Shigenobu Yoshida's research while affiliated with National Agriculture and Food Research Organization and other places
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Publications (62)
In this study, we developed an effective and stable technique for suppressing seedling rot of rice caused by Burkholderia glumae using bacterial communities cultured from nursery soils for organic farming (OF) of rice that have disease-suppressive activity. When culturable bacterial communities (CBCs) isolated from OF soils by growth on nutrient-ag...
Increased plant phosphorus uptake and growth as a result of inoculation with arbuscular mycorrhizal (AM) fungi is observed less often under field conditions than in pot experiments. Interaction between introduced and indigenous AM fungi is one of the reasons for ineffectiveness of inoculation in the field. We aimed to distinguish the effect of intr...
Fusarium head blight (FHB) of cereals is a severe disease caused by the Fusarium graminearum species complex. It leads to the accumulation of the mycotoxin deoxynivalenol (DON) in grains and other plant tissues and causes substantial economic losses throughout the world. DON is one of the most troublesome mycotoxins because it is a virulence factor...
The potential of the active ingredient of a commercial bioinsecticide, XenTari® (Bacillus thuringiensis [BT] serovar aizawai strain ABTS‐1857), to suppress gray mold in tomato plants was elucidated. First, a suspension of the active ingredient of XenTari® and a liquid culture of the bacterial strain as BT inocula were sprayed onto detached leaves o...
Natural farming has attracted attention due to its low environmental loading. However, research on the soil microbial community during natural farming is limited. In the present study, soil bacterial community diversity in naturally farmed and conventionally farmed apple orchards was evaluated using 16S rRNA gene sequencing as a case study. We comp...
Actinomycete Nocardioides sp. strain LS1, isolated from wheat leaf, is a bacterium that degrades and assimilates the mycotoxin deoxynivalenol (DON) as the carbon source. This is the first study of the genome sequence of the DON-degrading genus Nocardioides , and it facilitates the study of genes encoding the DON-degrading pathway.
Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as a...
The phylloplane yeast Pseudozyma antarctica secretes an esterase, named PaE, and xylanase when cultivated with xylose. We previously observed that the lipophilic layer of Micro-Tom tomato leaves became thinner after the culture filtrate treatment. The leaves developed reduced water-holding ability and became wilted. In this study, the purified enzy...
Inoculation with arbuscular mycorrhizal fungi (AMF) can increase the growth of host plants, especially under condition of low phosphate (P) availability. Although this effect is shown relatively easily in simplified systems such as pot experiments, it is often hard to show in the field because of complicating factors such as competition with indige...
Arbuscular mycorrhizal (AM) fungi associate with most land plants and deliver phosphorus to the host. Identification of biotic/abiotic factors that determine crop responses to AM fungal inoculation is an essential step for successful application of the fungi in sustainable agriculture. We conducted three field trials on soybean with a commercial in...
To survive in harsh environments, phyllosphere microorganisms have developed numerous adaptive strategies against stressors. One such strategy is the synthesis of compounds that absorb ultraviolet A radiation (UVA). The chemical structure of a UVA-absorbing compound from Methylobacterium sp. strain W-213 was elucidated by spectroscopic analyses. ¹H...
The outbreak of rice plant diseases can be effectively suppressed in organic farming systems. However, the mechanisms of disease suppression by organic farming systems are not well understood. When Burkholderia-infected rice seeds were sown and cultivated on nine organic-farmed soils which were supplied by nine independent organic rice farmers or s...
Agricultural mulch films made from biodegradable polymers (BP) have been used to decrease the burden of plastic waste recovery and recycling. However, their degradations depend largely on environmental conditions and sometimes do not proceed as desired. Yeast strains of Pseudozyma antarctica often isolated from rice husks were found to secrete an e...
Microbes inhabiting the phyllosphere encounter harmful ultraviolet rays, and must develop adaptive strategies against this irradiation. In this study, we screened bacterial isolates originating from the phyllosphere of various plants which harbored absorbers of ultraviolet A (UVA), a wavelength range which is recognized as harmful to human skin. Of...
The fungal strain B47-9, isolated from barley, was previously selected as an effective degrader of various biodegradable plastic (BP) films such as poly(butylene succinate-co-adipate) (PBSA) and poly(butylene succinate) (PBS). The strain has not been identified based on mycological methods because it does not form fruiting bodies, which are the key...
Yeast host-vector systems are useful tools for the production of recombinant proteins. Here, we report the construction of a new high-level expression plasmid pPAX1-neo for the basidiomycetous yeast, Pseudozyma antarctica. pPAX1-neo harbours a xylose-inducible expression cassette under control of the xylanase promoter and terminator of P. antarctic...
The yeast strain, Cryptococcus flavus GB-1, isolated from rice husks as a candidate producer of a biodegradable plastic (BP)-degrading enzyme. The genomic DNA sequence encoding the BP-degrading enzyme of GB-1 was determined. The enzyme was named CfCLE because the deduced amino acid sequence (239 amino acids) was found to be 93% identical to that of...
To investigate the effects of mannosylerythritol lipids (MELs) on the hydrophobicity of solid surfaces, their suppressive activity against the early infection behaviors of several phytopathogenic fungal conidia, and their suppressive activity against disease occurrences on fungal host plant leaves.
The changes in the hydrophobicity of plastic film...
The spreading property of mannosylerythritol lipids (MELs) was investigated in connection with our search for new application in agriculture. The wetting ability of MEL solutions for hydrophobic surfaces was evaluated based on contact angle measurements for several surfactant solutions on abiotic and biotic surfaces. The contact angle of MEL-A solu...
Aerial plant surface (phylloplane) is a primary key habitat for many microorganisms but is generally recognized as limited in nutrient resources. Pseudozyma antarctica, a nonpathogenic yeast, is commonly isolated from plant surfaces and characterized as an esterase producer with fatty acid assimilation ability. In order to elucidate the biological...
Although there has been much research on soil microbial communities in organic farming, little research has been reported on those in natural farming (no fertilizer use). Soil chemical properties and microbial and nematode communities in naturally (Orchard-N) and conventionally (Orchard-C) farmed apple orchards were compared over 3 years as a case...
![Fig. 5. Each-lane variations of band positions [ln(L-SDM)s]. ln(L-SDM)s...](profile/Bao-Zhihua-2/publication/273134658/figure/fig4/AS:664565943656448@1535456276081/Each-lane-variations-of-band-positions-lnL-SDMs-lnL-SDMs-obtained-by-loading-DGGE_Q320.jpg)
Variation in band position between gels is a well-known problem in denaturing gradient gel electrophoresis (DGGE). However, few reports have evaluated the degree of variation in detail. In this study, we investigated the variation in band positions of DNA samples extracted from soil, normalized using reference positions within marker lanes for DGGE...
Cheese whey is a by-product of cheese production and has high concentrations of lactose (about 5%) and other nutrients. Pseudozyma antarctica produces a unique cutinase-like enzyme, named PaE, that efficiently degrades biodegradable plastics. A previous study showed that a combination of 1% oil and 0.5% lactose increased cutinase-like enzyme produc...
The suppressive potentials of Bacillus and Paenibacillus strains isolated from the tomato phyllosphere were investigated to obtain new biocontrol candidates against Fusarium crown and root rot of tomato. The suppressive activities of 20 bacterial strains belonging to these genera were examined using seedlings and potted tomato plants, and two Paeni...
The biological function of mannosylerythritol lipids (MELs) towards their producer, Pseudozyma antarctica, on plant surfaces was investigated. MEL-producing wild-type strain and its MEL production-defective mutant strain (ΔPaEMT1) were compared in terms of their phenotypic traits on the surface of plastic plates, onion peels, and fresh leaves of ri...
Paraphoma-related fungal strain B47-9 secreted a biodegradable plastic (BP)-degrading enzyme which amounted to 68 % (w/w) of the total secreted proteins in a culture medium containing emulsified poly(butylene succinate-co-adipate) (PBSA) as sole carbon source. The gene for this enzyme was found to be composed of an open reading frame consisting of...
Key message:
Activation of SA-dependent signaling pathway and suppression of JA-dependent signaling pathway seem to play key roles inB. thuringiensis-induced resistance toR. solanacearumin tomato plants. Bacillus thuringiensis, a well-known and effective bio-insecticide, has attracted considerable attention as a potential biological control agent...
There is a need to speed up the degradation of used agricultural mulch films that are made of biodegradable plastics (BPs) in the field. Treating them with BP-degrading enzymes could be a solution to this problem. A cutinase-like enzyme of yeast Pseudozyma antarctica (PaE) has wide specificity of BPs degradation, but needs to be produced efficientl...
Enzymatic degradation of polyester films by a cutinase-like enzyme from Pseudozyma antarctica JCM10317 (PaE) was analyzed by surface plasmon resonance (SPR). The adsorption of PaE and the degradation rate for polyester films were quantitatively monitored by a positive and negative SPR signal shifts, respectively. The decrease in SPR signal and the...
![FIG 3 Mitochondrial-type [2Fe-2S] Fdxs and FAD-dependent FdRs among...](profile/Ikuo-Sato/publication/234012134/figure/fig3/AS:300069128556547@1448553463470/Mitochondrial-type-2Fe-2S-Fdxs-and-FAD-dependent-FdRs-among-KSM1-and-its-relative_Q320.jpg)
Deoxynivalenol (DON) is a natural toxin of fungi that cause Fusarium head blight disease of wheat and other small-grain cereals. DON accumulates in infected grains and promotes the spread of
the infection on wheat, posing serious problems to grain production. The elucidation of DON-catabolic genes and enzymes in
DON-degrading microbes will provide...
Bacillus thuringiensis is a naturally abundant Gram-positive bacterium and a well-known, effective bio-insecticide. Recently, B. thuringiensis has attracted considerable attention as a potential biological control agent for the suppression of plant diseases. In this study, the bacterial wilt disease-suppressing activity of B. thuringiensis was exam...
To improve the biodegradation of biodegradable plastic (BP) mulch films, 1227 fungal strains were isolated from plant surface (phylloplane) and evaluated for BP-degrading ability. Among them, B47-9 a strain isolated from the leaf surface of barley showed the strongest ability to degrade poly-(butylene succinate-co-butylene adipate) (PBSA) and poly-...
Pseudozyma antarctica JCM 10317 exhibits a strong degradation activity for biodegradable plastics (BPs) such as agricultural mulch films composed of poly(butylene succinate) (PBS) and poly(butylene succinate-co-adipate) (PBSA). An enzyme named PaE was isolated and the gene encoding PaE was cloned from the strain by functional complementation in Sac...
Deoxynivalenol (DON) is a hazardous and globally prevalent mycotoxin in cereals. It commonly accumulates in the grain of wheat, barley and other small grain cereals affected by Fusarium head blight (caused by several Fusarium species). The concept of reducing DON in naturally contaminated grain of wheat or barley using a DON-degrading bacterium is...
The specificity of culturable bacteria on healthy and Fusarium head blight (FHB)-infected spikelets of wheat heads was investigated to find a candidate of biocontrol agents against FHB. The bacterial genus Pseudomonas was commonly isolated from the tissues, and phylogenetic analysis using 16S ribosomal RNA gene sequences of isolates of the genera r...
The use of biodegradable plastics can reduce the accumulation of environmentally persistent plastic wastes. The rate of degradation of biodegradable plastics depends on environmental conditions and is highly variable. Techniques for achieving more consistent degradation are needed. However, only a few microorganisms involved in the degradation proc...
The mycotoxin deoxynivalenol (DON), a secondary metabolite produced by species of the plant pathogen Fusarium, causes serious problems in cereal crop production because of its toxicity towards humans and livestock. A biological approach for the degradation of DON using a DON-degrading bacterium (DDB) appears to be promising, although information ab...
Culturable bacterial communities on rice plants were investigated from 2001 to 2003. In total, 1,394 bacterial isolates were obtained from the uppermost leaf sheaths at 1 month before heading time and from leaf sheaths and panicles at heading time. The average culturable bacterial population on the leaf sheaths was larger at heading time than at 1...
Various preservation methods at low temperature have been reported for several powdery mildew fungi, but the conidia of Podosphaera aphanis causing powdery mildew of strawberry could not be preserved either at low temperature or by freeze-drying and liquid-drying of conidial suspensions or diseased leaf discs. Here, we developed a new technique for...
The mycotoxin deoxynivalenol (DON) causes serious problems worldwide in the production of crops such as wheat and barley because of its toxicity toward humans and livestock. A bacterial culture capable of degrading DON was obtained from soil samples collected in wheat fields using an enrichment culture procedure. The isolated bacterium, designated...
The phyllosphere is one of the most common habitats for terrestrial bacteria. However, little is known about the populations of bacteria, including unculturable bacteria, that thrive on plant surfaces. Here, we developed a fluorescent nuclear staining technique to easily and rapidly observe and enumerate populations of total and living epiphytic ba...
In 2006, stem rot and blue-green crusty lesions were found on the stems of tomato plants in Chiba Prefecture, Japan. Penicillium oxalicum was isolated repeatedly from the diseased plants. The causal fungus reproduced natural symptoms after artificial inoculation
of tomato plants and was re-isolated from symptomatic plant tissue. P. oxalicum is a ne...
In 2002, rotted flower clusters and blighted shoot tips and leaves were observed on highbush blueberry (Vaccinium corymbosum L.) and rabbiteye blueberry (V. ashei Reade) plants in Chiba, Japan. The causal fungus isolated from the diseased plants was morphologically identified as Sclerotinia sclerotiorum (Libert) de Bary. The fungus reproduced natur...
Culturable leaf-associated bacteria inhabiting a plant have been considered as promising biological control agent (BCA) candidates because they can survive on the plant. We investigated the relationship between bacterial groups of culturable leaf-associated bacteria on greenhouse- and field-grown tomato leaves and their antifungal activities agains...
The production of quorum-sensing-related signal molecules (QSRMs) among culturable bacteria comprising the community on wheat heads was investigated. The taxonomic position of 186 bacterial isolates obtained from ten heads was inferred based on 16S rRNA gene sequences, and their QSRM production was determined using two bioreporter strains of N-acyl...
The pathogen of brown stripe in leaves of Cynodon dactylon (bermudagrass) and Zoysia japonica (Zoysia grass) in Japan is identical with Bipolaris heveae, a rubber tree pathogen, based on morphological and phylogenetic characteristics, following pathogenicity studies. Crossing isolates used in the study with each other, the obtained teleomorph is de...
The polygalacturonase (PG)-encoding gene (rpg1) of Rhizopus oryzae, the causal pathogen of rhizopus rot of mulberry, was cloned and sequenced. PGs were partially purified from incubation mixture of 2% pectin medium and their N-terminal amino acid sequences were determined by a gas-phase protein sequencer. RT-PCR was performed using degenerate prime...
Bacillus amyloliquefaciens strain RC-2 produced seven antifungal compounds (1-7) secreted into the culture filtrate. These compounds inhibited the development of mulberry anthracnose caused by the fungus, Colletotrichum dematium. Chemical structural analyses by NMR and FAB-MS revealed that all these compounds were iturins (cyclic peptides with the...
To develop effective control techniques against mulberry anthracnose caused by Colletotrichum dematium, ecological and biocontrol studies on the disease were carried out. It was confirmed that the causal fungus overwinters mainly in infected mulberry leaves on the ground, then first infects the leaves adjacent to the ground in the rainy season. The...
Shoot blight and leaf spots were found on highbush blueberry trees in Tsukuba, Ibaraki, in 1999. The causal fungus was identified
morphologically as Colletotrichum acutatum Simmonds ex Simmonds. This is the first report of blueberry anthracnose caused by C. acutatum in Japan.
Compounds in mulberry leaves inducing sporulation of C. dematium, mulberry anthracnose fungus, were detected. Dissolved or suspended aqueous solutions (1%) of 16 amino acids and 10 vitamins
occurring in mulberry leaves were applied individually at the margin of the fungal colony growing on PSA plate. Sporulation
was induced only where a biotin solu...
Colletotrichum acutatum, a causal fungus of mulberry anthracnose, has been observed on the leaves of a particular mulberry tree in Tsukuba. To elucidate its life cycle on the tree, the fungus was isolated throughout the year from various asymptomatic organs; leaves, bark, xylem and winter buds were periodically collected from November 1995 to Janua...
In late June 1994, a severe form of leaf spot disease suddenly appeared on mulberry seedlings of improved varieties which were transplanted into a nursery bed at the institute. Red-brown necrotic lesions formed on the leaves. In more severe cases, infected leaves fell. Colletotrichum dematium, the mulberry anthracnose fungus, was consistently isola...
Development of mulberry anthracnose caused by Colletotrichum dematium was surveyed in a tree at a fixed point from August to November over a period of 2 or 3 years at field. Disease was observed only in lower foliage of trees in August, and subsequently the disease reached the middle and upper foliage in later months, resulting in the increase in t...
Citations
... Several meta-analyses point to an increased microbial diversity or changes in community composition due to organic farming [16][17][18]. In addition, organic amendments may act as disease-suppressive soils, decreasing the incidence or severity of soil-derived plant diseases [18][19][20][21]. Interactions in the soil are complex, and practices related to tillage, fertilization and irrigation regimes alter the soil microbiota and their related functions [22,23]. ...
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... Bender et al. [56] reported that the abundance of established inoculum was negatively correlated with that of native AMF species. Sato et al. [93] also demonstrated that the indigenous AMF community affected the establishment of introduced species, which had an abundance of 48.3% of all the AMF species, compared to fumigated soil, where it accounted for two-thirds (89.6%). ...
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... /fmicb. . correlated with 3-AcDON in winter wheat, and its production by F. culmorum is believed to play a role in pathogenesis (Morimura et al., 2020). Mycotoxin accumulation affects germination rates, seedling growth, pathogen aggressiveness, and overall disease severity (Bruins et al., 1993;Scherm et al., 2011;Winter et al., 2019). ...
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... Asterisks represent statistically significant infestation rate or damage severity reduction in the indicated treatment over control, in a two-tailed t-test with Welch's correction. *p-value < 0.05; **p-value < 0.01; ***p-value < 0.001; ns-non-significant cinerea (Yoshida et al., 2019) and X. euvesicatoria (Hernández-Huerta et al., 2023). To the best of our knowledge, the present report is however, the first showing Bt-induced plant resistance toward powdery mildew diseases (here, L. taurica and O. neolycopersici). ...
... At the phylum level, Proteobacteria, Bacteroidetes and Verrucomicrobia in oil cake fertilized soil were significantly higher compared to NPK fertilized soil. These trends are also observed in other studies showing inorganic fertilization regimes decrease the population of Proteobacteria and Verrucomicrobia [38,39]. Additionally, Proteobacteria contains bacterial populations that are important for carbon, nitrogen and sulfur cycling in soil [40]. ...
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... Based on the observed difference between the DON-degradation phenotypes of both groups, the authors postulated that the Gram-positive strains represent native DON destroyers, which DON-degrading ability plays a key role for their survival, while Gram-negative bacteria are rather casual DON degraders. Note further sequencing of the Nocardioides strain LS1 indicated the lack of genes similar to the earlier described genes encoding DON-degrading enzymes [121] resulting in a conclusion that LS1 possesses a novel DON-degrading pathway. ...
... The majority of the 13 active mainly saprotrophic fungal taxa were linked to members of the diazotrophic genus Sphingomonas. A cross-kingdom association between ectomycorrhizal and arbuscular mycorrhizal fungi and Sphingomonas was shown several times [52,53], and the presence of Sphingomonas enriched the system with additional N [52]. Moreover, Sphingomonas were mainly found in the early stage of deadwood decay [54], indicating that they are of high importance to initiate accelerated deadwood decay by atmospheric N addition like in our study. ...
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... In the context of the observed differential leaf ionome and microbiome, this raises the intriguing possibility that each leaf within a plant is a distinct habitat having an adapted corresponding distinctive leaf-resident community. This adaptation could be through several mechanisms such as ability to extract nutrients, production of hormones and surfactants, as well as motility and biofilm formation (Nadakuduti et al., 2012;Ueda et al., 2018;Leveau, 2019;Oso et al., 2019). Dolan, L., Janmaat, K., Willemsen, V., Linstead, P., Poethig, S., Roberts, K., et al. (1993). ...
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... A distinct pink pigmentation is a frequently recognizable characteristic of Methylobacterium, however some exceptions to this have been established (Methylobacterium jeotgali) [33]. The presence of carotenoids have been suggested to cause the pink pigmentation which may in fact confer the ultraviolet (UV) and gamma radiation tolerance observed in earlier studies [30,[47][48][49][50][51][52]. Morphologically, Methylobacterium are rodshaped, and exhibit polar growth. ...
... R10 consistently enhanced SDW and other shoot growth parameters of both rice and pearl millet around flowering time in both years (Tables 1, S1), confirming its potential utility. Enhancement of plant growth by this commercial inoculant has been reported in maize in pot (Karasawa et al., 2000) and soybean in long-term bare fallow fields (Hayashi et al., 2018). Here, we showed that in rice and pearl millet grown in upland fields, the positive effect of inoculation on SDW was stronger in pearl millet (I × G), and also in well-irrigated conditions (W100) (I × W; Table 1, I × W × G in 2021 in Table S1). ...
