Soil-borne Plant Pathogenic Fungi Research Articles

Inoculation of Bacillus velezensis Bv-116 and its bio-organic fertilizer serve as an environmental friendly biocontrol strategy against cucumber Fusarium wilt.

The aim of this study was to evaluate the effects of Bacillus velezensis Bv-116 and its bio-organic fertilizer on the control of cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. Cucumerinum (FOC), the promotion of growth of cucumber seedlings, and the soil microbial community. B. velezensis Bv-116 exhibited an inhibition rate of 84.93% against FOC, as well as broad-spectrum inhibitory activities against other soil-borne plant pathogenic fungi. Fermentation products of B. velezensis Bv-116 destroyed the cell structure of FOC and inhibited the growth of FOC mycelium. These products were identified as volatile antimicrobial gases, proteases and cellulases. In the greenhouse pot experiment, both B. velezensis Bv-116 and its bio-organic fertilizer exhibited significant promoting effects on cucumber growth, and a significant reduction in the incidence and disease severity index of cucumber wilt (p < 0.05). Analysis of the microbial community structure of cucumber rhizosphere soil revealed that inoculation of B. velezensis Bv-116 and its bio-organic fertilizer increased the abundance of genera with biocontrol capabilities against plant pathogens. In addition, inoculation of the bio-organic fertilizer reversed the excessive proliferation of Fusarium and Acidobacteria. Our results suggest the potential of inoculating B. velezensis Bv-116 and its bio-organic fertilizer as an environmentally friendly biocontrol strategy against cucumber wilt.

Unraveling the ecological niche signals of Verticillium dahliae: Insights from Mediterranean landscapes.

Verticillium wilt (VW), caused by the soil-borne plant pathogenic fungus Verticillium dahliae, is a major disease impacting olive crops globally. In view of the lack of effective post-infection treatments, exclusion and avoidance strategies are essential in disease management. Assessing the risks posed by this pathogen is essential to prevent the spread and to ensure selection of suitable sites for new plantations. This study aimed to elucidate the environmental factors driving V. dahliae establishment in the Andalusia region, in southern Spain, an emblematic Mediterranean landscape for olive cultivation. To this end, we explored ecological niche signals for this fungal pathogen by analyzing 62 environmental variables across 1.6 million hectares dedicated to olive and cotton cultivation, using a 15-yr survey data on VW incidence on presence-absence from both olive and cotton fields. To ensure robust identification of ecological niche signals, we employed randomization-based, non-parametric univariate tests to compare presence records with the broader sampling universe (including absence records). Our findings identified key environmental variables that are associated significantly with V. dahliae presence, including temperature range seasonality (including mean diurnal and annual ranges), summer temperature (maximum of the warmest month, mean of the warmest quarter), and moisture and water availability (near-surface humidity, potential evapotranspiration, vapor pressure) as core niche variables for V. dahliae. Our results replicated the pathogen's known distribution, identifying the Guadalquivir Valley as a particularly high-risk area in view of its mild winters and distinct rainy seasons, providing new insights into the specific environmental conditions that facilitate the pathogen's survival and spread. Furthermore, this study introduces a novel approach to niche modeling that prioritizes variables with consistent effects and significant impact on the presence and distribution of V. dahliae and identifies potential data artifacts. This approach enhances our understanding of ecological requirements in V. dahliae and informs targeted management strategies.

GC-MS analysis and antifungal potential of flower extract of Acacia nilotica subsp. Indica against Macrophomina phaseolina

Macrophomina phaseolina is a wide host ranged soil-borne fungal plant pathogen. It infects more than 500 host plant species belonging to 100 families. Many important oil-seed and leguminous crops are known to be attacked by this devastating plant pathogen. In the present study, antifungal potential of flowers of a leguminous tree Acacia nilotica subsp. indica, was assessed against this pathogen through bioassays guided fractionation. Initially, methanolic extracts of 1 %–5 % of leaf, flower, root-bark and stem-bark of the plant species under consideration were evaluated for their antifungal potential against the target pathogen. Among these, the best antifungal activity was shown by flower extract. The reduction in growth of the test fungal strain was 27–49 %, 4–40 % and 2–27 % due to flower, root-bark and leaf extracts, respectivey, over control. Flower extract was partitioned using n-hexane, chloroform, ethyl acetate and n-butanol as the solvents. Bioassays guided study of these fractions of methanolic extract of flower revealed that high antifungal potential was shown by n-hexane and chloroform fractions against M. phaseolina causing 26–53 % and 28–50 % decline in fungal biomass, respectively, as compared to that of control. GC-MS analysis of chloroform fraction revealed the presence of 27 compounds in this fraction. Among these cyclopentanol,-1-methyl (10.93 %) was the predominant compound followed by methyl, 4,4-dimethyl butanoate (7.04 %), 1-pentanol (6.80 %), 2-propanol, 1-cyclopropyl (6.11 %), 1H,imidazole-4-5-dihydro-2-methyl (5.93 %), trichloroethane (5.91 %), carbonic acid-ethyl hexyl ester (4.59 %), 1,4-butandiol,2,3-bis(methylene)- (4.54 %) and [S]-3,4-dimethyl pentanol (4.48 %).

Characterization and evaluation of actinomycete from the Protaetia brevitarsis Larva Frass.

Protaetia brevitarsis larvae (PBL) are soil insects important for the soil organic carbon cycle, and PBL frass not only contains a large amount of humic acid but also affects the diversity, novelty, and potential functions of actinomycetes. Here, we characterized and assessed the actinomycete. The operational taxonomic unit (OTU) data showed that 90% of the actinomycetes cannot be annotated to species, and pure culture and genome analysis showed that 35% of the strains had the potential to be new species, indicating the novelty of PBL frass actinomycetes. Additionally, genome annotation showed that many gene clusters related to antifungal, antibacterial and insecticidal compound synthesis were identified, and confrontation culture confirmed the antifungal activities of the actinomycetes against soil-borne plant pathogenic fungi. The incubation experiment results showed that all isolates were able to thrive on media composed of straw powder and alkaline lignin. These results indicated that PBL hindgut-enriched actinomycetes could survive in soil by using the residual lignocellulose organic matter from plant residues, and the antibiotics produced not only give them a competitive advantage among soil microflora but also have a certain inhibitory effect on plant diseases and pests. This study suggests that the application of PBL frass can not only supplement soil humic acid but also potentially affect the soil microbiota of cultivated land, which is beneficial for the healthy growth of crops.

A Bacillus velezensis strain shows antimicrobial activity against soilborne and foliar fungi and oomycetes.

Biological control uses naturally occurring antagonists such as bacteria or fungi for environmentally friendly control of plant pathogens. Bacillus spp. have been used for biocontrol of numerous plant and insect pests and are well-known to synthesize a variety of bioactive secondary metabolites. We hypothesized that bacteria isolated from agricultural soil would be effective antagonists of soilborne fungal pathogens. Here, we show that the Delaware soil isolate Bacillus velezensis strain S4 has in vitro activity against soilborne and foliar plant pathogenic fungi, including two with a large host range, and one oomycete. Further, this strain shows putative protease and cellulase activity, consistent with our prior finding that the genome of this organism is highly enriched in antifungal and antimicrobial biosynthetic gene clusters. We demonstrate that this bacterium causes changes to the fungal and oomycete hyphae at the inhibition zone, with some of the hyphae forming bubble-like structures and irregular branching. We tested strain S4 against Magnaporthe oryzae spores, which typically form germ tubes and penetration structures called appressoria, on the surface of the leaf. Our results suggest that after 12 hours of incubation with the bacterium, fungal spores form germ tubes, but instead of producing appressoria, they appear to form rounded, bubble-like structures. Future work will investigate whether a single antifungal molecule induces all these effects, or if they are the result of a combination of bacterially produced antimicrobials.

Soil microbial communities along elevational gradients in the Madrean Sky Islands.

The Madrean Sky Islands are mountain ranges isolated by a 'desert sea'. This area is a biodiversity hotspot currently threatened by climate change. Here, we studied soil microbial communities along elevational gradients in eight Madrean Sky Islands in southeastern Arizona (USA). Our results showed that while elevational microbial richness gradients were weak and not consistent across different mountains, soil properties strongly influenced microbial community composition (overall composition and the abundance of key functional groups) along elevational gradients. In particular, warming is associated with a higher abundance of soil-borne fungal plant pathogens that concomitantly might facilitate upward elevational shifts of plant species released from negative plant-soil feedbacks. Furthermore, projected warming and drought in the area aggravated by anthropogenic nitrogen deposition on mountain tops (and thus, decreasing nitrogen limitation) can enhance a shift from ectomycorrhizal to arbuscular mycorrhizal fungi. Overall, these results indicate that climate change effects on plant-soil interactions might have profound ecosystem consequences.

The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization.

Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.

Temperature sensitivity of soil-borne fungal phytopathogens depends on niche breadth and land use types

Soil-borne fungal plant pathogens pose great threats to agricultural productivity and native ecosystems. However, the roles of niche breadth and land-use types in regulating the response of soil-borne fungal plant pathogens to temperature changes largely remain unclear. Here, we surveyed soil pathogens from different valleys where croplands, grasslands, and woodlands scattered in mosaic patterns. We found that pathogen richness increased with increasing temperature in grasslands but not in croplands and woodlands. After classifying the pathogens based on temperature niche, we found that the richness of specialists was sensitive to temperature changes and increased with increasing temperature in grasslands and croplands. By contrast, the richness of neutrals (those taxa not defined as generalists or specialists) did not change with temperature gradients regardless of land-use types. Additionally, pathogens were more abundant and diverse in croplands than those in grasslands and woodlands, and this pattern persisted across the temperature gradient. Our results provide evidence that temperature change and land use types could additively affect the diversity of plant pathogens in soils. This work advances our understanding of how niche breadth affects the response of pathogens to temperature, highlighting the importance of climate change and land use in regulating the abundance and diversity of pathogens.

Screening of microRNAs and target genes involved in Sclerotinia sclerotiorum (Lib.) infection in Brassica napus L.

BackgroundRapeseed (Brassica napus L.) is the third largest source of vegetable oil in the world, and Sclerotinia sclerotiorum (Lib.) is a major soil-borne fungal plant pathogen that infects more than 400 plant species, including B. napus. Sclerotinia stem rot caused an annual loss of 10 − 20% in rapeseed yield. Exploring the molecular mechanisms in response to S. sclerotiorum infection in B. napus is beneficial for breeding and cultivation of resistant varieties. To gain a better understanding of the mechanisms regarding B. napus tolerance to Sclerotinia stem rot, we employed a miRNAome sequencing approach and comprehensively investigated global miRNA expression profile among five relatively resistant lines and five susceptible lines of oilseed at 0, 24, and 48 h post-inoculation.ResultsIn this study, a total of 40 known and 1105 novel miRNAs were differentially expressed after S. sclerotiorum infection, including miR156, miR6028, miR394, miR390, miR395, miR166, miR171, miR167, miR164, and miR172. Furthermore, 8,523 genes were predicted as targets for these differentially expressed miRNAs. These target genes were mainly associated with disease resistance (R) genes, signal transduction, transcription factors, and hormones. Constitutively expressing miR156b (OX156b) plants strengthened Arabidopsis resistance against S. sclerotiorum accompanied by smaller necrotic lesions, whereas blocking miR156 expression in Arabidopsis (MIM156) led to greater susceptibility to S. sclerotiorum disease, associated with extensive cell death of necrotic lesions.ConclusionsThis study reveals the distinct difference in miRNA profiling between the relatively resistant lines and susceptible lines of B. napus in response to S. sclerotiorum. The identified differentially expressed miRNAs related to sclerotinia stem rot resistance are involved in regulating resistance to S. sclerotiorum in rapeseed by targeting genes related to R genes, signal transduction, transcription factors, and hormones. miR156 positively modulates the resistance to S. sclerotiorum infection by restricting colonization of S. sclerotiorum mycelia. This study provides a broad view of miRNA expression changes after S. sclerotiorum infection in oilseed and is the first to elucidate the function and mechanism underlying the miR156 response to S. sclerotiorum infection in oilseed rape.

Biomolecules from Chaetomium globosum Possessing Antimicrobial Compounds Potentially Inhibits Fusarium Wilt of Tomato.

Wilt disease caused by Fusarium solani, a soil-borne plant pathogenic fungus, is a serious disease in tomato causing economic losses. In the present study, among the nine isolates of Chaetomium globosum Kunze (Chg1-Chg9), screened against F. solani No. Fs-1, Chg2 exhibited the maximum inhibition (49.2 %), followed by the isolates Chg6 (47.4%) and Chg1 (46.3%) in dual culture. Further, the crude secondary metabolites from these three isolates showed maximum reduction of the mycelial growth of Fs-1 compared to control. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of the metabolites from Chg2 revealed the presence of major compounds, viz., benzothiazole, 2-(2-hydroxyethylthio) (7.51%); 9,12,15- octadecatrienoic acid, 2,3-bis[(trimethylsilyl)oxy] propyl ester (3.13%); and hexadecanoic acid, 1- (hydroxymethyl)-1,2-ethanediyl ester (2.69%). Fourier transform infrared (FTIR) spectroscopy revealed the presence of alcohol, secondary amine, aliphatic primary amine, carboxylic acid, allene, conjugated ketone, imine/oxime, sulphate, and halo compound groups with a weak to strong range of intensity. Pure compound of benzothiazole @ 5000 ppm exhibited higher antagonistic activity of Fs-1which decreased at lower concentration. In pot culture experiment, dipping tomato seedlings cv. PKM1 in 2% ethyl acetate-fractionated biomolecules of Chg2 recorded a minimum disease incidence of 20.0%, whereas seedlings dipped in the culture filtrate of Chg2 showed a disease incidence of 26.6% compared to control (86.6%). Besides, these seedlings treated with the culture filtrate showed the highest plant height of 37.68 cm and the maximum number of leaves and flowers (39.6 and 5.48, respectively), followed by those treated with the biomolecules of Chg2 (C. globosum) and the culture filtrate of T. asperellum. The results revealed that the antifungal efficacy of C. globosum Chg2 is due to the presence of antimicrobial metabolites including benzothiazole. Exploring the use of this novel antifungal compound in the management of plant diseases is highly warranted.

Distinct distribution patterns and functional potentials of rare and abundant microorganisms between plastisphere and soils

The increasing application of plastic film has caused the “white pollution” of farmlands in greenhouses. To date, most studies on the ecology of the plastisphere have focused on the whole microbial community, with few on the rare and abundant taxa, especially in the terrestrial ecosystems. To understand the plastisphere rare and abundant taxa of bacterial and fungal communities, we collected residues of plastic film from plastic-covered soils in the greenhouse. The plastisphere was significantly different from surrounding soils in terms of alpha- and beta-diversities of abundant and rare taxa. Such discrepancies were greater in rare taxa than in abundant taxa. Besides, the enrichment of soil-borne plant pathogenic fungi in the plastisphere implied that plastic film residues can act as vectors for pathogen transmission. In the plastisphere, the stochastic process governed the assemblies of rare taxa, while deterministic assemblies dominated that of abundant taxa. However, in surrounding soils, the stochastic process played a larger role in abundant taxa as compared to rare taxa. The plastisphere showed a network of less complexity, more competitive connections, and more modules compared to surrounding soils, and rare taxa played greater roles than abundant taxa. There existed obvious discrepancies in the microbial functions between surrounding soils and plastisphere, including carbon, sulfur, nitrogen, and phosphorus cycling, and rare taxa contribute large proportions to the above cycling processes. Altogether, the findings advance our understanding of ecological mechanisms of abundant and rare taxa in the plastisphere in terrestrial ecosystems.

Detection of Mycovirus in Sclerotium Rolfsii, A Phytopathogenic Fungus in Bangladesh

A research project was conducted to detect presence of mycovirus, a probable virocontrol agent in Sclerotium rolfsii, a destructive soil-borne plant pathogenic fungus. A total of 500 isolates of the pathogen was isolated from infected wheat, bush bean, tomato, eggplant, lentil, chickpea, eggplant, chilli and okra grown Bangladesh following tissue planting methods and brought to the Virology laboratory of Okayama University, Japan. After brought to Japan, a total of 472 isolates were re-isolated and the fungal isolates were cultured on potato dextrose agar for extraction of DNA and dsRNA. The extracted nucleic acids were tested for the presence of viruses using rolling circle amplification (RCA) (for DNA viruses) and cellulose column chromatography (for RNA viruses). The detected S. rolfsii viruses were further characterized molecularly. For detection of DNA virus, a total of 120 isolates were tested, none were found positive for DNA viruses. For detection of dsRNA virus, a total of 472 isolates were tested, 7 isolates showed possible dsRNA positive band. The partial cDNA sequences of the dsRNA segments isolated from the strain SR336 were obtained. BlastX database search with the partial sequence from SR336 isolates showed similarities with randorna like virus. To screen the presence of randorna like virus in S. rolfsii isolates, 64 isolates were selected from 472 isolates of S. rolfsii. The isolates of S. rolfsii were tested by RT-PCR using randorna virus specific primers. Out of 64 isolates 13, (20.31%) isolates were randorna virus positive strain and rest of the isolates were absent of randorna virus.&#x0D; Bangladesh J. Agril. Res. 46(3): 331-341, September 2021

The secreted FoAPY1 peptidase promotes Fusarium oxysporum invasion.

The secretion of peptidases from several pathogens has been reported, but the biological function of these proteins in plant-pathogen interactions is poorly understood. Fusarium oxysporum, a soil-borne plant pathogenic fungus that causes Fusarium wilt in its host, can secrete proteins into host plant cells during the infection process to interfere with the host plant defense response and promote disease occurrence. In this study, we identified a peptidase, FoAPY1, that could be secreted from F. oxysporum depending on the N-terminal signal peptide of the protein. FoAPY1 belongs to the peptidase M28 family and exerts peptidase activity in vitro. Furthermore, the FoAYP1 gene knockout strain (∆FoAYP1) presented reduced virulence to tomato plants, but its mycelial growth and conidiation were unchanged. Moreover, FoAYP1 overexpression tomato seedlings exhibited enhanced susceptibility to F. oxysporum and Botrytis cinerea strains. These data demonstrated that FoAYP1 contributes to the virulence of F. oxysporum may through peptidase activity against host plant proteins.

Soil-borne plant pathogenic fungi biodiversity of sunflower

Diseases caused by soil-borne phytopathogenic fungi are a serious problem for agricultural crops, including sunflower crops. The limited possibilities of measures to control them further increases the interest and focus on them. This article reveals data on the species composition, occurrence rate of soil-borne plant pathogenic fungi isolated from the soil of sunflower. Here, 11 species of true fungi and 1 species of oomycetes have been isolated. The highest incidence rate was recorded in the Fusarium oxysporum fungi species. During the study, pathogenic fungi specific to sunflower have also been isolated.

In-silico analysis of the regulatory region of effector protein genes in Verticillium dahliae

Verticillium dahliae is a soil-borne fungal plant pathogen that infects more than 400 plant species throughout the world, causing huge economic losses annually. Due to its wide host range and adaptation strategy of producing resting structures, Verticillium infection and spread are difficult to control. The resting dormant melanized structures called microsclerotia, produced during the dormant stage of the pathogen can persist in soil for years and are the primary source of infection as they germinate after being stimulated by root exudates. The fungus secrets effector proteins that facilitate the primary infection and subsequent spread. In the current study, we used in silico tools to analyze effector proteins belonging to hydrophobin, necrosis, and ethylene inducing like-protein and polysaccharide lyase 3 protein family which are required for virulence and pathogenicity of the pathogen. Our study showed that the genes for these protein families consist of many paralogs. Some of these paralogous proteins display similar functions but differential expression during pathogenicity establishment. This study will provide information about cis-acting factors regulating differential regulation of paralogs during infection.

Biological Characteristics of Verticillium dahliae MAT1-1 and MAT1-2 Strains.

Verticillium dahliae is a soil-borne plant pathogenic fungus that causes Verticillium wilt on hundreds of dicotyledonous plant species. V. dahliae is considered an asexually (clonal) reproducing fungus, although both mating type idiomorphs (MAT1-1 and MAT1-2) are present, and is heterothallic. Most of the available information on V. dahliae strains, including their biology, pathology, and genomics comes from studies on isolates with the MAT1-2 idiomorph, and thus little information is available on the MAT1-1 V. dahliae strains in the literature. We therefore evaluated the growth responses of MAT1-1 and MAT1-2 V. dahliae strains to various stimuli. Growth rates and melanin production in response to increased temperature, alkaline pH, light, and H2O2 stress were higher in the MAT1-2 strains than in the MAT1-1 strains. In addition, the MAT1-2 strains showed an enhanced ability to degrade complex polysaccharides, especially starch, pectin, and cellulose. Furthermore, several MAT1-2 strains from both potato and sunflower showed increased virulence on their original hosts, relative to their MAT1-1 counterparts. Thus, compared to MAT1-1 strains, MAT1-2 strains derive their potentially greater fitness from an increased capacity to adapt to their environment and exhibit higher virulence. These competitive advantages might explain the current abundance of MAT1-2 strains relative to MAT1-1 strains in the agricultural and sylvicultural ecosystems, and this study provides the baseline information on the two mating idiomorphs to study sexual reproduction in V. dahliae under natural and laboratory conditions.

Bacterial community analysis on Sclerotium-suppressive soil.

Difficulties in controlling the soil-borne plant pathogenic fungus Sclerotium rolfsii favoured the analysis of its suppressive soil for better understanding. In the present study, culture-independent molecular technique was used to analyse the bacterial communities of suppressive soil and conducive soil. Hence, metagenomic DNAs from both kinds of soils were directly extracted and their sequence polymorphism was analysed by targeting hypervariable domains, V4 + V5, of the 16S rRNA gene. The results of 16S rRNA gene-driven bacterial community diversity analysis along with soil physicochemical and biological properties clearly discriminated S. rolfsii suppressive soil from conducive soil. The dominant phylogenetic group of suppressive soil is Actinobacteria followed by Proteobacteria. The other groups include Acidobacteria, Firmicutes and Cyanobacteria. In contrast, conducive soil had very few Actinobacterial sequences and was dominated by Gamma- and Betaproteobacteria. Based on the relative proportion of different bacterial communities, their diversity and species richness were observed more in suppressive soil than in conducive soil. The present study identifies the dominant bacterial community which shares S. rolfsii suppressiveness.

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics.

ABSTRACTDisease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10× metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype.IMPORTANCE Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops. Our approach to develop novel sustainable strategies to control this fungal root pathogen is to explore and exploit an effective, yet poorly understood naturally occurring protection, i.e., disease-suppressive soils. After screening 28 agricultural soils, we recently identified four soils that were suppressive to root disease of wheat caused by Fusarium culmorum. We also confirmed, via sterilization and transplantation, that the microbiomes of these soils play a significant role in the suppressive phenotype. By adopting nonribosomal peptide synthetase (NRPS) functional amplicon screening of suppressive and conducive soils, we here show how computationally driven comparative analysis of combined functional amplicon and metagenomic data can unravel putative mechanisms underlying microbiome-associated plant phenotypes.

Successful biocontrol of major postharvest and soil-borne plant pathogenic fungi by antagonistic yeasts

Fungal pathogens are the main biotic burden of productivity for economically important crops under field, greenhouse or postharvest conditions. The discovery and development of new environmental-friendly solutions, such as application of living organisms and their derivatives to control plant diseases and pests, are of enormous interest. This study presents the results of a mass screening designed to detect yeast strains with antagonistic activity against postharvest pathogens (Alternaria alternata, Penicillium expansum and Botrytis cinerea) and soil-borne diseases (Verticillium dahliae and Fusarium oxysporum). In fact, this is the first study that focuses on screening the antagonistic potential of a wide variety of yeast genera (13) and species (30) against vascular wilts. The results from in vivo trials demonstrated that fungal infected tomato plants, grown under hydroponic or soil conditions, showed a significant reduction in disease severity after yeast treatment. Wickerhamomyces anomalus Wa-32 was able to antagonise both pathogens and reduce the disease severity up to 40% (V. dahliae) and 50% (F. oxysporum) in soil conditions. In addition, this strain became endophytic in tomato plants. The features of Wa-32 are of enormous interest since no effective antagonistic biocontrol product is available for the simultaneous control of these two fungal pathogens. Postharvest assays with wounded tomato fruits showed that several strains displayed very high biocontrol levels against P. expansum and B. cinerea (up to 86 and 97% reduction in disease severity, respectively) but none of them showed protection against A. alternata. The best protection against B. cinerea was again achieved with W. anomalus Wa-32 and two Metschnikowia pulcherrima strains (Mp-22 and Mp-30). However, the best antagonistic strains of P. expansum were Candida lusitaniae Cl-28, Candida oleophila Co-13, Debaryomyces hansenii Dh-67 and Hypopichia pseudoburtonii Hp-54. These biocontrol effects were also demonstrated in grapes and apples.

Antifungal effect of some plant extracts and their combination with Moncut fungicide on sugar beet root rot

Sugar beet (Beta vulgaris L. Chenopodiaceae) has become the first Egyptian crop for sugar production because it contributed with 59.5% of total sugar production. Sclerotium rolfsii is a soil-borne plant pathogenic fungi incident of southern sclerotium rot in sugar beet. The aim of the present study was to investigate the effect of some plant extracts in different solvents as inhibitory control agents against the growth plant pathogen S. rolfsii. Five plant extracts; Roselle, pomegranate, rosemary, black pepper and chamomile were evaluated as inhibitors for Sclerotium rolfsii of sugar beet root rot under laboratory and greenhouse conditions during 2016/2017 growing season at Gemmeiza Agricultural Research Station, (ARC). The results indicated that all tested plant extracts caused remarkable growth inhibition of S. rolfsii compared with control. However, black pepper extract was the most effective against S. rolfsii (recorded 93.33% inhibition). On the other hand, Pomegranate extract in methanol solvent showed also high inhibition percentage (93.30%). All plant extracts mixed with Moncut fungicides demonstrated an antagonistic effect. The pomegranate and black pepper treatments showed the lowest disease severity compared with control. Furthermore, the pomegranate and black paper treatments recorded the highest root weight, root yield/plot, total soluble solids percentage and sucrose content. Also, pomegranate and black pepper treatments reflected the highest amount of total phenols, free phenols, and conjugated phenols. Additionally, the interaction of pomegranate and black pepper treatments with S. rolfsii pathogen, showed the highest activity of oxidative enzymes peroxidase and polyphenol oxidase. This study recommends the application of pomegranate and black pepper as natural alternative fungicides against Sclerotium rolfsii plant infection.