Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness

BACKGROUND

Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.

RESULTS

The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.

CONCLUSION

Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.

Akanthomyces diversity in Brazil and their pathogenicity to plant-sucking insects

Currently, species within the genus Akanthomyces are poorly studied and explored compared to other hypocrealean entomopathogenic fungi employed as commercial biocontrol agents. This study aimed to molecularly identify 23 Brazilian Akanthomyces strains, most originally isolated from aphids and scales (n = 22), and one from the coffee leaf rust, and further investigate their pathogenicity to six plant-sucking insects as a means to better understand their host spectra. We also explored the capacity of A. muscarius CG935 for blastospore production via liquid fermentation. Akanthomyces dipterigenus, A. muscarius, A. lecanii, and two unidentified species were recognized as naturally occurring in Brazil. Akanthomyces dipterigenus CG829 and A. muscarius CG935 were highly virulent to nymphs of Bemisia tabaci (67.5-85.4% confirmed mortality) and the aphid Aphis fabae (74.6-75.3%), but only the first strain was virulent to the mealybug Planococcus sp. (80.9%). Akanthomyces lecanii CG824 was weakly virulent to all tested insects. None of the strains were pathogenic to the thrips Caliothrips phaseoli, and all strains showed low virulence to the wooly whitefly Aleurothrixus floccosus and the scale Duplachionaspis divergens. Submerged liquid fermentation yields varied from 1.72 × 109 (day 2) to 3.90 × 109 (day 5) blastospores mL-1. Blastospores or aerial conidia from A. muscarius CG935, at a single concentration of 1 × 107 viable propagules mL-1, resulted in 67.5-83.1% mortality of B. tabaci nymphs within 8 days post-treatment. Overall, these results encourage additional studies that could lead to the development of new mycopesticides based on Akanthomyces strains.

Bacillus subtilis and Bacillus licheniformis promote tomato growth

Bacillus spp. are widely marketed and used in agricultural systems as antagonists to various phytopathogens, but it can also benefit the plant as plant growth promoters. Therefore, the longer presence of the bacterium in the rhizosphere would result in a prolonged growth-promoting benefit, but little is yet known about its persistence in the rhizosphere after seed coating. The objectives of this study were to evaluate the tomato growth promotion mediated by Bacillus licheniformis FMCH001 and Bacillus subtilis FMCH002 and the survival rate of these bacteria both in shoots and in the rhizosphere. The Bacillus strains used throughout this study were obtained from Quartzo® produced by Chr. Hansen. The application of a mixture of B. subtilis and B. licheniformis (Quartzo®) at concentrations 1 × 108, 1 × 109, and 1 × 1010 CFU mL-1, as well as the application of B. subtilis and B. licheniformis individually at concentration 1 × 108 CFU mL-1, increased fresh and dry masses of shoot and root system, volume of root system, and length of roots of tomato plants when compared to control. Both Bacillus strains produced IAA after 48 h of in vitro. Bacillus colonies obtained from plant sap were morphologically similar to colonies of B. subtilis and B. licheniformis strains and were detected in inoculated on plants and not detected in control ones. A similar pattern was obtained through DNA-based detection (qPCR). Therefore, B. subtilis and B. licheniformis were able to produce auxin, promote tomato growth, and colonize and persist in the rhizosphere.

Population Genomics Provide Insights into the Global Genetic Structure of Colletotrichum graminicola, the Causal Agent of Maize Anthracnose

Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure. IMPORTANCE Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (Colletotrichum graminicola) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of C. graminicola being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.

Dual functionality of Trichoderma: Biocontrol of Sclerotinia sclerotiorum and biostimulant of cotton plants

Microbial crop protection products based on Trichoderma have the ability to display multifunctional roles in plant protection, such as pathogen parasitism, enhance nutrient availability and stimulate plant growth, and these traits can be used to enhance the overall agronomic performance of a variety of crops. In the current study, we explored the multifunctional potential of two indigenous Brazilian strains of Trichoderma (T. asperelloides CMAA 1584 and T. lentiforme CMAA 1585) for their capability of controlling Sclerotinia sclerotiorum, a key plant pathogen of cotton, and for their ability of growth promotion in cotton plants (Gossypium hirsutum). Both strains were able to solubilize mineral phosphorus (CaHPO₄), to release volatile organic compounds that impaired the mycelial growth of S. sclerotiorum, and to promote the growth of cotton plants under greenhouse conditions. In dual culture, Trichoderma strains reduced the growth rate and the number of sclerotia formed by S. sclerotiorum. By treating sclerotia with conidial suspensions of these Trichoderma strains, a strong inhibition of the myceliogenic germination was observed, as a result of the marked mycoparasitic activity exerted on the sclerotia. The parasitism over S. sclerotiorum was more effective with T. asperelloides CMAA 1584, whilst the biostimulant effects on cotton growth were more pronounced with T. lentiforme CMAA 1585, which also showed a higher capacity of phosphate solubilization. Thus, T. asperelloides CMAA 1584 displays higher efficiency in controlling S. sclerotiorum, while T. lentiforme CMAA 1585 is more suitable as a biostimulant due to its ability to promote growth in cotton plants. Overall, these Trichoderma strains may be used in mixture to provide both pathogen control and promotion of plant growth, and this strategy will support growers in minimizing the use of synthetic fertilizers and fungicides against white mold in cotton crops.

Clonostachys rosea: Production by Submerged Culture and Bioactivity Against Sclerotinia sclerotiorum and Bemisia tabaci

Among the prospective biocontrol agents, the saprophytic filamentous fungus Clonostachys rosea is an excellent necrotrophic mycoparasite of numerous plant pathogenic fungi. However, its commercial development has been hampered by mass production difficulties during solid-state fermentation. Conversely, the submerged liquid fermentation shortens the cultivation time while increasing yields of fungal propagules. However, this method has been overlooked for C. rosea. In this work, we investigated the impact of liquid pre-culture inoculum on the spore production by the two-stage fermentation process using rice grains in comparison to the traditional solid-state fermentation. In parallel, we studied the submerged cultivation of C. rosea by manipulating carbon-to-nitrogen (C:N) ratio and nitrogen source, with the further optimization of spore production in a benchtop bioreactor. Additional bioassays included assessing the bioactivity of water-dispersible microgranules (that contained a submerged conidia) against the whitefly (Bemisia tabaci biotype B) and Sclerotinia sclerotiorum (causal agent of the white mold). Our results showed a maximum concentration of 1.1 × 109 conidia/g-dry-matter after 7 days of cultivation by two-stage fermentation process. The liquid fermentation yielded 1.4 × 109 submerged conidia/ml after 7 days using a medium with a 50:1 C:N ratio, and it also induced the production of microsclerotia (MS) up to 1.35 × 104/ml within 6 days with 10:1 C:N ratio; both media were supplemented with dextrose monohydrate and soybean meal. The fermentation batches carried out in a benchtop bioreactor with medium 50:1 C:N ratio and amended with soybean meal rendered a production peak on the fourth day, corresponding to 1.11 × 109 conidia/ml and 4.35 × 108 colony forming units (CFU)/ml. Following air-drying, the conidia production from air-dried microgranules of C. rosea biomass was estimated at 3.4 × 1010 conidia/g of formulated product upon re-hydration for 7 days. Both submerged conidia and MS of C. rosea inhibited 100% germination of S. sclerotiorum sclerotia by direct parasitism. The air-dried submerged conidia exhibited a suppressive activity on sclerotia (88% mycoparasitism) and early whitefly nymphs (76.2% mortality) that rendered LC50 values of 3.2 × 104 CFU/g soil and 1.5 × 107 CFU/ml, respectively. Therefore, the submerged liquid culture of C. rosea may offer a feasible and cost-effective method for its large-scale production, alleviating critical constraints to their commercial use while providing an additional tool for management of B. tabaci and S. sclerotiorum.

Bio-based composite granules with simultaneous biocontrol and phosphorus fertilization roles: outcomes from a lab-scale in-vitro assessment

The use of phosphate rocks as low-solubility phosphorus fertilizers has been promoted to reduce the environmental impacts of agriculture, but adequate nutrient uptake by plants depends on solubilization of the rock, driven by soil microorganisms. Here, investigation was made of the microbial solubilization of low-solubility phosphate rocks, together with simultaneous bioprotective action involving the biocontrol of microorganisms. The aim was to enhance function and value by delivering two effects using a single bio-based product, in accordance with the concept of a "bioreactor-in-a-granule" system. A composite structure was developed, based on a starch matrix, comprising a combination of Trichoderma asperelloides, as a biocontrol agent, and Aspergillus niger, as an acidulant. A significant increase of up to 150% in P solubilization was achieved, indicating the positive effect of the microorganism-composite interaction. In vitro assays showed that the ability of T. asperelloides to inhibit Fusarium oxysporum mycelial growth was maintained in the presence of A. niger. Moreover, the estimated cost of the composite granule (0.35 US$/kg of product on a dry basis) revealed competitive. The results indicated that the association of T. asperelloides and A. niger is an effective way to increase nutrient availability and to inhibit plant pathogens, opening up possibilities for the design of multifunctional bio-based fertilizer composites. This article is protected by copyright. All rights reserved.

Multifaceted intervention of Bacillus spp. against salinity stress and Fusarium wilt in tomato

AIM

This study aimed to screen halotolerant Bacillus strains able to promote growth and protect tomato plants against salt stress and Fusarium wilt (Fusarium oxysporum f. sp. lycopersici).

METHODS AND RESULTS

We evaluated some halotolerant strains of Bacillus spp. (Bacillus velezensis (AP-3) and Bacillus spp. (AP-6, AP-85 and AP-100)) to promote growth of tomato plants grown under salinity stress conditions and to protect them against Fusarium wilt disease. Such strains had been previously selected among 154 bacterial strains through biochemical tests (siderophores and indoleacetic acid productions, cellulase and catalase activity, nitrogen fixation and phosphate solubilization) in the presence of 100-mmol l^-1 NaCl. Besides the above-mentioned strains, B. subtilis QST-713 (Serenade^TM ) was also evaluated. Compared to control plants, aboveground dry weight increased in plants inoculated with AP-6, AP-85, AP-3, AP-100 and QST-713 strains developed in the absence of salt stress. The same tendency occurred for root dry weight; however, AP-3 strain was more effective, promoting an increase of 163%, when compared to control. Chlorophyll index and height increased >40 and 53%, respectively, for all Bacillus strains. Saline stress reduced plant growth regardless of the presence of Bacillus. Height, stem diameter, and aboveground and root dry weights increased in plants treated with Bacillus strains grown under saline conditions when compared to control. Bacillus velezensis AP-3 reduced the severity of Fusarium wilt in tomato by 50% when compared to control.

CONCLUSION

Halotolerant Bacillus strains controlled tomato Fusarium wilt, increased growth as well as tolerance to salt stress.

SIGNIFICANCE AND IMPACT OF THE STUDY

We demonstrated the efficacy of halotolerant Bacillus strains to control Fusarium wilt and improve tomato growth. We also demonstrated that these Bacillus strains protect tomato plants against salt stress. Bacillus can be used in an eco-friendly way because they are considered Generally Recognized As Safe.

Optimizing mass production of Trichoderma asperelloides by submerged liquid fermentation and its antagonism against Sclerotinia sclerotiorum

Commercial products based on Trichoderma are obtained mainly from solid-state fermentation. Submerged liquid fermentation is the most appropriate method compared to the solid medium for large-scale production of Trichoderma spp. The present study aimed to optimize the combination of key variables that influence the liquid fermentation process of Trichoderma asperelloides LQC-96 for conidial production coupled with its efficiency in the control of Sclerotinia sclerotiorum. In addition, we verified whether the optimized culture conditions can be used for the conidial production of Trichoderma erinaceum T-12 and T-18 and Trichoderma harzianum T-15. Fermentation studies were performed in shake flasks following a planned experimental design to reduce the number of tests and consumable costs. The effect of temperature, pH, photoperiod, carbon:nitrogen ratio and water activity on conidial production were assessed, which of pH was the only meaningful factor contributing to increased conidial production of T. asperelloides LQC-96. From the five variables studied initially, pH and C:N ratio were further used in the second design (rotational central composite design-RCCD). Hence, the best conditions for the production of T. asperelloides LQC-96 conidia by liquid fermentation consisted of initial pH of 3.5, C:N ratio of 200:1 at 30 °C, without glycerol, and under 24 h photoperiod. The highest conidial concentration was observed after seven days of fermentation. Under these optimal conditions, T. erinaceum T-12 and T-18, and T. harzianum T-15 were also cultivated, but only LQC-96 efficiently parasitized S. sclerotiorum, precluding sclerotium myceliogenic germination. Our findings propose optimal fermentation conditions that maximize conidial production of T. asperelloides as a potential biofungicide against S. sclerotiorum.

The Combination of Trichoderma harzianum and Chemical Fertilization Leads to the Deregulation of Phytohormone Networking, Preventing the Adaptive Responses of Tomato Plants to Salt Stress

Plants have evolved effective mechanisms to avoid or reduce the potential damage caused by abiotic stresses. In addition to biocontrol abilities, Trichoderma genus fungi promote growth and alleviate the adverse effects caused by saline stress in plants. Morphological, physiological, and molecular changes were analyzed in salt-stressed tomato plants grown under greenhouse conditions in order to investigate the effects of chemical and biological fertilizations. The application of Trichoderma harzianum T34 to tomato seeds had very positive effects on plant growth, independently of chemical fertilization. The application of salt stress significantly changed the parameters related to growth and gas-exchange rates in tomato plants subject to chemical fertilization. However, the gas-exchange parameters were not affected in unfertilized plants under the same moderate saline stress. The combined application of T34 and salt significantly reduced the fresh and dry weights of NPK-fertilized plants, while the opposite effects were detected when no chemical fertilization was applied. Decaying symptoms were observed in salt-stressed and chemically fertilized plants previously treated with T34. This damaged phenotype was linked to significantly higher intercellular CO2 and slight increases in stomatal conductance and transpiration, and to the deregulation of phytohormone networking in terms of significantly lower expression levels of the salt overlay sensitivity 1 (SOS1) gene, and the genes involved in signaling abscisic acid-, ethylene-, and salicylic acid-dependent pathways and ROS production, in comparison with those observed in salt-challenged NPK-fertilized plants.

Nitrogen Metabolism and Growth Enhancement in Tomato Plants Challenged with Trichoderma harzianum Expressing the Aspergillus nidulans Acetamidase amdS Gene

Trichoderma is a fungal genus that includes species that are currently being used as biological control agents and/or as biofertilizers. In addition to the direct application of Trichoderma spp. as biocontrol agents in plant protection, recent studies have focused on the beneficial responses exerted on plants, stimulating the growth, activating the defenses, and/or improving nutrient uptake. The amdS gene, encoding an acetamidase of Aspergillus, has been used as a selectable marker for the transformation of filamentous fungi, including Trichoderma spp., but the physiological effects of the introduction of this gene into the genome of these microorganisms still remains unexplored. No evidence of amdS orthologous genes has been detected within the Trichoderma spp. genomes and the amdS heterologous expression in Trichoderma harzianum T34 did not affect the growth of this fungus in media lacking acetamide. However, it did confer the ability for the fungus to use this amide as a nitrogen source. Although a similar antagonistic behavior was observed for T34 and amdS transformants in dual cultures against Rhizoctonia solani, Botrytis cinerea, and Fusarium oxysporum, a significantly higher antifungal activity was detected in amdS transformants against F. oxysporum, compared to that of T34, in membrane assays on media lacking acetamide. In Trichoderma-tomato interaction assays, amdS transformants were able to promote plant growth to a greater extent than the wild-type T34, although compared with this strain the transformants showed similar capability to colonize tomato roots. Gene expression patterns from aerial parts of 3-week-old tomato plants treated with T34 and the amdS transformants have also been investigated using GeneChip Tomato Genome Arrays. The downregulation of defense genes and the upregulation of carbon and nitrogen metabolism genes observed in the microarrays were accompanied by (i) enhanced growth, (ii) increased carbon and nitrogen levels, and (iii) a higher sensitivity to B. cinerea infections in plants treated with amdS transformants as detected in greenhouse assays. These observations suggest that the increased plant development promoted by the amdS transformants was at expense of defenses.

Combined Effects of Soil Biotic and Abiotic Factors, Influenced by Sewage Sludge Incorporation, on the Incidence of Corn Stalk Rot

The objectives of this study were to evaluate the combined effects of soil biotic and abiotic factors on the incidence of Fusarium corn stalk rot, during four annual incorporations of two types of sewage sludge into soil in a 5-years field assay under tropical conditions and to predict the effects of these variables on the disease. For each type of sewage sludge, the following treatments were included: control with mineral fertilization recommended for corn; control without fertilization; sewage sludge based on the nitrogen concentration that provided the same amount of nitrogen as in the mineral fertilizer treatment; and sewage sludge that provided two, four and eight times the nitrogen concentration recommended for corn. Increasing dosages of both types of sewage sludge incorporated into soil resulted in increased corn stalk rot incidence, being negatively correlated with corn yield. A global analysis highlighted the effect of the year of the experiment, followed by the sewage sludge dosages. The type of sewage sludge did not affect the disease incidence. A multiple logistic model using a stepwise procedure was fitted based on the selection of a model that included the three explanatory parameters for disease incidence: electrical conductivity, magnesium and Fusarium population. In the selected model, the probability of higher disease incidence increased with an increase of these three explanatory parameters. When the explanatory parameters were compared, electrical conductivity presented a dominant effect and was the main variable to predict the probability distribution curves of Fusarium corn stalk rot, after sewage sludge application into the soil.

The importance of chorismate mutase in the biocontrol potential of Trichoderma parareesei

Species of Trichoderma exert direct biocontrol activity against soil-borne plant pathogens due to their ability to compete for nutrients and to inhibit or kill their targets through the production of antibiotics and/or hydrolytic enzymes. In addition to these abilities, Trichoderma spp. have beneficial effects for plants, including the stimulation of defenses and the promotion of growth. Here we study the role in biocontrol of the T. parareesei Tparo7 gene, encoding a chorismate mutase (CM), a shikimate pathway branch point leading to the production of aromatic amino acids, which are not only essential components of protein synthesis but also the precursors of a wide range of secondary metabolites. We isolated T. parareesei transformants with the Tparo7 gene silenced. Compared with the wild-type, decreased levels of Tparo7 expression in the silenced transformants were accompanied by reduced CM activity, lower growth rates on different culture media, and reduced mycoparasitic behavior against the phytopathogenic fungi Rhizoctonia solani, Fusarium oxysporum and Botrytis cinerea in dual cultures. By contrast, higher amounts of the aromatic metabolites tyrosol, 2-phenylethanol and salicylic acid were detected in supernatants from the silenced transformants, which were able to inhibit the growth of F. oxysporum and B. cinerea. In in vitro plant assays, Tparo7-silenced transformants also showed a reduced capacity to colonize tomato roots. The effect of Tparo7-silencing on tomato plant responses was examined in greenhouse assays. The growth of plants colonized by the silenced transformants was reduced and the plants exhibited an increased susceptibility to B. cinerea in comparison with the responses observed for control plants. In addition, the plants turned yellowish and were defective in jasmonic acid- and ethylene-regulated signaling pathways which was seen by expression analysis of lipoxygenase 1 (LOX1), ethylene-insensitive protein 2 (EIN2) and pathogenesis-related protein 1 (PR-1) genes.

Potential of non-pathogenic Fusarium oxysporum isolates for control of Fusarium wilt of tomato

This study was done to evaluate the efficiency of non-pathogenic Fusarium oxysporum isolates (141/3, 233, 233/1, 245, 245/1, 251, 251/2, 251/5, and 257) in controlling vascular wilt caused by F. oxysporum f. sp. lycopersici, race 2 (isolates C-21A, TO11, and TO245) in tomato (Lycopersicon esculentum) cv. Viradoro seedlings. In order to determine the effect of non-pathogenic F. oxysporum isolates in tomato plants, the root system of 30-day-old seedlings was immersed in conidial suspensions (10(6) ml-1) of each isolate and the seedlings were transplanted to a cultivation substrate. Thirty-five days after transplanting it was observed that the non-pathogenic F. oxysporum isolates were not pathogenic to the cv. Viradoro nor did they affect seedling development. The efficiency of the non-pathogenic F. oxysporum isolates in controlling Fusarium wilt was determined by immersing the tomato seedling roots in the conidial suspension (10(6) ml-1) of each isolate and then transplanting them into substrates previously infested with isolates of F. oxysporum f.sp. lycopersici, race 2 (10(5) conidia ml-1 of substrate). Evaluations were performed 35 days after transplanting, for severity in scale with 1=healthy plant to 6=dead plant or plant showing vessel browning and wilted leaves up to the leader shoot and seedling height. The non-pathogenic F. oxysporum isolates were efficient in reducing the severity of the disease and maintaining normal plant development. These results provide evidence of the antagonistic activity of non-pathogenic F. oxysporum isolates in controlling vascular wilt caused by F. oxysporum f. sp. lycopersici race 2 in tomato.