Genetics and gibberellin production in Gibberella fujikuroi

Does nest occupancy by birds influence the microbial composition?

Nest microbiota plays a vital role in the breeding and development of birds, which not only provides protection to bird hosts but also negatively affects the host. At present, it is unclear whether the composition of the microbes in the nests is affected by nesting. For this reason, we hung artificial nest boxes to simulate the natural nesting environment and combined 16S rRNA and ITS high-throughput sequencing technology to further study the differences in microbial composition and richness between used nests and control nests of Japanese tits (Parus minor). The study found that the bacteria in used nests and control nests showed significant differences at the phylum level (p < 0.05). It is also worth noting that the predominant bacteria in used nests were Proteobacteria (51.37%), Actinobacteria (29.72%), Bacteroidetes (6.59%), and Firmicutes (3.82%), while the predominant bacteria in control nests were Proteobacteria (93.70%), Bacteroidetes (2.33%), and Acidobacteria (2.06%). Both used nests and control nests showed similar fungi at the phylum level, which consisted mainly of Ascomycota and Basidiomycota, although significant differences were found in their relative abundance between both groups. The results of alpha diversity analysis showed significant differences in bacteria between the two groups and not in fungi. However, the beta diversity analysis showed significant differences between both bacteria and fungi. In summary, our results showed that the used nests had a higher abundance of beneficial microbiota and a lower presence of pathogenic microbiota. Therefore, we speculate that birds will change the characteristics of the nest microbial composition in the process of nest breeding to ensure their smooth reproductive development.

Application of direct PCR for phylogenetic analysis of Fusarium fujikuroi species complex isolated from rice seeds

Plant pathogenic fungi cause severe yield losses and mycotoxin contamination in crops. The precise and rapid detection of fungal pathogens is essential for effective disease management. Sequencing universal DNA barcodes has become the standard method for the diagnosis of fungal diseases, as well as for identification and phylogenetic analysis. A major bottleneck in obtaining DNA sequence data from many samples was the laborious and time-consuming process of sample preparation for genomic DNA. Here, we describe a direct PCR approach that bypasses the DNA extraction steps to streamline the molecular identification of fungal species. Using a direct PCR approach, we successfully sequenced the nuclear ribosomal internal transcribed spacer (ITS) region for the representatives of major fungal lineages. To demonstrate the usefulness of this approach, we performed a phylogenetic analysis of the Fusarium fujikuroi species complex, which causes bakanae ("foolish seedling") disease of rice and mycotoxin contamination. A total of 28 candidate strains were isolated from rice seeds in the Republic of Korea, and the identity of the isolates was determined using the DNA sequence of both ITS and translation elongation factor 1-α regions. In addition, 17 F. fujikuroi isolates were examined for fumonisin (FB) production in rice medium using an enzyme-linked immunosorbent assay. Phylogenetic and toxigenic analyses showed that the F. fujikuroi strains could be distinguished into two groups: FB producers (B14-type) and non-producers (B20-type). These results will accelerate the molecular identification of fungal pathogens and facilitate the effective management of fungal diseases.

Molecular Diagnosis of Thiophanate-Methyl-Resistant Strains of Fusarium fujikuroi in Japan

Fusarium fujikuroi is the pathogen of rice bakanae disease and is subclassified into gibberellin and fumonisin groups (G and F groups). Thiophanate-methyl (TM), a benzimidazole fungicide, has been used extensively to control F. fujikuroi. Previous investigation showed that F-group strains are TM sensitive (TMS), whereas most G-group strains are TM resistant (TMR) in Japan. The minimum inhibitory concentration in TMS strains was 1 to 10 μg ml^-1, whereas that in TMR strains was >100 μg ml^-1. E198K and F200Y mutations in β₂-tubulin were detected in TMR strains. A loop-mediated isothermal amplification-fluorescent loop primer method was developed for diagnosis of these mutations and applied to 37 TMR strains and 56 TMS strains. The results indicated that 100% of TMR strains were identified as having either the E198K mutation (41%) or the F200Y mutation (59%), whereas none of the TMS strains tested showed either mutation. We found one remarkable TMR strain in the F group that had an F200Y mutation. These results suggest that E198K and F200Y mutations in β₂-tubulin contribute to TM resistance in F. fujikuroi.

Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds

Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents.

Fusarium fujikuroi Species Complex Associated With Rice, Maize, and Soybean From Jiangsu Province, China: Phylogenetic, Pathogenic, and Toxigenic Analysis

Species belonging to the Fusarium fujikuroi species complex (FFSC) are of vital importance and are a major concern for food quantity and quality worldwide, as they not only cause serious diseases in crops but also produce various mycotoxins. To characterize the population structure and evaluate the risk of poisonous secondary metabolites, a total of 237 candidate strains were isolated from rice, maize, and soybean samples in Jiangsu Province, China. Species identification of the individual strain was accomplished by sequencing the translation elongation factor 1α gene (TEF-1α) and the fumonisin (FB) synthetic gene (FUM1). The distribution of Fusarium species among the different crops was observed. The maize seeds were dominated by F. proliferatum (teleomorph, Gibberella intermedia) and F. verticillioides (teleomorph, G. moniliformis), whereas F. fujikuroi (teleomorph, G. fujikuroi) was the most frequently isolated species from rice and soybean samples. In addition, phylogenetic analyses of these strains were performed, and the results suggested clear groups showing no obvious relationship with the origin source. FFSC species pathogenicity and toxigenicity were studied. All of the species reduced the rice seed germination rate, with no significant differences. F. fujikuroi showed two distinct patterns of influencing the length of rice seedlings, which were correlated with FBs and gibberellic acid synthesis. FBs were mainly produced by F. verticillioides and F. proliferatum. F. proliferatum and F. fujikuroi also produced moniliformin and beauvericin. The toxigenicity of F. andiyazi (teleomorph, G. andiyazi) was extremely low. Further analysis indicated that the sequence variations in TEF-1α and the differences in the expression levels of the toxin synthesis genes were associated with the diversity of secondary metabolites in F. fujikuroi strains. These findings provide insight into the population-level characterization of the FFSC and might be helpful in the development of strategies for the management of diseases and mycotoxins.

Species composition of and fumonisin production by the Fusarium fujikuroi species complex isolated from Korean cereals

To assess the risk of fumonisin contamination in Korean cereals, we isolated colonies of the Fusarium fujikuroi species complex (FFSC) from barley, maize, rice and soybean samples from 2011 to 2015. A total of 878 FFSC strains were isolated mostly from maize and rice, and species identity of the isolates were determined using the DNA sequence of the translation elongation factor 1-α (TEF-1α) and RNA polymerase II (RPB2) genes. Fusaria recovered from Korean cereals included F. fujikuroi (317 isolates and a frequency of 36%), F. proliferatum (212 isolates and 24.1%), F. verticillioides (170 isolates and 19.4%), F. concentricum (86 strains and 9.8%), F. andiyazi (56 isolates and 6.4%), F. subglutinans (28 isolates and 3.2%), F. thapsinum (5 isolates and 0.6%), and F. circinatum (2 isolates and 0.2%). The rice samples were dominated by F. fujikuroi (47.4%), F. proliferatum (27.3%), and F. concentricum (15.1%), whereas maize samples were dominated by F. verticillioides (33.9%), F. fujikuroi (25.3%), and F. proliferatum (21.1%). A phylogenetic analysis of 70 representative isolates demonstrated that each species was resolved as genealogically exclusive in the ML tree. Fumonisin production potential was evaluated using a PCR assay for the fumonisin biosynthesis gene, FUM1 in all of the isolates. Most of the isolates tested (94%) were positive for FUM1. All of the isolates assigned to F. fujikuroi, F. proliferatum, F. verticillioides and F. thapsinum were positive for FUM1 irrespective of their host origin. Seventy-seven representative isolates positive for FUM1 were examined for fumonisin production in rice medium. The majority of F. proliferatum (26/27, 96.3%), F. verticillioides (16/17, 94.1%) and F. fujikuroi (19/25, 76.0%) produced both FB₁ and FB₂. Notably, 16 of 19 fumonisin-producing F. fujikuroi produced >1000μg/g of fumonisins (FB₁+FB₂) in rice medium, which is higher than that in previous reports. These results suggest that F. fujikuroi can produce high levels of fumonisins similar to F. verticillioides and F. proliferatum.

Bioconversion of Gibberellin Fermentation Residue into Feed Supplement and Organic Fertilizer Employing Housefly (Musca domestica L.) Assisted by Corynebacterium variabile

The accumulation of a considerable quantity of gibberellin fermentation residue (GFR) during gibberellic acid A3 (GA3) production not only results in the waste of many resources, but also poses a potential hazard to the environment, indicating that the safe treatment of GFR has become an urgent issue for GA3 industry. The key to recycle GFR is converting it into an available resource and removing the GA3 residue. To this end, we established a co-bioconversion process in this study using house fly larvae (HFL) and microbes (Corynebacterium variabile) to convert GFR into insect biomass and organic fertilizer. About 85.5% GA3 in the GFR was removed under the following optimized solid-state fermentation conditions: 60% GFR, 40% rice straw powder, pH 8.5 and 6 days at 26°C. A total of 371g housefly larvae meal and 2,064g digested residue were bio-converted from 3,500g raw GFR mixture contaning1, 400g rice straw in the unit of (calculated) dry matter. HFL meal derived from GFR contained 56.4% protein, 21.6% fat, and several essential amino acids, suggesting that it is a potential alternative animal feed protein source. Additionally, the digested GFR could be utilized as an organic fertilizer with a content of 3.2% total nitrogen, 2.0% inorganic phosphorus, 1.3% potassium and 91.5% organic matter. This novel GFR bio-conversion method can mitigate potential environmental pollution and recycle the waste resources.

Investigation of the gibberellic acid optimization with a statistical tool from Penicillium variable in batch reactor

The culture conditions for gibberellic acid (GA3) production by the fungus Penicillium variable (P. variable) was optimized using a statistical tool, response surface methodology (RSM). Interactions of culture conditions and optimization of the system were studied using Box-Behnken design (BBD) with three levels of three variables in a batch flask reactor. Experimentation showed that the model developed based on RSM and BBD had predicted GA3 production with R(2) = 0.987. The predicted GA3 production was optimum (31.57 mg GA3/kg substrate) when the culture conditions were at 7 days of incubation period, 21% v/w of inoculum size, and 2% v/w of olive oil concentration as a natural precursor. The results indicated that RSM and BBD methods were effective for optimizing the culture conditions of GA3 production by P. variable mycelia.

Further data on the production of beauvericin, enniatins and fusaproliferin and toxicity to Artemia salina by Fusarium species of Gibberella fujikuroi species complex

The knowledge of toxigenic profiles of fungal plant pathogens is of extreme importance for evaluating the potential toxicity of infected plant products. Ninety-six fungal isolates belonging to 28 species in the Gibberella fujikuroi complex were studied for the production of beauvericin, enniatins and fusaproliferin in rice cultures. Toxin production ranged from 5 to 3000 microg/g for beauvericin, 2 to 131 microg/g for enniatins, and 4 to 440 microg/g for fusaproliferin. Beauvericin was the most common metabolite produced by 16 species followed by fusaproliferin with 11 species and enniatins with 4 species. The production of beauvericin by F. bulbicola, F. denticulatum, F. lactis, F. phyllophilum, F. pseudocircinatum, and F. succisae and fusaproliferin by F. antophilum, F. begoniae, F. bulbicola, F. circinatum, F. concentricum, F. succisae, and F. udum is reported here for the first time. Brine shrimp larvae were most sensitive to culture extracts of F. acutatum (up to 94+/-3%), F. concentricum (up to 99+/-1%), F. denticuatum (up to 100%) and F. sacchari (up to 100%). Toxicity towards brine shrimp was significantly correlated with the beauvericin content of the fungal extracts with few exceptions. These data indicate that beauvericin and fusaproliferin are common metabolites of species of the G. fujikuroi complex and pose a risk for a possible toxin accumulation in their respective host plant products. However, data from the brine shrimp bioassay showed that further toxic metabolites within this complex need to be characterized.

Species diversity of and toxin production by Gibberella fujikuroi species complex strains isolated from native prairie grasses in Kansas

Fusarium species from agricultural crops have been well studied with respect to toxin production and genetic diversity, while similar studies of communities from nonagricultural plants are much more limited. We examined 72 Fusarium isolates from a native North American tallgrass prairie and found that Gibberella intermedia (Fusarium proliferatum), Gibberella moniliformis (Fusarium verticillioides), and Gibberella konza (Fusarium konzum) dominated. Gibberella thapsina (Fusarium thapsinum) and Gibberella subglutinans (Fusarium subglutinans) also were recovered, as were seven isolates that could not be assigned to any previously described species on the basis of either morphological or molecular characters. In general, isolates from the prairie grasses produced the same toxins in quantities similar to those produced by isolates of the same species recovered from agricultural hosts. The G. konza isolates produce little or no fumonisins (up to 120 micro g/g by one strain), and variable but generally low to moderate amounts of beauvericin (4 to 320 micro g/g) and fusaproliferin (50 to 540 micro g/g). Toxicity to Artemia salina larvae within most species was correlated with the concentration of either beauvericin or fusaproliferin produced. Organic isolates from some cultures of G. moniliformis were highly toxic towards A. salina even though they produced little, if any, beauvericin or fusaproliferin. Thus, additional potentially toxigenic compounds may be synthesized by G. moniliformis strains isolated from prairie grasses. The Fusarium community from these grasses appears to contain some species not found in surrounding agricultural communities, including some that probably are undescribed, and could be capable of serving as a reservoir for strains of potential agricultural importance.

Production of beauvericin, moniliformin, fusaproliferin, and fumonisins b(1), b(2), and b(3) by fifteen ex-type strains of fusarium species

Fifteen Fusarium species were analyzed by high-performance liquid chromatography for the production of six mycotoxins in corn grits cultures. Production of mycotoxins ranged from 66 to 2,500 micro g/kg for fumonisin B(1), 0.6 to 1,500 micro g/g for moniliformin, 2.2 to 720 micro g/g for beauvericin, and 12 to 130 micro g/g for fusaproliferin. Fumonisin B(2) (360 micro g/kg) was produced by two species, fumonisin B(3) was not detected in any of the 15 species examined, and Fusarium bulbicola produced none of the six mycotoxins that we analyzed.

Microbial transformation of ent-kaurenoic acid and its 15-hydroxy derivatives by the SG138 mutant of Gibberella fujikuroi

Feeding experiments with ent-kaurenoic acid (4), 15 alpha-hydroxy-ent-kaurenoic acid (5), 15 beta-hydroxy-ent-kaurenoic acid (6), and mixtures of 4 plus 5 and 4 plus 6 were conducted using the SG138 mutant of Gibberella fujikuroi, to gain information about the phenotype of this unique strain. The biotransformation of 5 gave 7 beta,15 alpha-dihydroxykaurenolide (9) and 7 beta,15 alpha-dihydroxy-ent-kaurenoic acid (13). The incubation of 6 produced 7 beta,15 beta-dihydroxy-ent-kaurenoic acid (7) and 7 beta,15 beta-dihydroxykaurenolide (10). No 15-hydroxylated gibberellins were detected in any of these experiments. The results indicated that a hydroxy group at C-15 does not inhibit 7 beta-hydroxylase activity but in the SG138 strain obstructs the enzymatic ring-B contraction of ent-kaurenoids to gibberellins. Exogenous 4 stimulated both the excretion of ent-kaurene and the fungal metabolism of 5 and 6.

Separate compartments for the production of sterols, carotenoids and gibberellins in Gibberella fujikuroi

Substrate flows in the sterol, carotenoid and gibberellin pathways of Gibberella fujikuroi were examined by isotope-dilution experiments. The wild type and two carotenoid mutants of this fungus were grown in minimal medium with abundant glucose, limiting ammonium nitrate and a radioactively labelled precursor (either acetate, mevalonate or leucine). The precursors did not affect growth or terpenoid production, with two exceptions; leucine allowed additional growth, as expected from the nitrogen limitation in the medium, and mevalonate inhibited the accumulation of gibberellins, but only if added before the onset of gibberellin production. The relative contributions of glucose, mevalonate, leucine and acetate as terpenoid precursors, calculated from the specific radioactivities of ergosterol, neurosporaxanthin and phytoene, were different for different products and different precursors. We conclude that the biosyntheses of sterols, gibberellins and carotenoids in Gibberella are physically separated in different subcellular compartments with independent substrate pools. The same results were obtained with the three strains, except for carotenoid production, indicating that this pathway is regulated independently from other terpenoid pathways.

A genetic map of Gibberella fujikuroi mating population A (Fusarium moniliforme)

We constructed a recombination-based map of the fungal plant pathogen Gibberella fujikuroi mating population A (asexual stage Fusarium moniliforme). The map is based on the segregation of 142 restriction fragment length polymorphism (RFLP) markers, two auxotrophic genes (arg1, nic1), mating type (matA+/matA-), female sterility (ste1), spore-killer (Sk), and a gene governing the production of the mycotoxin fumonisin B1 (fum1) among 121 random ascospore progeny from a single cross. We identified 12 linkage groups corresponding to the 12 chromosome-sized DNAs previously observed in contour-clamped homogeneous electric field (CHEF) gels. Linkage groups and chromosomes were correlated via Southern blots between appropriate RFLP markers and the CHEF gels. Eleven of the 12 chromosomes are meiotically stable, but the 12th (and smallest) is subject to deletions in 3% (4/121) of the progeny. Positive chiasma interference occurred on five of the 12 chromosomes, and nine of the 12 chromosomes averaged more than one crossover per chromosome. The average kb/cM ratio in this cross is approximately 32.

Gibberellin biosynthesis in gib mutants of Gibberella fujikuroi

The Ascomycete Gibberella fujikuroi synthesizes gibberellins, fujenal, carotenoids, and other terpenoids. Twelve gib mutants, isolated through the modified gibberellin fluorescence of their culture media, were subjected to chemical and biochemical analyses. Two mutants were specifically defective in the hydroxylation of carbon 13; their total gibberellin production was normal, but their main gibberellin was GA7 instead of GA3. Four mutants were blocked in the early reactions between geranylgeranyl pyrophosphate and 7-hydroxy-kaurenoic acid; two of them could not synthesize kaurene and another one was blocked in several oxidative steps. Six mutants had partial defects in early reactions, leading to the production of one-fifth to one-third of the wild type amounts of gibberellins and fujenal. Two of these produced considerable amounts of kaurenolides due to a defect in the conversion of kaurenoic acid to 7-hydroxykaurenoic acid. Another one produced no carotenoids, but attempts to isolate mutants of reactions shared by the carotenoid and gibberellin pathways failed. The gib mutations did not modify the ability of the fungus to live as a saprophyte.