Brazil and Paraguay. Its cultivation in the Province of Misiones (Argentina) supports various sectors, contributes to regional development, and provides employment opportunities. However, the transition from extractive practices to monoculture, accompanied with increased demand, has led to phytosanitary challenges. Imbalanced native microbiota, disease development, and pathogen dispersion have become prevalent issues. Understanding the known pathogens associated with yerba mate plants is crucial for developing effective agricultural strategies. The primary objective of this study is to synthesise current knowledge on prevalent fungal diseases in yerba mate cultivation, as well as to provide agricultural management recommendations for effective disease control. Fungal diseases can cause significant damage to different parts of the plant, resulting in economic losses. The proximity of neighbouring plantations to yerba mate crops may contribute to the cross-contamination of pathogens, emphasizing the need for comprehensive epidemiology and accurate diagnosis. Multiple fungal genera have been reported to cause pathologies in yerba mate. Among the fungi causing foliar diseases are Ceratobasidium niltonsouzanum, Cylindrocladium spathulatum, Pseudocercospora mate, Asterina sphaerelloides, Colletotrichum gloeosporioides aff var. yerbae, and Phyllosticta sp. Caulinary diseases are caused by Alternaria sp., Phoma sp., Colletotrichum sp., and Ceratocystis fimbriata. Regarding root rot, the genera Rhizoctonia sp., Pythium sp., Fusarium sp., and Rosellinia sp. have been reported. Proper crop management practices and monitoring are essential for effective disease control. To reduce reliance on chemical compounds, the use of biocontrol agents like Trichoderma sp. has shown promise in regulating phytopathogenic fungi populations. Continued research is vital to preserve the yerba mate industry and ensure its long-term viability while minimizing environmental impact.

Pattern recognition receptors as potential therapeutic targets for developing immunological engineered plants

There is an urgent need to combat pathogen infestations in crop plants to ensure food security worldwide. To counter this, plants have developed innate immunity mediated by Pattern Recognition Receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) and damage- associated molecular patterns (DAMPs). PRRs activate Pattern-Triggered Immunity (PTI), a defence mechanism involving intricate cell-surface and intracellular receptors. The diverse ligand-binding ectodomains of PRRs, including leucine-rich repeats (LRRs) and lectin domains, facilitate the recognition of MAMPs and DAMPs. Pathogen resistance is mediated by a variety of PTI responses, including membrane depolarization, ROS production, and the induction of defence genes. An integral part of intracellular immunity is the Nucleotide-binding Oligomerization Domain, Leucine-rich Repeat proteins (NLRs) which recognize and respond to effectors in a potent manner. Enhanced understanding of PRRs, their ligands, and downstream signalling pathways has contributed to the identification of potential targets for genetically modified plants. By transferring PRRs across plant species, it is possible to create broad-spectrum resistance, potentially offering innovative solutions for plant protection and global food security. The purpose of this chapter is to provide an update on PRRs involved in disease resistance, clarify the mechanisms by which PRRs recognize ligands to form active receptor complexes and present various applications of PRRs and PTI in disease resistance management for plants.

Bacillus velezensis RC218 and emerging biocontrol agents against Fusarium graminearum and Fusarium poae in barley: in vitro, greenhouse and field conditions

Fusarium head blight (FHB) is one of the most common diseases in Argentina, affecting the quality and yield of barley grains. Fusarium graminearum sensu stricto (ss) and Fusarium poae are causal agents of FHB and potential sources of mycotoxin contamination in barley. Conventional management strategies do not lead to a complete control of FHB; therefore, biological control emerges as an eco-friendly alternative in the integrated management of the disease. In the present work, Bacillus velezensis, Bacillus inaquosorum, Bacillus nakamurai and Lactobacillus plantarum were evaluated as potential biocontrol agents against F. graminearum ss and F. poae on barley-based media. Bacillus velezensis RC218 was selected to carry out greenhouse and field trials in order to reduce FHB and mycotoxin accumulation. This strain was able to control growth of both Fusarium species and reduced deoxynivalenol (DON) and nivalenol (NIV) production by 66 % and 79 %, respectively. Bacillus inaquosorum and B. nakamurai were more effective in controlling F. poae growth, and the mean levels of reduction in DON accumulation were 50 and 38 %, and 93 and 26 % for NIV, respectively. Lactobacillus plantarum showed variable biocontrol capacity depending on the strain, with no significant mycotoxin reduction. The biocontrol on incidence and severity of FHB in the greenhouse and field trials was effective, being more efficient against F. graminearum ss and DON accumulation than against F. poae and NIV occurrence. This study provides valuable data for the development of an efficient tool based on biocontrol agents to prevent FHB-producing Fusarium species development and mycotoxin occurrence in barley, contributing to food safety.

National-scale investigation reveals the dominant role of phyllosphere fungal pathogens in sorghum yield loss

Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity.

Bimetallic nanoparticles and biochar produced by Adansonia Digitata shell and their effect against tomato pathogenic fungi

Adansonia digitata L. is a royal tree that is highly valued in Africa for its medicinal and nutritional properties. The objective of this study was to use its fruit shell extract to develop new, powerful mono and bimetallic nanoparticles (NPs) and biochar (BC) using an eco-friendly approach. Silver (Ag), iron oxide (FeO), the bimetallic Ag-FeO NPs, as well as (BC) were fabricated by A. digitata fruit shell extract through a reduction process and biomass pyrolysis, respectively, and their activity against tomato pathogenic fungi Alternaria sp., Sclerotinia sclerotiorum, Fusarium equiseti, and Fusarium venenatum were detected by agar dilution method. The Ag, FeO, Ag-FeONPs, and BC were characterized using a range of powerful analytical techniques such as ultraviolet-visible (UV-Vis) spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier Transform-Infra Red (FT-IR), dynamic light scatter (DLS), and zeta potential analysis. The fabricated Ag, FeO and Ag-FeO NPs have demonstrated a remarkable level of effectiveness in combating fungal strains. UV-Vis spectra ofAg, FeO, Ag-FeONPs, and BC show broad exhibits peaks at 338, 352, 418, and 480 nm, respectively. The monometallic, bimetallic NPs, and biochar have indicated the presence in various forms mostly in Spherical-shaped. Their size varied from 102.3 to 183.5 nm and the corresponding FTIR spectra suggested that the specific organic functional groups from the plant extract played a significant role in the bio-reduction process. Ag and Ag-FeO NPs exhibited excellent antifungal activity against pathogenic fungi Alternaria sp., S. sclerotiorum, F. equiseti, and F. venenatum. The current study could be a significant achievement in the field of antifungal agents since has the potential to develop new approaches for treating fungal infections.

Aeromicrobiology: A global review of the cycling and relationships of bioaerosols with the atmosphere

Airborne microorganisms and biological matter (bioaerosols) play a key role in global biogeochemical cycling, human and crop health trends, and climate patterns. Their presence in the atmosphere is controlled by three main stages: emission, transport, and deposition. Aerial survival rates of bioaerosols are increased through adaptations such as ultra-violet radiation and desiccation resistance or association with particulate matter. Current research into modern concerns such as climate change, global gene transfer, and pathogenicity often neglects to consider atmospheric involvement. This comprehensive review outlines the transpiring of bioaerosols across taxa in the atmosphere, with significant focus on their interactions with environmental elements including abiotic factors (e.g., atmospheric composition, water cycle, and pollution) and events (e.g., dust storms, hurricanes, and wildfires). The aim of this review is to increase understanding and shed light on needed research regarding the interplay between global atmospheric phenomena and the aeromicrobiome. The abundantly documented bacteria and fungi are discussed in context of their cycling and human health impacts. Gaps in knowledge regarding airborne viral community, the challenges and importance of studying their composition, concentrations and survival in the air are addressed, along with understudied plant pathogenic oomycetes, and archaea cycling. Key methodologies in sampling, collection, and processing are described to provide an up-to-date picture of ameliorations in the field. We propose optimization to microbiological methods, commonly used in soil and water analysis, that adjust them to the context of aerobiology, along with other directions towards novel and necessary advancements. This review offers new perspectives into aeromicrobiology and calls for advancements in global-scale bioremediation, insights into ecology, climate change impacts, and pathogenicity transmittance.

Physiological, metabolic and hormonal responses of two Pinus spp. with contrasting susceptibility to brown-spot needle blight disease

Needle blights are serious fungal diseases affecting European natural and planted pine forests. Brown-spot needle blight (BSNB) disease, caused by the fungus Lecanosticta acicola, causes canopy defoliation and severe productivity losses, with consequences depending on host susceptibility. To gain new insights into BSNB plant-pathogen interactions, constitutive and pathogen-induced traits were assessed in two host species with differential disease susceptibility. Six-month-old Pinus radiata D. Don (susceptible) and Pinus pinea L. (more resistant) seedlings were needle inoculated with L. acicola under controlled conditions. Eighty days after inoculation, healthy-looking needles from symptomatic plants were assessed for physiological parameters and sampled for biochemical analysis. Disease progression, plant growth, leaf gas-exchanges and biochemical parameters were complemented with hormonal and untargeted primary metabolism analysis and integrated for a holistic analysis. Constitutive differences between pine species were observed. Pinus pinea presented higher stomatal conductance and transpiration rate and higher amino and organic acids, abscisic acid as well as putrescine content than P. radiata. Symptoms from BSNB disease were observed in 54.54% of P. radiata and 45.45% of P. pinea seedlings, being more pronounced and generalized in P. radiata. For both species, plant height, sub-stomatal CO2 concentration and water-use efficiency were impacted by infection. In P. radiata, total soluble sugars, starch and total flavonoids content increased after infection. No differences in hormone content after infection were observed. However, secondary metabolism was induced in P. pinea visible through total phenolics, flavonoids and putrescine accumulation. Overall, the observed results suggest that P. pinea constitutive and induced traits may function as two layers of a defence strategy which contributed to an increased BSNB resistance in comparison with P. radiata. This is the first integrative study linking plant physiological and molecular traits in Pinus-Lecanosticta acicola pathosystem, contributing to a better understanding of the underlying resistance mechanisms to BSNB disease in pines.

Plant community diversity alters the response of ecosystem multifunctionality to multiple global change factors

Biodiversity is considered important to the mitigation of global change impacts on ecosystem multifunctionality in terrestrial ecosystems. However, potential mechanisms through which biodiversity maintains ecosystem multifunctionality under global change remain unclear. We grew 132 plant communities with two levels of plant diversity, crossed with treatments based on 10 global change factors (nitrogen deposition, soil salinity, drought, plant invasion, simulated grazing, oil pollution, plastics pollution, antibiotics pollution, heavy metal pollution, and pesticide pollution). All global change factors negatively impacted ecosystem multifunctionality, but negative impacts were stronger in high compared with low diversity plant communities. We explored potential mechanisms for this unexpected result, finding that the inhibition of selection effects (i.e., selection for plant species associated with high ecosystem functioning) contributed to sensitivity of ecosystem multifunctionality to global change. Specifically, global change factors decreased the abundance of novel functional plants (i.e., legumes) in high but not low diversity plant communities. The negative impacts of global change on ecosystem multifunctionality were also mediated by increased relative abundance of fungal plant pathogens (identified from metabarcoding of soil samples) and their negative relationship with the abundance of novel functional plants. Taken together, our experiment highlights the importance of protecting high diversity plant communities and legumes, and managing fungal pathogens, to the maintenance of ecosystem multifunctionality in the face of complex global change.

Evaluating the contribution of historical and contemporary temperature to the oospore production of self-fertile Phytophthora infestans

Reproductive systems play an important role in the ecological function of species, but little is known about how climate change, such as global warming, may affect the reproductive systems of microbes. In this study, 116 Phytophthora infestans isolates sampled from five different altitudes along a mountain were evaluated under five temperature regimes to determine the effects of historical and experimental temperature on the reproductive system of the pathogen. Both altitude, a proxy for historical pathogen adaptation to temperature, and temperature used in the experiment affected the sexual reproduction of the pathogen, with experimental temperature, that is, contemporary temperature, playing a role several times more important than historical temperature. Furthermore, the potential of sexual reproduction, measured by the number of oospores quantified, increased with the temperature breadth (i.e., difference between the highest and lowest temperature at which sexual reproduction takes place) of the pathogen and reached the maximum at the experimental temperature of 21°C, which is higher than the annual average temperature in many potato-producing areas. The results suggest that rising air temperature associated with global warming may increase the potential of sexual reproduction in P. infestans. Given the importance of sexuality in pathogenicity and ecological adaptation of pathogens, these results suggest that global warming may increase the threat of P. infestans to agricultural production and other ecological services and highlight that new epidemiological strategies may need to be implemented for future food security and ecological resilience.

Pseudomonas syringae coffee blight is associated with the horizontal transfer of plasmid-encoded type III effectors

The emergence of new pathogens is an ongoing threat to human health and agriculture. While zoonotic spillovers received considerable attention, the emergence of crop diseases is less well studied. Here, we identify genomic factors associated with the emergence of Pseudomonas syringae bacterial blight of coffee. Fifty-three P. syringae strains from diseased Brazilian coffee plants were sequenced. Comparative and evolutionary analyses were used to identify loci associated with coffee blight. Growth and symptomology assays were performed to validate the findings. Coffee isolates clustered in three lineages, including primary phylogroups PG3 and PG4, and secondary phylogroup PG11. Genome-wide association study of the primary PG strains identified 37 loci, including five effectors, most of which were encoded on a plasmid unique to the PG3 and PG4 coffee strains. Evolutionary analyses support the emergence of coffee blight in PG4 when the coffee-associated plasmid and associated effectors derived from a divergent plasmid carried by strains associated with other hosts. This plasmid was only recently transferred into PG3. Natural diversity and CRISPR-Cas9 plasmid curing were used to show that strains with the coffee-associated plasmid grow to higher densities and cause more severe disease symptoms in coffee. This work identifies possible evolutionary mechanisms underlying the emergence of a new lineage of coffee pathogens.

Population genomic analyses suggest recent dispersal events of the pathogen Cercospora zeina into East and Southern African maize cropping systems

A serious factor hampering global maize production is gray leaf spot disease. Cercospora zeina is one of the causative pathogens, but population genomics analysis of C. zeina is lacking. We conducted whole-genome Illumina sequencing of a representative set of 30 C. zeina isolates from Kenya and Uganda (East Africa) and Zambia, Zimbabwe, and South Africa (Southern Africa). Selection of the diverse set was based on microsatellite data from a larger collection of the pathogen. Pangenome analysis of the C. zeina isolates was done by (1) de novo assembly of the reads with SPAdes, (2) annotation with BRAKER, and (3) protein clustering with OrthoFinder. A published long-read assembly of C. zeina (CMW25467) from Zambia was included and annotated using the same pipeline. This analysis revealed 790 non-shared accessory and 10,677 shared core orthogroups (genes) between the 31 isolates. Accessory gene content was largely shared between isolates from all countries, with a few genes unique to populations from Southern Africa (32) or East Africa (6). There was a significantly higher proportion of effector genes in the accessory secretome (44%) compared to the core secretome (24%). PCA, ADMIXTURE, and phylogenetic analysis using a neighbor-net network indicated a population structure with a geographical subdivision between the East African isolates and the Southern African isolates, although gene flow was also evident. The small pangenome and partial population differentiation indicated recent dispersal of C. zeina into Africa, possibly from 2 regional founder populations, followed by recurrent gene flow owing to widespread maize production across sub-Saharan Africa.

Oomycete Soil Diversity Associated with Betula and Alnus in Forests and Urban Settings in the Nordic-Baltic Region

This study aimed to determine the differences and drivers of oomycete diversity and community composition in alder- and birch-dominated park and natural forest soils of the Fennoscandian and Baltic countries of Estonia, Finland, Lithuania, Norway, and Sweden. For this, we sequenced libraries of PCR products generated from the DNA of 111 soil samples collected across a climate gradient using oomycete-specific primers on a PacBio high-throughput sequencing platform. We found that oomycete communities are most affected by temperature seasonality, annual mean temperature, and mean temperature of the warmest quarter. Differences in composition were partly explained by the higher diversity of Saprolegniales in Sweden and Norway, as both total oomycete and Saprolegniales richness decreased significantly at higher longitudes, potentially indicating the preference of this group of oomycetes for a more temperate maritime climate. None of the evaluated climatic variables significantly affected the richness of Pythiales or Peronosporales. Interestingly, the relative abundance and richness of Pythiales was higher at urban sites compared to forest sites, whereas the opposite was true for Saprolegniales. Additionally, this is the first report of Phytophthora gallica and P. plurivora in Estonia. Our results indicate that the composition of oomycetes in soils is strongly influenced by climatic factors, and, therefore, changes in climate conditions associated with global warming may have the potential to significantly alter the distribution range of these microbes, which comprise many important pathogens of plants.

Secondary metabolites in grapevine: crosstalk of transcriptional, metabolic and hormonal signals controlling stress defence responses in berries and vegetative organs

Abiotic stresses, such as temperature, heat waves, water limitation, solar radiation and the increase in atmospheric CO₂ concentration, significantly influence the accumulation of secondary metabolites in grapevine berries at different developmental stages, and in vegetative organs. Transcriptional reprogramming, miRNAs, epigenetic marks and hormonal crosstalk regulate the secondary metabolism of berries, mainly the accumulation of phenylpropanoids and of volatile organic compounds (VOCs). Currently, the biological mechanisms that control the plastic response of grapevine cultivars to environmental stress or that occur during berry ripening have been extensively studied in many worlds viticultural areas, in different cultivars and in vines grown under various agronomic managements. A novel frontier in the study of these mechanisms is the involvement of miRNAs whose target transcripts encode enzymes of the flavonoid biosynthetic pathway. Some miRNA-mediated regulatory cascades, post-transcriptionally control key MYB transcription factors, showing, for example, a role in influencing the anthocyanin accumulation in response to UV-B light during berry ripening. DNA methylation profiles partially affect the berry transcriptome plasticity of different grapevine cultivars, contributing to the modulation of berry qualitative traits. Numerous hormones (such as abscisic and jasmomic acids, strigolactones, gibberellins, auxins, cytokynins and ethylene) are involved in triggering the vine response to abiotic and biotic stress factors. Through specific signaling cascades, hormones mediate the accumulation of antioxidants that contribute to the quality of the berry and that intervene in the grapevine defense processes, highlighting that the grapevine response to stressors can be similar in different grapevine organs. The expression of genes responsible for hormone biosynthesis is largely modulated by stress conditions, thus resulting in the numeourous interactions between grapevine and the surrounding environment.

Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose

Colletotrichum lupini, the causative agent of lupin anthracnose, affects lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the diversity, evolutionary dynamics, and molecular basis of the interaction of this notorious lupin pathogen with its host. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction site-associated DNA sequencing, resulting in a data set of unparalleled resolution. Phylogenetic and structural analysis could distinguish four independent lineages (I-IV). The strong population structure and high overall standardized index of association (r̅d ) indicates that C. lupini reproduces clonally. Different morphologies and virulence patterns on white lupin (Lupinus albus) and Andean lupin (Lupinus mutabilis) were observed between and within clonal lineages. Isolates belonging to lineage II were shown to have a minichromosome that was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this minichromosome could imply a role in host-pathogen interaction. All four lineages were present in the South American Andes region, which is suggested to be the centre of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seedborne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.

Modeling plant diseases under climate change: evolutionary perspectives

Infectious plant diseases are a major threat to global agricultural productivity, economic development, and ecological integrity. There is widespread concern that these social and natural disasters caused by infectious plant diseases may escalate with climate change and computer modeling offers a unique opportunity to address this concern. Here, we analyze the intrinsic problems associated with current modeling strategies and highlight the need to integrate evolutionary principles into polytrophic, eco-evolutionary frameworks to improve predictions. We particularly discuss how evolutionary shifts in functional trade-offs, relative adaptability between plants and pathogens, ecosystems, and climate preferences induced by climate change may feedback to future plant disease epidemics and how technological advances can facilitate the generation and integration of this relevant knowledge for better modeling predictions.

Semi-VOCs of Wood Vinegar Display Strong Antifungal Activities against Oomycete Species Globisporangium ultimum and Pythium aphanidermatum

Plant disease outbreaks are increasingly exacerbated by climate change and the conditions of stress combinations. They are negatively affecting crop yield and driving threats to food security in many areas of the world. Although synthetic pesticides offer relative success in the control of pests and plant diseases, they are often overused, and this method faces numerous drawbacks, including environmental toxicity, soil degradation, and adverse effects on human health. Therefore, alternatives are being developed and examined, including the biocontrol of pests and pathogens and biomass pyrolysis leading to wood vinegar that has shown great promise in agriculture and organic farming. However, while wood vinegar use is expanding and allows the control of numerous pests and bacterial and fungal diseases, its application to control oomycete diseases is limited. This study aimed to test wood vinegar for the control of oomycete plant pathogens from which six wood vinegars of pistachio, pomegranate, almond, pine, cypress, and walnut were produced. The inhibitory effects of volatile metabolites (semi-VOCs) of different wood vinegars concentrations (100%, 50%, 25%, 12.5%, and 6.25%) were examined against the hyphal growth of Globisporangium ultimum and Pythium aphanidermatum isolates. An in vitro analysis unambiguously demonstrated that for Globisporangium ultimum, the wood vinegar semi-VOCs of almond, pistachio (C 100% and 50%), and walnut (C 100%) totally inhibited mycelial growth. On the other hand, Pythium aphanidermatum, pistachio (C 100%, 50%, and 25%), and cypress (C 100%) expressed their abilities to completely inhibit the mycelial growth. Other treatments, including relevant concentrations of pine and pomegranate significantly inhibited the growth of mycelia of both species compared to the control (p ≤ 0.05). Therefore, wood vinegar could be considered a natural and organic product to use in agriculture to cope not only against pests, bacterial and fungal pests but also against emerging oomycete plant diseases.

Fusarioid community diversity associated with conifer seedlings in forest nurseries across the contiguous USA

INTRODUCTION

Fusarioid fungi that cause damping-off and root diseases can result in significant losses to conifer crops produced in forest nurseries across the USA. These nurseries are vital to reforestation and forest restoration efforts. Understanding the diversity of Fusarioid fungi associated with damping-off and root diseases of conifer seedlings can provide an approach for targeted management techniques to limit seedling losses and pathogen spread to novel landscapes.

METHODS

This study identifies 26 Fusarium spp. (F. acuminatum, F. annulatum, F. avenaceum, F. brachygibbosum, F. clavus, F. commune, F. cugenangense, F. diversisporum, F. elaeagni, F. elaeidis, F. flocciferum, F. fredkrugeri, F. fujikuroi, F. grosmichelii, F. ipomoeae, F. lactis, F. languescens, F. luffae, F. odoratissimum, F. oxysporum, F. queenslandicum, F. redolens, F. torulosum, F. triseptatum, F. vanleeuwenii, & F. verticillioides), 15 potential species within Fusarium and Neocosmospora species complexes (two from F. fujikuroi species complex, nine from F. oxysporum species complex, three from F. tricinctum species complex, and one from Neocosmospora species complex), and four Neocosmospora spp. (N. falciforme, N. metavorans, N. pisi, & N. solani) and associated host information collected from conifer-producing nurseries across the contiguous USA.

RESULTS

Phylogenetic analyses identified Fusarioid fungi haplotypes that were associated with 1) host specificity, 2) localization to geographic regions, or 3) generalists found on multiple hosts across diverse geographic regions.

DISCUSSION

The haplotypes and novel species identified on conifer seedlings should be considered for further analysis to determine pathogenicity, pathogen spread, and assess management practices.

Carboxylic Acid Amide but Not Quinone Outside Inhibitor Fungicide Resistance Mutations Show Clade-Specific Occurrence in Pseudoperonospora cubensis Causing Downy Mildew in Commercial and Wild Cucurbits

Since its reemergence in 2004, Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew (CDM), has experienced significant changes in fungicide sensitivity. Presently, frequent fungicide applications are required to control the disease in cucumber due to the loss of host resistance. Carboxylic acid amides (CAA) and quinone outside inhibitors (QoI) are two fungicide groups used to control foliar diseases in cucurbits, including CDM. Resistance to these fungicides is associated with single nucleotide polymorphism (SNP) mutations. In this study, we used population analyses to determine the occurrence of fungicide resistance mutations to CAA and QoI fungicides in host-adapted clade 1 and clade 2 P. cubensis isolates. Our results revealed that CAA-resistant genotypes occurred more prominently in clade 2 isolates, with more sensitive genotypes observed in clade 1 isolates, while QoI resistance was widespread across isolates from both clades. We also determined that wild cucurbits can serve as reservoirs for P. cubensis isolates containing fungicide resistance alleles. Finally, we report that the G1105W substitution associated with CAA resistance was more prominent within clade 2 P. cubensis isolates while the G1105V resistance substitution and sensitivity genotypes were more prominent in clade 1 isolates. Our findings of clade-specific occurrence of fungicide resistance mutations highlight the importance of understanding the population dynamics of P. cubensis clades by crop and region to design effective fungicide programs and establish accurate baseline sensitivity to active ingredients in P. cubensis populations.

Climate change and plant pathogens

Global food security is threatened by climate change, both directly through responses of crop physiology and productivity, and indirectly through responses of plant-associated microbiota, including plant pathogens. While the interactions between host plants, pathogens and environmental drivers can be complex, recent research is beginning to indicate certain overall patterns in how plant diseases will affect crop production in future. Here, we review the results of three methodological approaches: large-scale observational studies, process-based disease models and experimental comparisons of pathosystems under current and future conditions. We find that observational studies have tended to identify rising temperatures as the primary driver of disease impact. Process-based models suggest that rising temperatures will lead to latitudinal shifts in disease pressure, but drying conditions could mitigate disease risk. Experimental studies suggest that rising atmospheric CO₂ will exacerbate disease impacts. Plant diseases may therefore counteract any crop yield increases due to climate change.

Optimal reduced-mixing for an SIS infectious-disease model

Which reduced-mixing strategy maximizes economic output during a disease outbreak? To answer this question, we formulate an optimal-control problem that maximizes the difference between revenue, due to healthy individuals, and medical costs, associated with infective individuals, for SIS disease dynamics. The control variable is the level of mixing in the population, which influences both revenue and the spread of the disease. Using Pontryagin's maximum principle, we find a closed-form solution for our problem. We explore an example of our problem with parameters for the transmission of Staphylococcus aureus in dairy cows, and we perform sensitivity analyses to determine how model parameters affect optimal strategies. We find that less mixing is preferable when the transmission rate is high, the per-capita recovery rate is low, or when the revenue parameter is much smaller than the cost parameter.

High Temporal Variability in Late Blight Pathogen Diversity, Virulence, and Fungicide Resistance in Potato Breeding Fields: Results from a Long-Term Monitoring Study

Long-term site-specific studies describing changes in the phenotypic variability of Phytophthora infestans populations allow quantitative predictions of pathogen spread and possible outbreaks of epidemics, and provide key input for regional resistance breeding programs. Late blight samples were collected from potato (Solanum tuberosum) breeding fields in Estonia during a twelve-year study period between 2001 and 2014. In total, 207 isolates were assessed for mating type and 235 isolates for metalaxyl resistance and 251 isolates for virulence factors. The frequency of mating types strongly fluctuated across the years, whereas the later period of 2010–2014 was dominated by the A2 mating. Despite fluctuations, both mating types were recorded in the same fields in most years, indicating sustained sexual reproduction of P. infestans with oospore production. Metalaxyl-resistant and intermediately resistant strains dominated in the first years of study, but with the progression of the study, metalaxyl-sensitive isolates became dominant, reaching up to 88%. Racial diversity, characterized by normalized Shannon diversity index decreased in time, varying from 1.00 in 2003 to 0.43 in 2013. The frequency of several virulence factors changed in a time-dependent manner, with R2 increasing and R6, R8, and R9 decreasing in time. Potato cultivar resistance background did not influence the frequency of P. infestans mating type, response to metalaxyl, and racial diversity. However, the diversity index decreased in time among isolates collected from resistant and susceptible cultivars, and remained at a high level in moderately resistant cultivars. These data demonstrate major time-dependent changes in racial diversity, fungicide resistance, and virulence factors in P. infestans, consistent with alterations in the control strategies and popularity of potato cultivars with different resistance.

Worldwide Population Structure of the Coffee Rust Fungus Hemileia vastatrix Is Strongly Shaped by Local Adaptation and Breeding History

The devastating disease coffee leaf rust, caused by Hemileia vastatrix, has been a major constraint to worldwide coffee production. Recently, H. vastatrix populations were shown to be structured into three divergent genetic lineages with marked host specialization (C1, C2, and C3). However, there is yet no overall understanding of the population dynamics and adaptation of the most widespread and epidemiological relevant H. vastatrix group (C3). We used restriction site-associated DNA sequencing to generate 13,804 single nucleotide polymorphisms (SNPs) across a worldwide collection of 99 H. vastatrix isolates. Phylogenetic analyses uncovered a well-supported structuring within C3, with three main subgroups (SGs; SGI, SGII, and SGIII), which seem to reflect the historical distribution, breeding, and exchange of coffee cultivars. SGI shows a ladder-like diversification pattern and occurs across all four continents sampled, SGII is mainly restricted to Africa, and SGIII is observed only in Timor, revealing a higher genetic differentiation. Outlier and association tests globally identified 112 SNPs under putative positive selection, which impacted population structure. In particular, 29 overlapping SNPs per se seemed to have an extremely strong effect on H. vastatrix population divergence. We also found exclusive and fixed alleles associated with the SGs supporting local adaptation. Functional annotation revealed that transposable elements may play a role in host adaptation. Our study provides a higher-resolution perspective on the evolutionary history of H. vastatrix on cultivated coffee, showing its strong ability to adapt and the strength of the selective force imposed by coffee hosts, which should be taken into account when designing strategies for pathogen dissemination control and selective breeding.

Assessing global fungal threats to humans

Fungi are an integral part of the earth's biosphere. They are broadly distributed in all continents and ecosystems and play a diversity of roles. Here, I review our current understanding of fungal threats to humans and describe the major factors that contribute to various threats. Among the 140,000 or so known species out of the estimated six million fungal species on Earth, about 10% directly or indirectly threaten human health and welfare. Major threats include mushroom poisoning, fungal allergies, infections of crop plants, food contamination by mycotoxins, and mycoses in humans. A growing number of factors have been identified to impact various fungal threats, including human demographics, crop distributions, anthropogenic activities, pathogen dispersals, global climate change, and/or the applications of antifungal drugs and agricultural fungicides. However, while models have been developed for analyzing various processes of individual threats and threat managements, current data are primarily descriptive and incomplete, and there are significant obstacles to integration of the diverse factors into accurate quantitative assessments of fungal threats. With increasing technological advances and concerted efforts to track the spatial and temporal data on climate and environmental variables; mycotoxins in the feed and food supply chains; fungal population dynamics in crop fields, human and animal populations, and the environment; human population demographics; and the prevalence and severities of fungal allergies and diseases, our ability to accurately assess fungal threats will improve. Such improvements should help us develop holistic strategies to manage fungal threats in the future.

Effect of No Tillage System on Soil Fungal Community Structure of Cropland in Mollisol: A Case Study

Conservation tillage is generally regarded as a sustainable farming system for the future. The fungal community structure has a strong response to conservation tillage. However, how the conservation tillage system affects the soil fungal community structure is little known. Using the high-throughput sequencing technology, the soil fungal community was explored under no tillage (NT) and conventional tillage (CT) in Northeast China Mollisol. The copy number of fungal genes in NT20 was significantly lower than that in other treatments. NT changed the composition of soil fungal communities at the taxonomic level of phylum and genus. The diversity indices of the soil fungal community in no tillage at soil depths of 0–5 cm (NT5) were significantly higher than those in soil depths of 5–20 cm (NT20). The fungal community under NT and CT could form a good cluster distribution and NT5, conventional tillage at soil depths of 0–5 cm (CT5) and 5–20 cm (CT20) had specific indicator species. Most of the potential pathogens were significantly higher in NT5 than in NT20. Tillage and soil depth could explain 64% of the diversity and 95% of the composition of the fungal community, which indirectly changed the diversity and composition of fungi by using soil organic carbon, pH value, and soil bulk density. Furthermore, soil organic carbon (SOC) best explained the soil fungal community, followed by soil pH. The study indicated that the NT system had a comprehensive effect on the soil fungal community and SOC is the most crucial factor in determining this community.

Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada

Several Peronospora species are carried by wind over short and long distances, from warmer climates where they survive on living plants to cooler climates. In eastern Canada, this annual flow of sporangia was thought to be the main source of Peronospora destructor responsible for onion downy mildew. However, the results of a recent study showed that the increasing frequency of onion downy mildew epidemics in eastern Canada is associated with warmer autumns, milder winters, and previous year disease severity, suggesting overwintering of the inoculum in an area where the pathogen is not known to be endogenous. In this study, genotyping by sequencing was used to investigate the population structure of P. destructor at the landscape scale. The study focused on a particular region of southwestern Québec-Les Jardins de Napierville-to determine if the populations were clonal and regionally differentiated. The data were characterized by a high level of linkage disequilibrium, characteristic of clonal organisms. Consequently, the null hypothesis of random mating was rejected when tested on predefined or nonpredefined populations, indicating that linkage disequilibrium was not a function of population structure and suggesting a mixed reproduction mode. Discriminant analysis of principal components performed with predefined population assignment allowed grouping P. destructor isolates by geographical regions, while analysis of molecular variance confirmed that this genetic differentiation was significant at the regional level. Without using a priori population assignment, isolates were clustered into four genetic clusters. These results represent a baseline estimate of the genetic diversity and population structure of P. destructor.

The Epidemiology of Sudden Oak Death Disease Caused by Phytophthora ramorum in a Mixed Bay Laurel-Oak Woodland Provides Important Clues for Disease Management

Epidemiological models are important for the understanding of disease progression in plants and for the design of control strategies. Phytophthora ramorum, the pathogen responsible for the disease known as Sudden Oak Death, causes lethal infection on several oaks but relies on California bay laurels for transmission. Here, repeated surveys of bay laurels and oaks indicated that bay laurel disease incidence was positively correlated with rainfall, bay laurel density, and an eastern aspect, and negatively correlated with bay laurel basal area. Oak infection only occurred in years when rainfall was higher than the 30-year average, and although infection rates were greater among larger trees, mortality was greater among smaller trees. Additionally, larger oaks closer to infected bay laurels exhibited greater infection rates. Disease incidence differed among sites, and only a fraction of bay laurels were disease superspreaders, while even fewer individuals were refugial trees harboring active infections during dry periods. Based on this study, reducing bay laurel density in denser stands and the number of superspreaders or refugial trees in less dense stands may reduce disease incidence. However, the selective removal of bay laurel trees 0–10 m from oaks is likely to be more effective in preventing infection of specific oaks.

Bluster or Lustre: Can AI Improve Crops and Plant Health?

In a changing climate where future food security is a growing concern, researchers are exploring new methods and technologies in the effort to meet ambitious crop yield targets. The application of Artificial Intelligence (AI) including Machine Learning (ML) methods in this area has been proposed as a potential mechanism to support this. This review explores current research in the area to convey the state-of-the-art as to how AI/ML have been used to advance research, gain insights, and generally enable progress in this area. We address the question-Can AI improve crops and plant health? We further discriminate the bluster from the lustre by identifying the key challenges that AI has been shown to address, balanced with the potential issues with its usage, and the key requisites for its success. Overall, we hope to raise awareness and, as a result, promote usage, of AI related approaches where they can have appropriate impact to improve practices in agricultural and plant sciences.

Towards a phylogenetic ecology of plant pests and pathogens

Plant-pathogens and insect pests, hereafter pests, play an important role in structuring ecological communities, yet both native and introduced pests impose significant pressure on wild and managed systems, and pose a threat to food security. Global changes in climate and land use, and transportation of plants and pests around the globe are likely to further increase the range, frequency and severity of pest outbreaks in the future. Thus, there is a critical need to expand on current ecological theory to address these challenges. Here, we outline a phylogenetic framework for the study of plant and pest interactions. In plants, a growing body of work has suggested that evolutionary relatedness, phylogeny, strongly structures plant-pest associations-from pest host breadths and impacts, to their establishment and spread in new regions. Understanding the phylogenetic dimensions of plant-pest associations will help to inform models of invasive species spread, disease and pest risk in crops, and emerging pest outbreaks in native plant communities-which will have important implications for protecting food security and biodiversity into the future. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Environmental monitoring of anthropogenic impacts and climate change: a case study from the national network of roads in Egypt

Economic development and land use/land cover (LULC) changes are deeply connected. Egypt has started the National Road Project to add 7000 km new roads to the 23.500 km existing network. The present study aimed at assessing anthropogenic impacts of the establishment and development of one of the newly developed arterial roads (Wadi Al-Natroun Al-Alamin road) on the LULC of surrounding region in relation to climate change during the period from 1986 to 2019. Using RS (remote sensing) techniques and four satellite images from 1986, 1999, 2011, and 2019, five classes were identified (vegetation, urban, water, agriculturally affected soils, and bare soils). The study area was divided based on different human activities into six areas of interest (AOIs). Results showed that massive changes have occurred during the 33-year period along the six AOIs and the five identified classes. Four climatic variables (annual mean temperature, maximum temperature of the warmest month, annual precipitation, precipitation of the wettest month) have been used to investigate climatic conditions of the study area in 1986 and 2018 and link it to the continuous development in the study area. Results showed an average increase of 2°C in annual temperature and maximum temperature of the hottest month. In contrary, a significant decrease in the annual precipitation and precipitation of the wettest month has been documented. Statistical analysis results showed significant correlations between climatic conditions and economic development along the study area. Climate change and human development stress on both natural and artificial ecosystems of the study area have been discussed, and recommended measures for sustainable development and natural resources perseveration have been provided.

A general trait-based modelling framework for revealing patterns of airborne fungal dispersal threats to agriculture and native flora

Fungal plant pathogens are of economic and ecological importance to global agriculture and natural ecosystems. Long-distance atmospheric dispersal of fungal spores (LAD) can pose threats to agricultural and native vegetation lands. An understanding of such patterns of fungal spore dispersal and invasion pathways can provide valuable insights into plant protection. Spore traits affect their dispersal abilities. We propose a general trait-based framework for modelling LAD to reveal dispersal patterns and pathways, and assess subsequent threats of arrival (TOA) quantitatively in the context of biosecurity. To illustrate the framework, we present a study of Australia and its surrounding land masses. The overall dispersal pattern covered almost the entire continent of Australia. Fungal spores in the size class of 10 and 20 µm (aerodynamic diameter) posed the greatest TOA. Our study shows the effects of morphological traits on these potential TOA, and how they varied between source regions, size classes, and seasons. Our framework revealed spore dispersal patterns and pathways. It also facilitates comparisons of spatio-temporal dispersal dynamics among fungal classes, gaining insights into atmospheric long-distance dispersal of fungi as a whole, and provides a basis for assessing fungal pest threats in potential source regions based on easily measured spore characteristics.

Precipitation increases the abundance of fungal plant pathogens in Eucalyptus phyllosphere

Understanding the current and future distributions of plant pathogens is critical to predict the plant performance and related economic benefits in the changing environment. Yet, little is known about the roles of environmental drivers in shaping the profiles of fungal plant pathogens in phyllosphere, an important habitat of microbiomes on Earth. Here, using a large-scale investigation of Eucalyptus phyllospheric microbiomes in Australia and the multiple linear regression model, we show that precipitation is the most important predictor of fungal taxonomic diversity and abundance. The abundance of fungal plant pathogens in phyllosphere exhibited a positive linear relationship with precipitation. With this empirical dataset, we constructed current and future atlases of phyllosphere plant pathogens to estimate their spatial distributions under different climate change scenarios. Our atlases indicate that the abundance of fungal plant pathogens would increase especially in the coastal regions with up to 100-fold increase compared with the current abundance. These findings advance our understanding of the distributions of fungal plant pathogens in phyllospheric microbiomes under the climate change, which can improve our ability to predict and mitigate their impacts on plant productivity and economic losses.

Plant and Fungal Genome Editing to Enhance Plant Disease Resistance Using the CRISPR/Cas9 System

Crop production has been substantially reduced by devastating fungal and oomycete pathogens, and these pathogens continue to threaten global food security. Although chemical and cultural controls have been used for crop protection, these involve continuous costs and time and fungicide resistance among plant pathogens has been increasingly reported. The most efficient way to protect crops from plant pathogens is cultivation of disease-resistant cultivars. However, traditional breeding approaches are laborious and time intensive. Recently, the CRISPR/Cas9 system has been utilized to enhance disease resistance among different crops such as rice, cacao, wheat, tomato, and grape. This system allows for precise genome editing of various organisms via RNA-guided DNA endonuclease activity. Beyond genome editing in crops, editing the genomes of fungal and oomycete pathogens can also provide new strategies for plant disease management. This review focuses on the recent studies of plant disease resistance against fungal and oomycete pathogens using the CRISPR/Cas9 system. For long-term plant disease management, the targeting of multiple plant disease resistance mechanisms with CRISPR/Cas9 and insights gained by probing fungal and oomycete genomes with this system will be powerful approaches.

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.

Disentangling the role of oomycete soil pathogens as drivers of plant-soil feedbacks

Interactions among plant species and their soil biota drive plant-soil feedbacks (PSFs) that play a major role in the dynamics and diversity of plant communities. Among the different components of the soil community, pathogens are considered to be the main drivers of negative PSFs. Despite this, the number of studies that have experimentally quantified the contribution of soil pathogens to PSFs remains considerably low. Here we conducted a greenhouse experiment with oomycete-specific fungicide to quantify the contribution of soil pathogens, and particularly oomycete pathogens, to individual and pairwise PSFs in forest communities. We used as a case study Mediterranean mixed forests dominated by Quercus suber and invaded by the oomycete pathogen Phytophthora cinnamomi. The fungicide treatment was crossed with a competition treatment to explore how conspecific neighbors might modify pathogen effects. To place the results of the experiment in a wider context, we also conducted a systematic review of published papers that explicitly used fungicide to explore the role of pathogens in PSF experiments. Our experimental results showed that oomycete pathogens were the main drivers of individual PSFs in the study forests. Oomycete effects varied among tree species according to their susceptibility to P. cinnamomi, driving negative PSFs in the highly susceptible Q. suber but not in the coexistent Olea europaea. Oomycete-driven PSFs were not modified by intraspecific competition. Oomycete pathogens were also major contributors to negative pairwise PSFs assumed to promote species coexistence. Results from the systematic review supported the novelty of our experimental results, since only three studies had previously used oomycete-specific fungicide in a PSF context and none in systems invaded by exotic oomycetes. Overall, our results provide novel evidence of oomycete pathogens (including the exotic P. cinnamomi) as fundamental drivers of negative individual and pairwise PSFs with implications for species coexistence in invaded communities. Although in the short-term invasive pathogens might contribute to species coexistence by causing self-limitation in dominant species, strong inter-specific variation in self-limitation might undermine coexistence in the long-term. Because of the increasing number of exotic oomycetes worldwide, further attention should be given to oomycetes as drivers of PSFs in plant communities.

Pathogenic Specialization of Venturia nashicola, Causal Agent of Asian Pear Scab, and Resistance of Pear Cultivars Kinchaku and Xiangli

Scab caused by Venturia nashicola is one of the most serious diseases of Asian pears, including Japanese pear (Pyrus pyrifolia var. culta) and Chinese pears (P. bretschneideri and P. ussuriensis). Breeding scab-resistant pear cultivars is essential to minimize fungicide use and development of fungicide resistance. A survey of pathogenic specialization in V. nashicola is needed to ensure durable scab resistance in cultivated pears. V. nashicola race 1, 2, and 3 isolates, each differing in pathogenicity to Japanese pear cultivar Kousui and Asian pear strain Mamenashi 12, have been reported in Japan. In this study, isolates collected from scabbed pears in China and Taiwan were classified as V. nashicola based on conidial size and mating ability. However, various isolates had pathogenicity distinct from races 1, 2, and 3 according to tests on seven differential host genotypes of pear cultivars from Japan (Kousui and strain Mamenashi 12), China (Jingbaili, Yali, Linyuli, and Nanguoli), and Taiwan (Hengshanli). These new races were designated as races 4 to 7. Progenies characteristic of race 3 isolates were produced using a cross between race 1 and race 2 isolates, suggesting the possible role of sexual recombination in the emergence of novel races. Japanese pear cultivar Kinchaku and Chinese P. sinkiangensis 'Xiangli' (a Korla fragrant pear grown in China) did not show visible symptoms after inoculation with any of the seven races. Broad scab resistance in Kinchaku and Xiangli makes them a promising genetic resource for resistance breeding programs.

Differential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicum

Pathogens that infect more than one host offer an opportunity to study how resistance mechanisms have evolved across different species. Exserohilum turcicum infects both maize and sorghum and the isolates are host-specific, offering a unique system to examine both compatible and incompatible interactions. We conducted transcriptional analysis of maize and sorghum in response to maize-specific and sorghum-specific E. turcicum isolates and identified functionally related co-expressed modules. Maize had a more robust transcriptional response than sorghum. E. turcicum responsive genes were enriched in core orthologs in both crops, but only up to 16% of core orthologs showed conserved expression patterns. Most changes in gene expression for the core orthologs, including hub genes, were lineage specific, suggesting a role for regulatory divergent evolution. We identified several defense-related shared differentially expressed (DE) orthologs with conserved expression patterns between the two crops, suggesting a role for parallel evolution of those genes in both crops. Many of the differentially expressed genes (DEGs) during the incompatible interaction were related to quantitative disease resistance (QDR). This work offers insights into how different hosts with relatively recent divergence interact with a common pathogen. Our results are important for developing resistance to this critical pathogen and understanding the evolution of host-pathogen interactions.

What Do We Know about Botryosphaeriaceae? An Overview of a Worldwide Cured Dataset

Botryosphaeriaceae-related diseases occur worldwide in a wide variety of plant hosts. The number of studies targeting the distribution, diversity, ecology, and pathogenicity of Botryosphaeriaceae species are consistently increasing. However, with the lack of consistency in species delimitation, the name of hosts, and the locations of studies, it is almost impossible to quantify the presence of these species worldwide, or the number of different host–fungus interactions that occur. In this review, we collected and organized Botryosphaeriaceae occurrences in a single cured dataset, allowing us to obtain for the first time a complete perspective on species’ global diversity, dispersion, host association, ecological niches, pathogenicity, communication efficiency of new occurrences, and new host–fungus associations. This dataset is freely available through an interactive and online application. The current release (version 1.0) contains 14,405 cured isolates and 2989 literature references of 12,121 different host–fungus interactions with 1692 different plant species from 149 countries.

Presence of the Weakly Pathogenic Fusarium poae in the Fusarium Head Blight Disease Complex Hampers Biocontrol and Chemical Control of the Virulent Fusarium graminearum Pathogen

Fusarium head blight (FHB) in wheat (Triticum aestivum L.) is caused by a consortium of mutually interacting Fusarium species. In the field, the weakly pathogenic F. poae often thrives on the infection sites of the virulent F. graminearum. In this ecological context, we investigated the efficacy of chemical and biocontrol agents against F. graminearum in wheat ears. For this purpose, one fungicide comprising prothioconazole + spiroxamine and two bacterial biocontrol strains, Streptomyces rimosus LMG 19352 and Rhodococcus sp. R-43120 were tested for their efficacy to reduce FHB symptoms and mycotoxin (deoxynivalenol, DON) production by F. graminearum in presence or absence of F. poae. Results showed that the fungicide and both actinobacterial strains reduced FHB symptoms and concomitant DON levels in wheat ears inoculated with F. graminearum. Where Streptomyces rimosus appeared to have direct antagonistic effects, Rhodococcus and the fungicide mediated suppression of F. graminearum was linked to the archetypal salicylic acid and jasmonic acid defense pathways that involve the activation of LOX1, LOX2 and ICS. Remarkably, this chemical- and biocontrol efficacy was significantly reduced when F. poae was co-inoculated with F. graminearum. This reduced efficacy was linked to a suppression of the plant's intrinsic defense system and increased levels of DON. In conclusion, our study shows that control strategies against the virulent F. graminearum in the disease complex causing FHB are hampered by the presence of the weakly pathogenic F. poae. This study provides generic insights in the complexity of control strategies against plant diseases caused by multiple pathogens.