Drought: A context-dependent damper and aggravator of plant diseases

Drought dynamically influences the interactions between plants and pathogens, thereby affecting disease outbreaks. Understanding the intricate mechanistic aspects of the multiscale interactions among plants, pathogens, and the environment-known as the disease triangle-is paramount for enhancing the climate resilience of crop plants. In this review, we systematically compile and comprehensively analyse current knowledge on the influence of drought on the severity of plant diseases. We emphasise that studying these stresses in isolation is not sufficient to predict how plants respond to combined stress from both drought and pathogens. The impact of drought and pathogens on plants is complex and multifaceted, encompassing the activation of antagonistic signalling cascades in response to stress factors. The nature, intensity, and temporality of drought and pathogen stress occurrence significantly influence the outcome of diseases. We delineate the drought-sensitive nodes of plant immunity and highlight the emerging points of crosstalk between drought and defence signalling under combined stress. The limited mechanistic understanding of these interactions is acknowledged as a key research gap in this area. The information synthesised herein will be crucial for crafting strategies for the accurate prediction and mitigation of future crop disease risks, particularly in the context of a changing climate.

Comprehensive bioremediation effect of phosphorus-mineralized bacterium Enterobacter sp. PMB-5 on cadmium contaminated soil-crop system

Phosphate-mineralizing bacteria (PMBs) have been widely studied by inducing phosphate heavy metal precipitation, but current researches neglect to study their effects on soil-microbe-crop systems on cadmium (Cd) contaminated. Based on this, a strain PMB, Enterobacter sp. PMB-5, was inoculated into Cd contaminated pots to detect soil characteristics, Cd occurrence forms, soil biological activities, plant physiological and biochemical indicators. The results showed that the inoculation of strain PMB-5 significantly increased the available phosphorus content (85.97%-138.64%), Cd-residual fraction (11.04%-29.73%), soil enzyme activities (31.94%-304.63%), plant biomass (6.10%-59.81%), while decreased the state of Cd-HOAc (11.50%-31.17%) and plant bioconcentration factor (23.76%-44.24%). These findings indicated that strain PMB-5 could perform the function of phosphorus solubilization to realize the immobilization of Cd in the complex soil environment. Moreover, SEM-EDS, FTIR, XPS, and XRD analysis revealed that strain PMB-5 does not significantly alter the soil morphology, structure, elemental distribution, and chemical composition, which suggested that remediation of Cd contamination using strain PMB-5 would not further burden the soil. This research implies that PMB-5 could be a safe and effective bioinoculant for remediating Cd-contaminated soils, contributing to the sustainable management of soil health in contaminated environments.

Mycorrhizal effects on crop yield and soil ecosystem functions in a long-term tillage and fertilization experiment

It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long-term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no-tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no-till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low-input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.

The potential of arbuscular mycorrhizal fungi to enhance metallic micronutrient uptake and mitigate food contamination in agriculture: prospects and challenges

Optimizing agroecosystems and crops for micronutrient uptake while reducing issues with inorganic contaminants (metal(loid)s) is a challenging task. One promising approach is to use arbuscular mycorrhizal fungi (AMF) and investigate the physiological, molecular and epigenetic changes that occur in their presence and that lead to changes in plant metal(loid) concentration (biofortification of micronutrients or mitigation of contaminants). Moreover, it is important to understand these mechanisms in the context of the soil microbiome, particularly those interactions of AMF with other soil microbes that can further shape crop nutrition. To address these challenges, a two-pronged approach is recommended: exploring molecular mechanisms and investigating microbiome management and engineering. Combining both approaches can lead to benefits in human health by balancing nutrition and contamination caused by metal(loid)s in the agro-ecosystem.

Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago

Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1-42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird's-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.

Domestication caused taxonomical and functional shifts in the wheat rhizosphere microbiota, and weakened the natural bacterial biocontrol against fungal pathogens

Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial-fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.

Metabolomics-guided utilization of beneficial microbes for climate-resilient crops

In the rhizosphere, plants and microbes communicate chemically, especially under environmental stress. Over millions of years, plants and their microbiome have coevolved, sharing various chemicals, including signaling molecules. This mutual exchange impacts bacterial communication and influences plant metabolism. Inter-kingdom signal crosstalk affects bacterial colonization and plant fitness. Beneficial microbes and their metabolomes offer eco-friendly ways to enhance plant resilience and agriculture. Plant metabolites are pivotal in this dynamic interaction between host plants and their interacting beneficial microbes. Understanding these associations is key to engineering a robust microbiome for stress mitigation and improved plant growth. This review explores mechanisms behind plant-microbe interactions, the role of beneficial microbes and metabolomics, and the practical applications for addressing climate change's impact on agriculture. Integrating beneficial microbes' activities and metabolomics' application to study metabolome-driven interaction between host plants and their corresponding beneficial microbes holds promise for enhancing crop resilience and productivity.

Improving crop health by synthetic microbial communities: Progress and prospects

Crop health directly affects yields and food security. At present, agrochemicals such as fertilizers and pesticides are mainly used in agricultural production to promote crop health. However, long-term excessive utilization of agrochemicals will damage the ecological environment of farmlands and increase the safety risk of agricultural products. It is urgent to explore efficient and environment-friendly agricultural products. Rhizosphere microbiome are considered as the second genome of plants, which are closely related to crop health. Understanding the key functional microbes, microbe-microbe interactions, and plant-microbe interactions are fundamental for exploring the potential of beneficial microbes in promoting crop health. However, due to the heterogeneity and complexity of the natural environment, stimulating the function of indigenous microorganisms remains uncertain. Synthetic microbial community (SynCom) is an artificial combination of two or more different strain isolates of microorganisms, with different taxonomic, genetic, or functional characteristic. Because of the advantages of maintaining species diversity and community stability, SynCom has been widely applied in the fields of human health, environmental governance and industrial production, and may also have great potential in promoting crop health. We summarized the concept and research status of SynCom, expounded the principles and methods of constructing SynCom, and analyzed the research on the promotion of crop health by exploring the mechanism of plant-microbe interactions, promoting plant growth and development, and improving stress resistance. Finally, we envisaged the future prospects to guide the using SynCom to improve crop health.

Biofilms formation in plant growth-promoting bacteria for alleviating agro-environmental stress

Biofilm formation represents a pivotal and adaptable trait among microorganisms within natural environments. This attribute plays a multifaceted role across diverse contexts, including environmental, aquatic, industrial, and medical systems. While previous research has primarily focused on the adverse impacts of biofilms, harnessing their potential effectively could confer substantial advantages to humanity. In the face of escalating environmental pressures (e.g., drought, salinity, extreme temperatures, and heavy metal pollution), which jeopardize global crop yields, enhancing crop stress tolerance becomes a paramount endeavor for restoring sufficient food production. Recently, biofilm-forming plant growth-promoting bacteria (PGPB) have emerged as promising candidates for agricultural application. These biofilms are evidence of microorganism colonization on plant roots. Their remarkable stress resilience empowers crops to thrive and yield even in harsh conditions. This is accomplished through increased root colonization, improved soil properties, and the synthesis of valuable secondary metabolites (e.g., ACC deaminase, acetin, 2,3-butanediol, proline, etc.). This article elucidates the mechanisms underpinning the role of biofilm-forming PGPB in bolstering plant growth amidst environmental challenges. Furthermore, it explores the tangible applications of these biofilms in agriculture and delves into strategies for manipulating biofilm formation to extract maximal benefits in practical crop production scenarios.

Effects of continuous cropping on fungal community diversity and soil metabolites in soybean roots

IMPORTANCE

Soybean yield can be affected by soybean soil fungal communities in different tillage patterns. Soybean is an important food crop with great significance worldwide. Continuous cultivation resulted in soil nutrient deficiencies, disordered metabolism of root exudates, fungal pathogen accumulation, and an altered microbial community, which brought a drop in soybean output. In this study, taking the soybean agroecosystem in northeast China, we revealed the microbial ecology and soil metabolites spectrum, especially the diversity and composition of soil fungi and the correlation of pathogenic fungi, and discussed the mechanisms and the measures of alleviating the obstacles.

Analysis of rhizosphere fungal community of agricultural crops cultivated in laboratory experiments on Chernevaya taiga soil

Chernevaya taiga of Western Siberia, Russia, is a unique ecosystem characterized by fertile soil, exceptionally large herbaceous plant sizes, and extraordinarily rapid rates of plant residue degradation. We expected that growing crops on soil collected from Chernevaya taiga, which has never been used for agricultural purposes before, would result in a distinct rhizospheric fungal community. This community could potentially yield novel, potent biostimulators and biocontrol fungi for modern agriculture. To check this idea, we used high-throughput ITS sequencing to examine the microbial communities in the rhizosphere of spring wheat and radish grown in greenhouse experiments on Chernevaya and control soils. Additionally, representative fungal strains were isolated and assessed for their ability to promote growth in wheat seedlings. The study revealed that the most abundant phyla in the rhizospheric fungal community were Mortierellomycota, primarily consisting of Mortierella species, and Ascomycota. Mucor and Umbelopsis comprised the majority of Mucoromycota in the control soils. Fusarium and Oidiodendron, two potentially plant-pathogenic fungi, were only found in the rhizosphere of crops grown in the control soil. Conversely, Chernevaya soil contained a diverse range of potential biocontrol fungi for plants. Tested novel fungal isolates showed a stimulating effect on the development of wheat seedlings and positively affected their rate of biomass accumulation. The results of the study demonstrate that the soil of Chernevaya taiga do indeed contain fungi with prominent potential to stimulate agricultural plants growth.

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

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

Engineering effector-triggered immunity in rice: Obstacles and perspectives

Improving rice immunity is one of the most effective approaches to reduce yield loss by biotic factors, with the aim of increasing rice production by 2050 amidst limited natural resources. Triggering a fast and strong immune response to pathogens, effector-triggered immunity (ETI) has intrigued scientists to intensively study and utilize the mechanisms for engineering highly resistant plants. The conservation of ETI components and mechanisms across species enables the use of ETI components to generate broad-spectrum resistance in plants. Numerous efforts have been made to introduce new resistance (R) genes, widen the effector recognition spectrum and generate on-demand R genes. Although engineering ETI across plant species is still associated with multiple challenges, previous attempts have provided an enhanced understanding of ETI mechanisms. Here, we provide a survey of recent reports in the engineering of rice R genes. In addition, we suggest a framework for future studies of R gene-effector interactions, including genome-scale investigations in both rice and pathogens, followed by structural studies of R proteins and effectors, and potential strategies to use important ETI components to improve rice immunity.

Plant host domestication and soil nutrient availability determine positive plant microbial response across the Solanum genus

Domestication of crops has changed how crops shape their associated microbial communities compared with their progenitors. However, studies testing how crop domestication-driven differences in rhizosphere microbial communities affect plant health are limited mostly to specific symbiont pairings. By conducting a soil manipulation greenhouse study, we examined plant growth and yield in response to differences in microbial communities and nutrient availability across a variety of wild, landrace, and commercially available 'Modern' potatoes. Coupled with this, we conducted 16S and internal transcribed spacer (ITS) amplicon sequencing to examine plant host- and soil treatment-driven differences in microbial community composition on potato plant roots. We found that the plant response to microbes (PRM) was context dependent. In low nutrient conditions, landraces responded positively to the presence of live soil microbial inocula. Conversely, modern potato varieties responded positively only in high nutrient conditions. Amplicon sequencing found differences in bacterial communities due to environmental and temporal factors. However, potato clade (e.g. Andigenum, Chiletanum, Solanum berthaultii, and 'Modern') alone did not lead to differences in microbial communities that accounted for PRM differences. Differences in PRM between landraces and modern potatoes, and the correlation of PRM to microbial diversity, suggest that domestication and subsequent breeding have altered the S. tuberosum response to rhizosphere microbiomes between Andigenum, Chiletanum, and North American potato varieties.

Biological nitrogen fixation in cereal crops: Progress, strategies, and perspectives

Nitrogen is abundant in the atmosphere but is generally the most limiting nutrient for plants. The inability of many crop plants, such as cereals, to directly utilize freely available atmospheric nitrogen gas means that their growth and production often rely heavily on the application of chemical fertilizers, which leads to greenhouse gas emissions and the eutrophication of water. By contrast, legumes gain access to nitrogen through symbiotic association with rhizobia. These bacteria convert nitrogen gas into biologically available ammonia in nodules through a process termed symbiotic biological nitrogen fixation, which plays a decisive role in ecosystem functioning. Engineering cereal crops that can fix nitrogen like legumes or associate with nitrogen-fixing microbiomes could help to avoid the problems caused by the overuse of synthetic nitrogen fertilizer. With the development of synthetic biology, various efforts have been undertaken with the aim of creating so-called "N-self-fertilizing" crops capable of performing autonomous nitrogen fixation to avoid the need for chemical fertilizers. In this review, we briefly summarize the history and current status of engineering N-self-fertilizing crops. We also propose several potential biotechnological approaches for incorporating biological nitrogen fixation capacity into non-legume plants.

Hedgerows increase the diversity and modify the composition of arbuscular mycorrhizal fungi in Mediterranean agricultural landscapes

Sustainable agriculture is essential to address global challenges such as climate change and biodiversity loss. Hedgerows enhance aboveground biodiversity and provide ecosystem services, but little is known about their impact on soil biota. Arbuscular mycorrhizal (AM) fungi are one of the key components of belowground biodiversity. We compared the diversity and composition of AM fungal communities at four farmland sites located in Central Spain, where 132 soil samples in total were collected to assess soil physical and chemical properties and the AM fungal communities. We compared the richness (number of AM fungal taxa), taxonomic, functional, and phylogenetic diversity, and structure of the AM fungal communities across three farmland habitat types, namely hedgerows, woody crops (olive groves and vineyard), and herbaceous crops (barley, sunflower, and wheat). Our results showed positive effects of hedgerows on most diversity metrics. Almost 60% of the AM fungal taxa were shared among the three farmland habitat types. Hedgerows increased AM fungal taxonomic richness (31%) and alpha diversity (25%), and especially so compared to herbaceous crops (45% and 28%, respectively). Hedgerows harbored elevated proportions of AM fungi with non-ruderal life-history strategies. AM fungal communities were more similar between hedgerows and woody crops than between hedgerows and adjacent herbaceous crops, possibly because of differences in tillage and fertilization. Unexpectedly, hedgerows reduced phylogenetic diversity, which might be related to more selective associations of AM fungi with woody plants than with herbaceous crops. Overall, the results suggest that planting hedgerows contributes to maintain belowground diversity. Thus, European farmers should plant more hedgerows to attain the goals of the EU Biodiversity Strategy for 2030.

The Perspective of Arbuscular Mycorrhizal Symbiosis in Rice Domestication and Breeding

In nature, symbiosis with arbuscular mycorrhizal (AM) fungi contributes to sustainable acquisition of phosphorus and other elements in over 80% of plant species; improving interactions with AM symbionts may mitigate some of the environmental problems associated with fertilizer application in grain crops such as rice. Recent developments of high-throughput genome sequencing projects of thousands of rice cultivars and the discovery of the molecular mechanisms underlying AM symbiosis suggest that interactions with AM fungi might have been an overlooked critical trait in rice domestication and breeding. In this review, we discuss genetic variation in the ability of rice to form AM symbioses and how this might have affected rice domestication. Finally, we discuss potential applications of AM symbiosis in rice breeding for more sustainable agriculture.

A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production

The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.

Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes

In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.

Foodmaking microbes bear marks of domestication

Bacteria and fungi behind cheese, soy, and more share genomic traits wth domesticated plants and animals.

The effect of phosphate mining activities on rhizosphere bacterial communities of surrounding vegetables and crops

The effects of phosphate mining on rhizosphere bacteria in surrounding vegetables and crops, including Lactuca sativa, Glycine max, and Triticum aestivum, are assessed in this study. As results, phosphate mining significantly increased the contents of some large elements, trace elements, and heavy metals in the surrounding agricultural soil, including phosphorus, magnesium, boron, cadmium, lead, arsenic, zinc, and chromium (P < 0.05). The community richness and diversity of bacteria in rhizosphere of the three crops were significantly reduced by phosphate mining (P < 0.05). Abundances of Sphingomonas and RB41 in the rhizosphere soil of phosphate mining area improved compared with the baseline in the non-phosphate mining area. Beta diversity analysis indicated that phosphate mining led to the differentiation of bacterial community structure in plant rhizospheres. Bacterial metabolic analysis indicated that different plant rhizosphere microbial flora developed various metabolic strategies in response to phosphate mining stress, including enriching unsaturated fatty acids, antibiological transport systems, cold shock proteins, etc. This study reveals the interaction between crops, rhizosphere bacteria, and soil pollutants. Select differentiated microbial strains suitable for specific plant rhizosphere environments are necessary for agricultural soil remediation. Additionally, the problem of destruction of agricultural soil and microecology caused by phosphate mining must be solved.

Aflatoxin Contamination, Its Impact and Management Strategies: An Updated Review

Aflatoxin, a type of mycotoxin, is mostly produced by Aspergillus flavus and Aspergillus parasiticus. It is responsible for the loss of billions of dollars to the world economy, by contaminating different crops such as cotton, groundnut, maize, and chilies, and causing immense effects on the health of humans and animals. More than eighteen different types of aflatoxins have been reported to date, and among them, aflatoxins B1, B2, G1, and G2 are the most prevalent and lethal. Early detection of fungal infection plays a key role in the control of aflatoxin contamination. Therefore, different methods, including culture, chromatographic techniques, and molecular assays, are used to determine aflatoxin contamination in crops and food products. Many countries have set a maximum limit of aflatoxin contamination (2-20 ppb) in their food and agriculture commodities for human or animal consumption, and the use of different methods to combat this menace is essential. Fungal infection mostly takes place during the pre- and post-harvest stage of crops, and most of the methods to control aflatoxin are employed for the latter phase. Studies have shown that if correct measures are adopted during the crop development phase, aflatoxin contamination can be reduced by a significant level. Currently, the use of bio-pesticides is the intervention employed in many countries, whereby atoxigenic strains competitively reduce the burden of toxigenic strains in the field, thereby helping to mitigate this problem. This updated review on aflatoxins sheds light on the sources of contamination, and the on occurrence, impact, detection techniques, and management strategies, with a special emphasis on bio-pesticides to control aflatoxins.

Salicylic acid carboxyl glucosyltransferase UGT87E7 regulates disease resistance in Camellia sinensis

Plant immune response following pathogenic infection is regulated by plant hormones, and salicylic acid (SA) and its sugar conjugates play important roles in establishing basal resistance. Here, the important pathogen Pseudopestalotiopsis camelliae-sinensis (Pcs) was isolated from tea gray blight, one of the most destructive diseases in tea plantations. Transcriptomic analysis led to the discovery of the putative Camellia sinensis UDP-glucosyltransferase CsUGT87E7 whose expression was significantly induced by SA application and Pcs infection. Recombinant CsUGT87E7 glucosylates SA with a Km value of 12 µM to form SA glucose ester (SGE). Downregulation reduced the accumulation of SGE, and CsUGT87E7-silenced tea plants exhibited greater susceptibility to pathogen infection than control plants. Similarly, CsUGT87E7-silenced tea leaves accumulated significantly less SA after infection and showed reduced expression of pathogenesis-related genes. These results suggest that CsUGT87E7 is an SA carboxyl glucosyltransferase that plays a positive role in plant disease resistance by modulating SA homeostasis through a mechanism distinct from that described in Arabidopsis (Arabidopsis thaliana). This study provides insight into the mechanisms of SA metabolism and highlights the role of SGE in the modulation of plant disease resistance.

Estimation of Tolerable Daily Intake (TDI) for Immunological Effects of Aflatoxin

Aflatoxins are toxic chemicals produced by the fungi Aspergillus flavus and Aspergillus parasiticus. In warm climates, these fungi frequently contaminate crops such as maize, peanuts, tree nuts, and sunflower seeds. In many tropical and subtropical regions of the world, populations are coexposed to dietary aflatoxin and multiple infectious pathogens in food, water, and the environment. There is increasing evidence that aflatoxin compromises the immune system, which could increase infectious disease risk in vulnerable populations. Our aim was to conduct a dose-response assessment on a noncarcinogenic endpoint of aflatoxin: immunotoxicological effects. We sought to determine a noncarcinogenic tolerable daily intake (TDI) of aflatoxin, based on the existing data surrounding aflatoxin and biomarkers of immune suppression. To conduct the dose response assessment, mammalian studies were assessed for appropriateness of doses (relevant to potential human exposures) as well as goodness of data, and two appropriate mouse studies that examined decreases in leukocyte counts were selected to generate dose response curves. From these, we determined benchmark dose lower confidence limits (BMDL) as points of departure to estimate a range of TDIs for aflatoxin-related immune impairment: 0.017-0.082 μg/kg bw/day. As aflatoxin is a genotoxic carcinogen, and regulations concerning its presence in food have largely focused on its carcinogenic effects, international risk assessment bodies such as the Joint Expert Committee on Food Additives (JECFA) have never established a TDI for aflatoxin. Our work highlights the importance of the noncarcinogenic effects of aflatoxin that may have broader public health impacts, to inform regulatory standard-setting.

Bioprospecting Plant Growth Promoting Rhizobacteria for Enhancing the Biological Properties and Phytochemical Composition of Medicinally Important Crops

Traditionally, medicinal plants have long been used as a natural therapy. Plant-derived extracts or phytochemicals have been exploited as food additives and for curing many health-related ailments. The secondary metabolites produced by many plants have become an integral part of human health and have strengthened the value of plant extracts as herbal medicines. To fulfil the demand of health care systems, food and pharmaceutical industries, interest in the cultivation of precious medicinal plants to harvest bio-active compounds has increased considerably worldwide. To achieve maximum biomass and yield, growers generally apply chemical fertilizers which have detrimental impacts on the growth, development and phytoconstituents of such therapeutically important plants. Application of beneficial rhizosphere microbiota is an alternative strategy to enhance the production of valuable medicinal plants under both conventional and stressed conditions due to its low cost, environmentally friendly behaviour and non-destructive impact on fertility of soil, plants and human health. The microbiological approach improves plant growth by various direct and indirect mechanisms involving the abatement of various abiotic stresses. Given the negative impacts of fertilizers and multiple benefits of microbiological resources, the role of plant growth promoting rhizobacteria (PGPR) in the production of biomass and their impact on the quality of bio-active compounds (phytochemicals) and mitigation of abiotic stress to herbal plants have been described in this review. The PGPR based enhancement in the herbal products has potential for use as a low cost phytomedicine which can be used to improve health care systems.

An insight to rhizosphere bacterial community composition and structure of consecutive winter-initiated sugarcane ratoon crop in Southern China

BACKGROUND

Ratooning in sugarcane is a crucial strategy for ensuring the long-term sustainability of the sugarcane industry. Knowledge gap relating to the interaction between rhizosphere microbiome and ratooning crop, particularly the impact of different sugarcane cultivars on the rhizosphere microbiome in consecutive ratooning, requires additional research. The response of two different sugarcane cultivars, viz ZZ-1 and ZZ-13, were evaluated in consecutive ratooning towards the rhizosphere microbial community and cane morphological characters.

RESULTS

Significant changes in the rhizosphere microbiome were observed in the second ratooning over the years. Several important genera were observed in high abundance during the second ratooning, including Burkholderia, Sphingomonas, Bradyzhizobium, and Acidothermus. Cultivar ZZ-13 caused more alterations in the rhizosphere microbiome than ZZ-1, resulting in a more favorable rhizosphere environment for sugarcane growth. The genotypes also varied in terms of nutrients and enzyme activity over the years. There were significant differences between the genotypes and year for number of stalks and yield was significant for genotypes, years and genotype × year.

CONCLUSION

This finding will help to understand thorough interactions between rhizosphere microorganisms and ratoon sugarcane and lay the foundation for promoting and maximizing yield as far as possible. In the future, this work can serve as guidance in sugarcane husbandry, mainly in Guangxi, China.

Breeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes

Grain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain legumes worldwide. Harnessing the untapped reserve of global grain legume germplasm, landraces, and crop wild relatives (CWRs) could help minimize yield losses caused by AB infection in grain legumes. Several genetic determinants controlling AB resistance in various grain legumes have been identified following classical genetic and conventional breeding approaches. However, the advent of molecular markers, biparental quantitative trait loci (QTL) mapping, genome-wide association studies, genomic resources developed from various genome sequence assemblies, and whole-genome resequencing of global germplasm has revealed AB-resistant gene(s)/QTL/genomic regions/haplotypes on various linkage groups. These genomics resources allow plant breeders to embrace genomics-assisted selection for developing/transferring AB-resistant genomic regions to elite cultivars with great precision. Likewise, advances in functional genomics, especially transcriptomics and proteomics, have assisted in discovering possible candidate gene(s) and proteins and the underlying molecular mechanisms of AB resistance in various grain legumes. We discuss how emerging cutting-edge next-generation breeding tools, such as rapid generation advancement, field-based high-throughput phenotyping tools, genomic selection, and CRISPR/Cas9, could be used for fast-tracking AB-resistant grain legumes to meet the increasing demand for grain legume-based protein diets and thus ensuring global food security.

Dynamic changes of rhizosphere soil bacterial community and nutrients in cadmium polluted soils with soybean-corn intercropping

BACKGROUND

Soybean-corn intercropping is widely practised by farmers in Southwest China. Although rhizosphere microorganisms are important in nutrient cycling processes, the differences in rhizosphere microbial communities between intercropped soybean and corn and their monoculture are poorly known. Additionally, the effects of cadmium (Cd) pollution on these differences have not been examined. Therefore, a field experiment was conducted in Cd-polluted soil to determine the effects of monocultures and soybean-corn intercropping systems on Cd concentrations in plants, on rhizosphere bacterial communities, soil nutrients and Cd availability. Plants and soils were examined five times in the growing season, and Illumina sequencing of 16S rRNA genes was used to analyze the rhizosphere bacterial communities.

RESULTS

Intercropping did not alter Cd concentrations in corn and soybean, but changed soil available Cd (ACd) concentrations and caused different effects in the rhizosphere soils of the two crop species. However, there was little difference in bacterial community diversity for the same crop species under the two planting modes. Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria and Firmicutes were the dominant phyla in the soybean and corn rhizospheres. In ecological networks of bacterial communities, intercropping soybean (IS) had more module hubs and connectors, whereas intercropped corn (IC) had fewer module hubs and connectors than those of corresponding monoculture crops. Soil organic matter (SOM) was the key factor affecting soybean rhizosphere bacterial communities, whereas available nutrients (N, P, K) were the key factors affecting those in corn rhizosphere. During the cropping season, the concentration of soil available phosphorus (AP) in the intercropped soybean-corn was significantly higher than that in corresponding monocultures. In addition, the soil available potassium (AK) concentration was higher in intercropped soybean than that in monocropped soybean.

CONCLUSIONS

Intercropped soybean-corn lead to an increase in the AP concentration during the growing season, and although crop absorption of Cd was not affected in the Cd-contaminated soil, soil ACd concentration was affected. Intercropped soybean-corn also affected the soil physicochemical properties and rhizosphere bacterial community structure. Thus, intercropped soybean-corn was a key factor in determining changes in microbial community composition and networks. These results provide a basic ecological framework for soil microbial function in Cd-contaminated soil.

Hollow-Structured Microporous Organic Networks Adsorbents Enabled Specific and Sensitive Identification and Determination of Aflatoxins

Aflatoxin (AFT) contamination, commonly in foods and grains with extremely low content while high toxicity, has caused serious economic and health problems worldwide. Now researchers are making an effort to develop nanomaterials with remarkable adsorption capacity for the identification, determination and regulation of AFT. Herein, we constructed a novel hollow-structured microporous organic networks (HMONs) material. On the basis of Fe3O4@MOF@MON, hydrofluoric acid (HF) was introduced to remove the transferable metal organic framework (MOF) to give hollow MON structures. Compared to the original Fe3O4@MOF@MON, HMON showed improved surface area and typical hollow cavities, thus increasing the adsorption capacity. More importantly, AFT is a hydrophobic substance, and our constructed HMON had a higher water contact angle, greatly enhancing the adsorption affinity. From that, the solid phase extraction (SPE-HPLC) method developed based on HMONs was applied to analyze four kinds of actual samples, with satisfied recoveries of 85-98%. This work provided a specific and sensitive method for the identification and determination of AFT in the food matrix and demonstrated the great potential of HMONs in the field of the identification and control of mycotoxins.

Fusarium Mycotoxins in Maize Field Soils: Method Validation and Implications for Sampling Strategy

While mycotoxins are generally regarded as food contamination issues, there is growing interest in mycotoxins as environmental pollutants. The main sources of trichothecene and zearalenone mycotoxins in the environment are mainly attributed to Fusarium infested fields, where mycotoxins can wash off in infested plants or harvest residues. Subsequently, mycotoxins inevitably enter the soil. In this context, investigations into the effects, fate, and transport are still needed. However, there is a lack of analytical methods used to determine Fusarium toxins in soil matrices. We aimed to validate an analytical method capable of determining the toxins nivalenol (NIV), deoxynivalenol (DON), 15-acetyl-deoxynivalenol (15-AcDON), and zearalenone (ZEN), at environmentally relevant concentrations, in five contrasting agricultural soils. Soils were spiked at three levels (3, 9 and 15 ng g-1), extracted by solid-liquid extraction assisted with ultrasonication, using a generic solvent composition of acetonitrile:water 84:16 (v:v) and measured by LC-HRMS. Method validation was successful for NIV, DON, and 15-AcDON with mean recoveries > 93% and RSDr < 10%. ZEN failed the validation criteria. The validated method was applied to eight conventionally managed maize field soils during harvest season, to provide a first insight into DON, NIV, and 15-AcDON levels. Mycotoxins were present in two out of eight sampled maize fields. Soil mycotoxin concentrations ranged from 0.53 to 19.4 ng g-1 and 0.8 to 2.2 ng g-1 for DON and NIV, respectively. Additionally, we found indication that "hot-spot" concentrations were restricted to small scales (<5 cm) with implications for field scale soil monitoring strategies.

Mycorrhizal symbiosis promotes the nutrient content accumulation and affects the root exudates in maize

BACKGROUND

Arbuscular mycorrhizal fungi (AMF) are a group of important symbiotic microorganisms found in ecosystems. Maize is the second most produced food crop globally. To investigate the mechanisms by which mycorrhizal symbiosis improves maize yields, the effects of mycorrhizal symbiosis on root vigor, nutrient accumulation in various tissues, and root exudates were investigated. We propose the following hypothesis: The secretion of organic acids in root exudates has antagonistic or synergistic effects, which are related to the rhizosphere environment. AMF symbiosis will enhance this effect.

RESULT

Rhizophagus aggreatus, Claroideoglomus etunicatum, and Funneliformis mosseae were used to inoculate maize plants separately; meanwhile, maize was inoculated with the above three fungi together for another processing. The plant tissues were sampled at five growth stages: V12 (twelve-leaf), VT (Tassel), R1 (Silking), R2 (Blister), and R4 (Dough stage). The root vigor, and nutrient content in different maize organs and organic acids in root exudates were determined in these stages. The results show that mycorrhizal symbiosis significantly improved the root vigor of maize, especially for plants inoculated with F. mosseae. AMF symbiosis significantly increased N, P, and K accumulation. Mixed inoculation with arbuscular mycorrhizal fungi significantly promoted the accumulation of N and K in maize. P accumulation was significantly promoted by C. etunicatum inoculation. Mycorrhizal symbiosis reduced the levels of protocatechuic, vanillic, citric, and ferulic acid in maize root exudates and increased the levels of p-hydroxybenzoic and caffeic acid. Except for syringic, chlorogenic and succinic acid, the levels of other organic acids in root exudates were higher in plants inoculated with F. mosseae than in other treatments.

CONCLUSION

This study demonstrates that mycorrhizal symbiosis improves root vigor and promotes nutrient accumulation at various sites; in addition, mycorrhizal symbiosis affects the content of organic acids in root exudates.

Search for host defense markers uncovers an apple agglutination factor corresponding with fire blight resistance

Pathenogenesis-related (PR) proteins are extensively used as molecular markers to dissect the signaling cascades leading to plant defense responses. However, studies focusing on the biochemical or biological properties of these proteins remain rare. Here, we identify and characterize a class of apple (Malus domestica) PR proteins, named M. domestica AGGLUTININS (MdAGGs), belonging to the amaranthin-like lectin family. By combining molecular and biochemical approaches, we show that abundant production of MdAGGs in leaf tissues corresponds with enhanced resistance to the bacterium Erwinia amylovora, the causal agent of the disease fire blight. We also show that E. amylovora represses the expression of MdAGG genes by injecting the type 3 effector DspA/E into host cells and by secreting bacterial exopolysaccharides. Using a purified recombinant MdAGG, we show that the protein agglutinates E. amylovora cells in vitro and binds bacterial lipopolysaccharides at low pH, conditions reminiscent of the intercellular pH occurring in planta upon E. amylovora infection. We finally provide evidence that negatively charged polysaccharides, such as the free exopolysaccharide amylovoran progressively released by the bacteria, act as decoys relying on charge-charge interaction with the MdAGG to inhibit agglutination. Overall, our results suggest that the production of this particular class of PR proteins may contribute to apple innate immunity mechanisms active against E. amylovora.

Revealing the early response of pear (Pyrus bretschneideri Rehd) leaves during Botryosphaeria dothideainfection by transcriptome analysis

Ring rot disease, which is caused by Botryosphaeria dothidea (B. dothidea), is one of the most serious diseases affecting the pear industry. Currently, knowledge of the mechanism about pear-pathogen interactions is unclear. To explore the early response of pear leaves to B. dothidea infection, we compared the early transcriptome of pear leaves infected with B. dothidea. The results revealed 3248 differentially expressed genes (DEGs) and 4862 DEGs at D2 and D4, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation of DEGs showed that these genes were predominately involved in plant-pathogen interactions, hormone signal transduction and other biosynthesis-related metabolic processes, including glucosinolate accumulation and flavonoid pathway enhancement. However, many hormone- and disease resistance-related genes and transcription factors (TFs) were differentially expressed during B. dothidea infection. These results were consistent with the changes in the physiological characteristics of B. dothidea. In addition, the expression of PbrPUB29, an E3 ubiquitin ligase with a U-box domain, was significantly higher than it was at 0 dpi. PbrPUB29 silencing enhanced the sensitivity of pear leaves to B. dothidea, reflected by more severe symptoms and higher reactive oxygen species (ROS) content in the defective pear seedlings after inoculation, revealing that PbrPUB29 has a significant role in pear disease resistance. In brief, we explored the interaction between pear leaves and B. dothidea at the transcriptome level, implied the early response of pear leaves to pathogens, and identified a hub gene in a B. dothidea-infected pear. These results provide a basis and new strategy for exploring the molecular mechanisms underlying pear-pathogen interactions and disease resistance breeding.

Fungal pathogens of cereal crops: Proteomic insights into fungal pathogenesis, host defense, and resistance

Fungal infections of cereal crops pose a significant risk to global food security through reduced grain production and quality, as well as contamination of animal feed and human products for consumption. To combat fungal disease, we need to understand how the pathogen adapts and survives within the hostile environment of the host and how the host's defense response can be modulated for protection from disease. Such investigations offer insight into fungal pathogenesis, host immunity, the development of resistance, and mechanisms of action for currently-used control strategies. Mass spectrometry-based proteomics provides a technologically-advanced platform to define differences among fungal pathogens and their hosts at the protein level, supporting the discovery of proteins critical for disease, and uncovering novel host responses driving susceptibly or resistance of the host. In this Review, we explore the role of mass spectrometry-based proteomics in defining the intricate relationship between a pathogen and host during fungal disease of cereal crops with a focus on recent discoveries derived from the globally-devastating diseases of Fusarium head blight, Rice blast, and Powdery mildew. We highlight advances made for each of these diseases and discuss opportunities to extrapolate findings to further our fight against fungal pathogens on a global scale.

Wide distribution of resistance to the fungicides fludioxonil and iprodione in Penicillium species

Fludioxonil and iprodione are effective fungicides widely used for crop protection and are essential for controlling plant pathogenic fungi. The emergence of fungicide-resistant strains of targeted pathogens is regularly monitored, and several cases have been reported. Non-targeted fungi may also be exposed to the fungicide residues in agricultural fields. However, there are no comprehensive reports on fungicide-resistant strains of non-targeted fungi. Here, we surveyed 99 strains, representing 12 Penicillium species, that were isolated from a variety of environments, including foods, dead bodies, and clinical samples. Among the Penicillium strains, including non-pathogenic P. chrysogenum and P. camembertii, as well as postharvest pathogens P. expansum and P. digitatum, 14 and 20 showed resistance to fludioxonil and iprodione, respectively, and 6 showed multi-drug resistance to the fungicides. Sequence analyses revealed that some strains of P. chrysogenum and Penicillium oxalicum had mutations in NikA, a group III histidine kinase of the high-osmolarity glycerol pathway, which is the mode of action for fludioxonil and iprodione. The single nucleotide polymorphisms of G693D and T1318P in P. chrysogenum and T960S in P. oxalicum were only present in the fludioxonil- or iprodione-resistant strains. These strains also exhibited resistance to pyrrolnitrin, which is the lead compound in fludioxonil and is naturally produced by some Pseudomonas species. This study demonstrated that non-targeted Penicillium strains distributed throughout the environment possess fungicide resistance.

Enriched HeK4me3 marks at Pm-0 resistance-related genes prime courgette against Podosphaera xanthii

Powdery mildew (PM) disease, caused by the obligate biotrophic fungal pathogen Podosphaera xanthii, is the most reported and destructive disease on cultivated Cucurbita species all over the world. Recently, the appearance of highly aggressive P. xanthii isolates has led to PM outbreaks even in resistant crops, making disease management a very difficult task. To challenge this, breeders rely on genetic characteristics for PM control. Analysis of commercially available intermediate resistance courgette (Cucurbita pepo L. var. cylindrica) varieties using cytological, molecular, and biochemical approaches showed that the plants were under a primed state and induced systemic acquired resistance (SAR) responses, exhibiting enhanced callose production, upregulation of salicylic acid (SA) defense signaling pathway genes, and accumulation of SA and defense metabolites. Additionally, the intermediate resistant varieties showed an altered epigenetic landscape in histone marks that affect transcriptional activation. We demonstrated that courgette plants had enriched H3K4me3 marks on SA-BINDING PROTEIN 2 and YODA (YDA) genes of the Pm-0 interval introgression, a genomic region that confers resistant to Cucurbits against P. xanthii. The open chromatin of SA-BINDING PROTEIN 2 and YDA genes was consistent with genes' differential expression, induced SA pathway, altered stomata characteristics, and activated SAR responses. These findings demonstrate that the altered epigenetic landscape of the intermediate resistant varieties modulates the activation of SA-BINDING PROTEIN 2 and YDA genes leading to induced gene transcription that primes courgette plants.

Asymmetric redundancy of soybean Nodule Inception (NIN) genes in root nodule symbiosis

Nodule Inception (NIN) is one of the most important root nodule symbiotic genes as it is required for both infection and nodule organogenesis in legumes. Unlike most legumes with a sole NIN gene, there are four putative orthologous NIN genes in soybean (Glycine max). Whether and how these NIN genes contribute to soybean-rhizobia symbiotic interaction remain unknown. In this study, we found that all four GmNIN genes are induced by rhizobia and that conserved CE and CYC binding motifs in their promoter regions are required for their expression in the nodule formation process. By generation of multiplex Gmnin mutants, we found that the Gmnin1a nin2a nin2b triple mutant and Gmnin1a nin1b nin2a nin2b quadruple mutant displayed similar defects in rhizobia infection and root nodule formation, Gmnin2a nin2b produced fewer nodules but displayed a hyper infection phenotype compared to wild type (WT), while the Gmnin1a nin1b double mutant nodulated similar to WT. Overexpression of GmNIN1a, GmNIN1b, GmNIN2a, and GmNIN2b reduced nodule numbers after rhizobia inoculation, with GmNIN1b overexpression having the weakest effect. In addition, overexpression of GmNIN1a, GmNIN2a, or GmNIN2b, but not GmNIN1b, produced malformed pseudo-nodule-like structures without rhizobia inoculation. In conclusion, GmNIN1a, GmNIN2a, and GmNIN2b play functionally redundant yet complicated roles in soybean nodulation. GmNIN1b, although expressed at a comparable level with the other homologs, plays a minor role in root nodule symbiosis. Our work provides insight into the understanding of the asymmetrically redundant function of GmNIN genes in soybean.

Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation

BACKGROUND

Brassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses. B. napus is susceptible to a variety of fungal diseases, so identify the BnLTPs and their expression in disease responses is very important. The common reference genome of B. napus does not contain all B. napus genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate BnLTP genes in the B. napus pangenome.

RESULTS

In the present study, the BnLTP genes were identified throughout the pangenome, and different BnLTP genes were presented among varieties. Totally, 246 BnLTP genes were identified and could be divided into five types (1, 2, C, D, and G). The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed. We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all BnLTP genes. RNA sequencing analysis showed that the BnLTP genes were involved in the response to Sclerotinia sclerotiorum infection. We identified 32 BnLTPs linked to blackleg resistance quantitative trait locus (QTL).

CONCLUSION

The identification and analysis of LTP genes in the B. napus pangenome could help to elucidate the function of BnLTP family members and provide new information for future molecular breeding in B. napus.

Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome

Fungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal following a rainfall gradient. We hypothesized that wild pearl millet could serve as a reservoir of endophytes for cultivated pearl millet. We therefore analyzed the soil factors influencing fungal community structure and whether cultivated and wild millet shared the same fungal communities. The fungal communities associated with pearl millet were significantly structured according to sites and plant type (wild vs cultivated). Besides, soil pH and phosphorus were the main factors influencing the fungal community structure. We observed a higher fungal diversity in cultivated compared to wild pearl millet. Interestingly, we detected higher relative abundance of putative pathotrophs, especially plant pathogen, in cultivated than in wild millet in semi-arid and semi-humid zones, and higher relative abundance of saprotrophs in wild millet in arid and semi-humid zones. A network analysis based on taxa co-occurrence patterns in the core mycobiome revealed that cultivated millet and wild relatives had dissimilar groups of hub taxa. The identification of the core mycobiome and hub taxa of cultivated and wild pearl millet could be an important step in developing microbiome engineering approaches for more sustainable management practices in pearl millet agroecosystems.

Silencing GhIAA43, a member of cotton AUX/IAA genes, enhances wilt resistance via activation of salicylic acid-mediated defenses

Auxin-mediated degradation of Aux/IAA proteins is a crucial step in auxin signaling. Recent researches indicate that Aux/IAA members also play a role in biotic and abiotic stresses. For example, Pseudomonas syringae infection causes Arabidopsis Aux/IAA protein (AXR2, AXR3) turnover. Here, by analyzing RNA-seq data we found that several cotton Aux/IAA genes are responsive to Verticillium dahliae infection, one of these named GhIAA43, was investigated for its role in cotton defense against V. dahliae infection. We demonstrate that the transcript levels of GhIAA43 were responsive to both V. dahliae infection and exogenous IAA application. By producing transgenic Arabidopsis plants overexpressing GhIAA43-GUS fusion, we show that IAA treatment and V. dahliae infection promoted GhIAA43 protein turnover. Silencing GhIAA43 in cotton enhanced wilt resistance, suggesting that GhIAA43 is a negative regulator in cotton defense against V. dahliae attack. By monitoring SA marker gene expression and measurement of SA content in GhIAA43-silenced cotton plants, we found that the enhanced resistance in GhIAA43-silenced cotton plants is due to the activation of SA-related defenses, and the activated defenses specifically occurred in the presence of V. dahliae. Furthermore, exogenous IAA application improve wilt resistance in cotton plants tested. Our results provide novel connection between auxin signaling and SA-related defenses in cotton upon V. dahliae attack.

Long Non-Coding RNAs profiling in pathogenesis of Verticillium dahliae: New insights in the host-pathogen interaction

Verticillium dahliae causes vascular wilt disease on cotton (Gossypium hirsutum), resulting in devastating yield loss worldwide. While little is known about the mechanism of long non-coding RNAs (lncRNAs), several lncRNAs have been implicated in numerous physiological processes and diseases. To better understand V. dahliae pathogenesis, lncRNA was conducted in a V. dahliae virulence model. Potential target genes of significantly regulated lncRNAs were predicted using cis/trans-regulatory algorithms. This study provides evidence for lncRNAs' regulatory role in pathogenesis-related genes. Interestingly, lncRNAs were identified and varying in terms of RNA length and nutrient starvation treatments. Efficient pathogen nutrition during the interaction with the host is a requisite factor during infection. Our observations directly link to mutated V. dahliae invasion, explaining infected cotton have lower pathogenicity and lethality compared to V. dahliae. Remarkably, lncRNAs XLOC_006536 and XLOC_000836 involved in the complex regulation of pathogenesis-related genes in V. dahliae were identified. For the first time the regulatory role of lncRNAs in filamentous fungi was uncovered, and it is our contention that elucidation of lncRNAs will advance our understanding in the development and pathogenesis of V. dahliae and offer alternatives in the control of the diseases caused by fungus V. dahliae attack.

The Bacteriophage Pf-10-A Component of the Biopesticide "Multiphage" Used to Control Agricultural Crop Diseases Caused by Pseudomonas syringae

Phytopathogenic pseudomonads are widespread in the world and cause a wide range of plant diseases. In this work, we describe the Pseudomonas phage Pf-10, which is a part of the biopesticide "Multiphage" used for bacterial diseases of agricultural crops caused by Pseudomonas syringae. The Pf-10 chromosome is a dsDNA molecule with two direct terminal repeats (DTRs). The phage genomic DNA is 39,424 bp long with a GC-content of 56.5%. The Pf-10 phage uses a packaging mechanism based on T7-like short DTRs, and the length of each terminal repeat is 257 bp. Electron microscopic analysis has shown that phage Pf-10 has the podovirus morphotype. Phage Pf-10 is highly stable at pH values from 5 to 10 and temperatures from 4 to 60 °C and has a lytic activity against Pseudomonas strains. Phage Pf-10 is characterized by fast adsorption rate (80% of virions attach to the host cells in 10 min), but has a relatively small number of progeny (37 ± 8.5 phage particles per infected cell). According to the phylogenetic analysis, phage Pf-10 can be classified as a new phage species belonging to the genus Pifdecavirus, subfamily Studiervirinae, family Autographiviridae, order Caudovirales.

Manipulating exudate composition from root apices shapes the microbiome throughout the root system

Certain soil microorganisms can improve plant growth, and practices that encourage their proliferation around the roots can boost production and reduce reliance on agrochemicals. The beneficial effects of the microbial inoculants currently used in agriculture are inconsistent or short-lived because their persistence in soil and on roots is often poor. A complementary approach could use root exudates to recruit beneficial microbes directly from the soil and encourage inoculant proliferation. However, it is unclear whether the release of common organic metabolites can alter the root microbiome in a consistent manner and if so, how those changes vary throughout the whole root system. In this study, we altered the expression of transporters from the ALUMINUM-ACTIVATED MALATE TRANSPORTER and the MULTIDRUG AND TOXIC COMPOUND EXTRUSION families in rice (Oryza sativa L.) and wheat (Triticum aestivum L.) and tested how the subsequent release of their substrates (simple organic anions, including malate, citrate, and γ-amino butyric acid) from root apices affected the root microbiomes. We demonstrate that these exudate compounds, separately and in combination, significantly altered microbiome composition throughout the root system. However, the root type (seminal or nodal), position along the roots (apex or base), and soil type had a greater influence on microbiome structure than the exudates. These results reveal that the root microbiomes of important cereal species can be manipulated by altering the composition of root exudates, and support ongoing attempts to improve plant production by manipulating the root microbiome.

The mitogen-activated protein kinase kinase TaMKK5 mediates immunity via the TaMKK5-TaMPK3-TaERF3 module

Sharp eyespot disease, caused by the soil-borne fungus Rhizoctonia cerealis, seriously threatens production of wheat (Triticum aestivum). Despite considerable advances in understanding the mechanisms of mitogen-activated protein kinase (MAPK) cascades in innate immunity in model plant species, the roles of MAPK cascades in wheat are unknown. In this study, we identified a wheat MAPK kinase TaMKK5, located on chromosome 6B, and deciphered its functional role in the innate immune responses to R. cerealis attack. The TaMKK5-6B transcript level was elevated after R. cerealis infection and was higher in resistant wheat genotypes compared to susceptible genotypes. Overexpressing TaMKK5-6B increased resistance to sharp eyespot and upregulated the expression of multiple defense-related genes in wheat, including the MAPK gene TaMPK3, the ethylene response factor gene TaERF3, the calcium-dependent protein kinase gene TaCPK7-D, the glutathione s-transferase-1 gene TaGST1, Defensin, and Chitinase 2, while TaMKK5 knock-down compromised the resistance and repressed the expression of these defense-related genes. Bimolecular fluorescence complementation, yeast two-hybrid, pull-down, and phosphorylation assays showed that TaMKK5 physically interacted with TaMPK3, and phosphorylated and activated TaMPK3, and that TaMPK3 interacted with and phosphorylated TaERF3. The TaMKK5-TaMPK3 cascade modulates the expression of TaGST1, Defensin, and Chitinase 2 through TaERF3. Collectively, TaMKK5 mediates resistance to sharp eyespot through the TaMKK5-TaMPK3-TaERF3 module and by upregulating the expression of defense-related genes in wheat. This study provides insights into the role of the wheat MAPK cascades in innate immunity. TaMKK5-6B is a promising gene for breeding wheat cultivars that are resistant to sharp eyespot.

Transgene pyramiding in wheat: Combination of deoxynivalenol detoxification with inhibition of cell wall degrading enzymes to contrast Fusarium Head Blight and Crown Rot

Fusarium Head Blight (FHB) and Crown Rot (FCR) are major diseases of wheat crops, causing extensive damages and mycotoxin contamination. In this work, we investigated the possibility to improve resistance to either or both diseases by combining different resistance mechanisms. To this aim, we stacked in the same wheat genotype transgenes controlling the DON-to-D3G conversion by specific UDP-glucosyltransferases (UGT) and the inhibition of cell wall degrading enzymes (CWDEs) by glycosidase inhibitors. We obtained: i) a durum wheat UGT+PMEI double-transgenic line constitutively expressing the HvUGT13248 and AcPMEI genes, coding for a barley UGT and a kiwi pectin methylesterase inhibitor, respectively; ii) a bread wheat UGT+PGIP line, expressing in floral tissues the HvUGT13248 gene and constitutively the PvPGIP2 gene, coding for a bean polygalacturonase inhibiting protein. We observed that both UGT+PMEI and UGT+PGIP plants exhibited increased resistance against Fusarium graminearum in FHB, further reducing by 10-20 % FHB symptoms as compared to the lines carrying the individual transgenes, and of up to 50 % as compared to wild-type plants. On the other hand, double-transgenic UGT+PMEI seedlings exhibited similar FCR symptoms as the UGT single transgenic line after infection with F. culmorum, indicating no contribution of the PMEI transgene to FCR resistance. This result is also supported by the inability of AcPMEI or PvPGIP2, constitutively expressed in durum wheat transgenic lines, to counteract F. graminearum in FCR. We also verified that F. graminearum produces PG and PME activity on infected wheat crown. We conclude that CWDEs inhibition combined with UGT-based DON detoxification contribute in an additive manner to limiting F. graminearum in FHB. Conversely, UGT-based DON detoxification is the only mechanism contributing to resistance observed against FCR. Indeed, the reinforcement of pectin does not enhance resistance against FCR.

Molecular signatures between citrus and Candidatus Liberibacter asiaticus

Citrus Huanglongbing (HLB), also known as citrus greening, is one of the most devastating citrus diseases worldwide. Candidatus Liberibacter asiaticus (CLas) is the most prevalent strain associated with HLB, which is yet to be cultured in vitro. None of the commercial citrus cultivars are resistant to HLB. The pathosystem of Ca. Liberibacter is complex and remains a mystery. In this review, we focus on the recent progress in genomic research on the pathogen, the interaction of host and CLas, and the influence of CLas infection on the transcripts, proteins, and metabolism of the host. We have also focused on the identification of candidate genes for CLas pathogenicity or the improvements of HLB tolerance in citrus. In the end, we propose potentially promising areas for mechanistic studies of CLas pathogenicity, defense regulators, and genetic improvement for HLB tolerance/resistance in the future.

Identification of a bio-signature for barley resistance against Pyrenophora teres infection based on physiological, molecular and sensor-based phenotyping

Necrotic and chlorotic symptoms induced during Pyrenophora teres infection in barley leaves indicate a compatible interaction that allows the hemi-biotrophic fungus Pyrenophora teres to colonise the host. However, it is unexplored how this fungus affects the physiological responses of resistant and susceptible cultivars during infection. To assess the degree of resistance in four different cultivars, we quantified visible symptoms and fungal DNA and performed expression analyses of genes involved in plant defence and ROS scavenging. To obtain insight into the interaction between fungus and host, we determined the activity of 19 key enzymes of carbohydrate and antioxidant metabolism. The pathogen impact was also phenotyped non-invasively by sensor-based multireflectance and -fluorescence imaging. Symptoms, regulation of stress-related genes and pathogen DNA content distinguished the cultivar Guld as being resistant. Severity of net blotch symptoms was also strongly correlated with the dynamics of enzyme activities already within the first day of infection. In contrast to the resistant cultivar, the three susceptible cultivars showed a higher reflectance over seven spectral bands and higher fluorescence intensities at specific excitation wavelengths. The combination of semi high-throughput physiological and molecular analyses with non-invasive phenotyping enabled the identification of bio-signatures that discriminates the resistant from susceptible cultivars.

QTL dissection and mining of candidate genes for Ascochyta fabae and Orobanche crenata resistance in faba bean (Vicia faba L.)

BACKGROUND

Ascochyta blight caused by Ascochyta fabae Speg. and broomrape (Orobanche crenata) are among the economically most significant pathogens of faba bean. Several QTLs conferring resistance against the two pathogens have been identified and validated in different genetic backgrounds. The aim of this study was to saturate the most stable QTLs for ascochyta and broomrape resistance in two Recombinant Inbred Line (RIL) populations, 29H x Vf136 and Vf6 x Vf136, to identify candidate genes conferring resistance against these two pathogens.

RESULTS

We exploited the synteny between faba bean and the model species Medicago truncatula by selecting a set of 219 genes encoding putative WRKY transcription factors and defense related proteins falling within the target QTL intervals, for genotyping and marker saturation in the two RIL populations. Seventy and 50 of the candidate genes could be mapped in 29H x Vf136 and Vf6 x Vf136, respectively. Besides the strong reduction of the QTL intervals, the mapping process allowed replacing previous dominant and pedigree-specific RAPD flanking markers with robust and transferrable SNP markers, revealing promising candidates for resistance against the two pathogens.

CONCLUSIONS

Although further efforts in association mapping and expression studies will be required to corroborate the candidate genes for resistance, the fine-mapping approach proposed here increases the genetic resolution of relevant QTL regions and paves the way for an efficient deployment of useful alleles for faba bean ascochyta and broomrape resistance through marker-assisted breeding.