Analysis of sources of oxolinic acid-resistant field strains of <Emphasis Type="Italic">Burkholderia glumae</Emphasis> based on rep-PCR analysis and nucleotide sequences of <Emphasis Type="Italic">gyrB</Emphasis> and <Emphasis Type="Italic">rpoD</Emphasis>

Repetitive sequence-based polymerase chain reaction (rep-PCR) analysis using BOX and ERIC as primers showed a highly divergent phylogeny among field strains of Burkholderia glumae. To elucidate the sources of oxolinic acid (OA) resistance in field strains of B. glumae isolated from rice seedlings cultivated in Mie, Toyama, and Iwate prefectures, Japan, the amino acid at position 83 of GyrA (GyrA83), which is involved in OA resistance, and the DNA patterns from the rep-PCR and the partial nucleotide sequences of gyrB and rpoD from various strains were analyzed. The ten Mie strains, in which GyrA83 was isoleucine (Ile), were divided into two groups based on the band patterns in rep-PCR analysis, although the nucleotide sequences of gyrB and rpoD were identical among the strains. Based on the band patterns in the rep-PCR analysis and the gyrB and rpoD sequences, two highly OA-resistant Toyama strains, Pg-13 and Pg-14, for which GyrA83 was serine (Ser) and Ile, respectively, were in the same lineage. This suggests that the bacteria might acquire OA resistance faster than phylogenic diversity as determined with the repetitive sequences BOX and ERIC and with gyrB and rpoD. Furthermore, three Iwate strains (H95, H101, and H104), isolated from seedlings of different cultivars grown in different years and having Ile at GyrA83, are probably in the same lineage, suggesting that OA-resistant bacteria might be transferred among different cultivars.     

Burkholderia gladioli associated with symptoms of bacterial grain rot and leaf-sheath browning of rice plants

Rice plants with bacterial leaf-sheath browning and grain rot were observed in Fukuoka Prefecture in Japan during the autumn seasons of 1995 and 1996. Burkholderia spp. were consistently isolated from the infected leaf sheaths and grains. These isolates were pathogenic and induced symptoms of seedling rot, grain rot, and leaf-sheath browning in rice plants, as well as in some orchidaceous plants (cymbidium, dendrobium, and oncidium leaves), gladiolus leaves, and onion bulbs. On the basis of morphological, physiological and pathological tests, and species-specific polymerase chain reaction, the isolates were identified as belonging to either Burkholderia glumae or Burkholderia gladioli. B. gladioli, as well as B. glumae, attacked rice plants after artificial inoculation and reproduced the symptoms similar to those after natural infections. We confirmed that rice is an additional natural host of B. gladioli. It is clarified that bacterial grain rot of rice is caused not only by B. glumae but also by B. gladioli.     

Phenotypic characterization of colony morphological mutants of Burkholderia glumae that emerged during subculture

Burkholderia glumae causes rice seedling rot and grain rot disease. It is genetically unstable in its pathogenicity, and colony morphological mutants (CMMs) also frequently emerge during subculture. In this study, three types of CMM were isolated during subculture, and we characterized virulence factors such as phytotoxin, oxalic acid, and N-acylhomoserine lactone (AHL) productivity and motility. The CMMs had various phenotypes and loss of pathogenicity or reduction of virulence on seedlings and spikelets. Quorum sensing system (QSS) plays a central role in the virulence of B. glumae. Although the phytotoxin production and motility were lost or reduced in CMMs, AHLs were produced normally by 16 h after incubation, and no mutations were associated with genes for QSS such as tofI, tofR and qsmR. Thus, QSS in the CMMs seemed to function normally, with virulence reduced by another unknown mechanism. Furthermore, culture pH values decreased in the wild-type strain but increased in the CMMs at 30 °C in Luria–Bertani medium. Since many bacteria have been known to increase pH values in LB medium, culture acidification in LB medium may be a specific character to B. glumae, and reduction or loss of phytotoxin production, motility and pathogenicity of the CMMs might be affected by the reduction in acid productivity. Studies on naturally emerged CMMs may enable us to understand any novel adaptive mechanism specific to B. glumae.     

Combination of a simple differential medium and toxA-specific PCR for isolation and identification of phytopathogenic Burkholderia gladioli

The NGM medium developed in a previous study was used for differential isolation of Pectobacterium chrysanthemi, Burkholderia gladioli, and B. glumae. P. chrysanthemi developed blue colonies, and all B. gladioli and B. glumae strains tested produced diffusible yellow pigments on the NGM medium, easily distinguishable from other Burkholderia spp. and plant pathogenic bacteria. The produced yellow pigments contained a toxoflavin determined by the TLC and orchid leaf chlorosis tests. A specific oligonucleotide primer pair was designed for the detection of toxA, which is involved in toxoflavin biosynthesis. All B. gladioli and B. glumae strains tested contained toxA as determined by PCR amplification. No amplification was observed with other plant pathogenic bacteria. In addition, the toxA-based species-specific PCR assays, based on the nucleotide sequence differences in the promoter region of toxA, were developed for identification of B. gladioli and B. glumae, respectively. The NGM medium and the toxA-based PCR assays were used to determine the causal agents of leaf rot of Phalaenopsis and Oncidium orchids at three cultivation areas in Taiwan. It was found that both P. chrysanthemi and B. gladioli are important pathogenic bacteria of orchid leaf rot in Taiwan. The results indicate that the combination of NGM medium with toxA-based PCR assays is a newly designed and efficient method for isolation and identification of leaf rot pathogenic bacteria especially from plant hosts on which P. chrysanthemi and B. gladioli (or B. glumae) could cause symptoms.     

Relationship between the incidence of latent infections caused by <Emphasis Type="Italic">Monilinia</Emphasis> spp<Emphasis Type="Italic">.</Emphasis> and the incidence of brown rot of peach fruit: factors affecting latent infection

Five field experiments were performed in commercial orchards located in Lleida (Spain) over three growing seasons, 2000–2002, in order to estimate the relationship between the incidence of latent infection caused by Monilinia spp. in peaches and the incidence of post-harvest brown rot. No latent infection was recorded at popcorn and the maximum incidence occurred pre-harvest; in some orchards a second peak was detected during the pit hardening period. Monilinia laxa is the most prevalent species isolated from peaches with brown rot. There was a positive correlation between the incidence of latent infection and that of post-harvest brown rot. The average incidence of latent infection during the crop season explained 55% of the total variation in the incidence of post-harvest brown rot. The effect of temperature (T) and duration of wetness (W) on the incidence of latent infection in peach and nectarine orchards was analysed using multiple regression. The regression analysis indicated that T and W jointly explained 83% of the total variation in the incidence of latent infection. The model predicts no latent infections when T < 8°C, and >22 h wetness are required when T = 8°C but only 5 h at 25°C are necessary for latent infection to occur. The incidence of brown rot and latent infection of peaches caused by M. laxa under controlled experimental conditions were also affected by T and W, as well as by fruit maturity and inoculum concentration. Latent infections were produced in fruit when T was not suitable for the development of brown rot symptoms. In these experiments more than 4–5 h of daily wetness were required after embryo growth in fruit sprayed to run-off with an inoculum concentration higher than 10⁴ conidia ml⁻¹ of M. laxa for brown rot and latent infections to develop. The fitted model obtained from the field data was able to predict the observed data obtained under controlled environmental conditions.     

Efficacy of new EC formulations of neem oil and pungam oil for the management of sheath rot disease of rice

Neem oil (NO) and pungam oil (PO) based emulsifiable concentrate (EC) formulations,viz., neem oil 60 EC (acetic acid) [NO 60 EC(A)], neem oil 60 EC (citric acid) [NO 60 EC(C] and neem oil + pungam oil 60 EC (citric acid) [NO+PO 60 EC(C)], which had been developed at Tamil Nadu Agricultural University, were evaluated for their efficacy against sheath rot of rice. All three formulations effectively inhibited the mycelial growth of the pathogen,Sarocladium oryzae, underin vitro conditions. There was no significant difference between efficacy of the freshly prepared and stored formulations in arresting the growth ofS. oryzae; efficacy was maintained even after 9 months of storage. These formulations effectively controlled rice sheath rot and led to increased yield in five field trials. Among the various treatments, the formulation NO 60 EC(A) achieved the highest grain yield in four out of five field trials, with a pooled mean grain yield of 4684 kg/havs 3882 kg/ha in the control. NO 60 EC(A) achieved the maximum cost-benefit ratio of 1:4.8, followed by NO+PO 60 EC(C), with 1:3.3.     

Survey of mutations of a histidine kinase gene BcOS1 in dicarboximide-resistant field isolates of Botrytis cinerea

Previously, we cloned a putative osmosensing histidine kinase gene (BcOS1) and revealed that a single amino acid substitution, isoleucine to serine at codon 365, conferred dicarboximide resistance in field isolates of Botrytis cinerea. This point mutation (type I) occurred within the restriction enzyme TaqI site of the wild-type BcOS1 gene. Thus, a procedure was developed for detecting the type I mutation of the BcOS1 gene using a polymerase chain reaction (PCR) in combination with restriction fragment-length polymorphism (RFLP). Diagnosis by PCR-RFLP was conducted on the 105 isolates isolated from 26 fields in Japan. All dicarboximide-sensitive isolates (49 isolates) had the wild-type BcOS1 gene, and the 43 isolates with the type I mutation were resistant to dicarboximides without exception. These data indicate that dicarboximide-resistant isolates with type I mutation are widespread throughout Japan. However, other types of dicarboximide resistance were detected among isolates from Osaka; among the 24 resistant isolates from Osaka, 12 had the BcOS1 gene without the type I mutation. BcOS1 gene sequencing of these resistant isolates classified them into two groups, type II and type III. The type II isolates have three amino acid substitutions within BcOS1p (³⁶⁸Val to Phe, ³⁶⁹Gln to His, and ⁴⁴⁷Thr to Ser). The type III isolates have two amino acid substitutions within BcOS1p (³⁶⁹Gln to Pro and ³⁷³Asn to Ser). These amino acid changes are located on the amino acid repeat domain in BcOS1p. The three types of resistant isolates were all moderately resistant to dicarboximides without significant osmotic sensitivity, and their pathogenicity on cucumber leaves was also very similar to that of the wild-type isolate.     

Induced resistance against Fusarium diseases of <Emphasis Type="Italic">Cymbidium</Emphasis> species by weakly virulent strain HPF-1 (<Emphasis Type="Italic">Fusarium</Emphasis> sp.)

The mechanism by which Fusarium diseases of cymbidium plants are suppressed by a weakly virulent strain HPF-1 of Fusarium sp. was studied. Strain HPF-1 produced microscopic, necrotic local lesions on cymbidium leaves, causing minor damage to palisade tissues at the infection sites. This weakly virulent strain remained near the site of infection and did not develop further. It systemically and nonselectively suppressed some diseases of cymbidium such as yellow spot of leaves caused by Fusarium proliferatum and F. fractiflexum, bulb and root rot caused by F. oxysporum, and dry rot of bulbs and roots caused by F. solani. Because endogenous salicylic acid levels increased in cymbidium leaves inoculated with strain HPF-1, the mechanism of disease suppression is thought to be systemic acquired resistance.     

Internal fruit rot of netted melon caused by <Emphasis Type="Italic">Pantoea ananatis</Emphasis> (=<Emphasis Type="Italic">Erwinia ananas</Emphasis>) in Japan

An internal fruit rot with a malodor was found in netted melons (Cucumis melo L.) in commercial greenhouses in Kochi Prefecture, Japan, in 1998, despite their healthy appearance and lack of water-soaking or brown spots on the surface. A yellow bacterium was consistently isolated from the affected fruits. To confirm the pathogenicity of eight representative isolates of the yellow bacterium, we stub-inoculated ovaries (immature-fruits) 5–7 days after artificial pollination, with a pin smeared with bacteria. After the melon fruits had grown for 60 more days, an internal fruit rot resembling the natural infection appeared, and the inoculated bacterium was reisolated. The melon isolates had properties identical with Pantoea ananatis, such as gram-negative staining, facultative anaerobic growth, indole production, phenylalanine deaminase absence, and acid production from melibiose, sorbitol, glycerol, and inositol. Phylogenetic analysis based on 16S rDNA sequences showed that the melon bacterium positioned closely with known P. ananatis strains. The melon bacterium had indole acetic acid (IAA) biosynthesis genes (iaaM and iaaH) and a cytokinin biosynthesis gene (etz). The bacterium could be distinguished from the other ‘Pantoea’ group strains by rep-PCR genomic fingerprinting. From these results, the causal agent of internal fruit rot was identified as a strain of P.ananatis [Serrano in (Philipp J Sci 36:271–305, 1928); Mergaert et al. in (Int J Syst Bacteriol 43:162–173, 1993)]. The nucleotide sequence data reported are available in the DDBJ database under accessions AB297969, AB373739, AB373740, AB373741, AB373742, AB373743 and AB373744.     

Epidemiology of root rot caused by <Emphasis Type="Italic">Leptosphaeria maculans</Emphasis> in <Emphasis Type="Italic">Brassica napus</Emphasis> crops

The infection of above-ground tissues of Brassica napus by Leptosphaeria maculans is well understood. However, root infection (root rot) under field conditions, the development of root rot over time and its relationship to other disease symptoms caused by L. maculans has not been described. A survey of B. napus crops was conducted in Australia to investigate the incidence and severity of root rot. Additionally, the pathway of root infection was examined in field experiments. Root rot was present in 95% of the 127 crops surveyed. The severity and incidence of root rot was significantly correlated with that of crown canker; however, the strength of this relationship was dependent on the season. Root rot symptoms appeared before flowering and increased in severity during flowering and at maturity, a pattern similar to crown canker suggesting that the infection of the root is an extension of the crown canker phase of the L. maculans lifecycle. All isolates of L. maculans tested in glasshouse experiments caused root rot and crown canker in B. napus and Brassica juncea. In the field, the main pathway of root infection is via invasion of cotyledons or leaves by airborne ascospores, rather than from inoculum in the soil. Root rot was present in crops in fields that had never been sown to B. napus previously, in plants grown in fumigated fields, and in glasshouse-grown plants inoculated in the hypocotyl with L. maculans.     

Root and stem rot of chrysanthemum caused by five <Emphasis Type="Italic">Pythium</Emphasis> species in Japan

Root and stem rot with wilt of above ground parts of cultivated chrysanthemums was first found in Ibaraki, Toyama and Kagawa prefectures, Japan in 2002 and 2003. Pythium species were isolated from the diseased tissues and identified as P. dissotocum, P. oedochilum, P. sylvaticum, P. ultimum var. ultimum and asexual strains of P. helicoides based on their morphologies and sequences of rDNA-ITS region. All the Pythium species were strongly pathogenic to chrysanthemums in pot conditions and were reisolated from the inoculated plants. Because Pythium root and stem rot of chrysanthemum has never been reported in Japan, we propose that this is a new disease that can be caused by the five Pythium species.     

Fusarium rot of hyacinth caused by <Emphasis Type="Italic">Gibberella zeae</Emphasis> (anamorph: <Emphasis Type="Italic">Fusarium</Emphasis><Emphasis Type="Italic"> graminearum</Emphasis>)

Severe rot of leaves, peduncles and flowers caused by Gibberella zeae (anamorph: Fusarium graminearum) was found on potted plants of hyacinth (Hyacinthus orientalis), a liliaceous ornamental, in greenhouses in Kagawa Prefecture, Japan, in January 2001. This disease was named “Fusarium rot of hyacinth” as a new disease because only the anamorph, F. graminearum, was identified on the diseased host plant. The authors contributed equally to this work. The fungal isolate and its nucleotide sequence data obtained in this study were deposited in the Genebank, National Institute of Agrobiological Sciences and the DDBJ/EMBL/GenBank databases under the accession numbers MAFF239499 and AB366161, respectively.     

Polygalacturonase S31PG1 from <Emphasis Type="Italic">Geotrichum candidum</Emphasis> citrus race S31 expressed in <Emphasis Type="Italic">Schizosaccharomyces pombe</Emphasis> versus S31PG2 regarding soft rot on lemon fruit

Gene S31pg1, which encodes a polygalacturonase (PG), was previously isolated from citrus race S31 of Geotrichum candidum, the causal agent of citrus sour rot. We have now isolated and sequenced an additional PG gene, S31pg2, with 95% identity to S31pg1 in the mature proteins. To evaluate the contribution of the two PG genes in the development of citrus sour rot, each gene was expressed in the fission yeast Schizosaccharomyces pombe. Both genes conferred PG activity to the yeast. Crude enzyme solutions containing S31PG1 severely degraded the albedo tissue of lemon peel, but those containing S31PG2 did not. Concentrated crude S31PG1 solutions also caused soft rot on lemon fruit, indicating that not S31PG2 but S31PG1 is an important pathogenicity factor in citrus sour rot. Next, the protopectinase (PP) activity of each PG was measured. Although S31PG1 and S31PG2 are highly homologous, S31PG1 had high PP activity, whereas S31PG2 had much lower activity. PG from G. candidum noncitrus race S63 (nonpathogenic to citrus fruits) was also assayed but did not have any PP activity at all. These results suggest that the different PP activities of the PGs are a key to the pathogenicity of G. candidum to lemon fruit.     

Fruit rot of Strawberry pear (pitaya) caused by <Emphasis Type="Italic">Bipolaris cactivora</Emphasis>

Strawberry pear (pitahaya, pitaya) [Hylocereus undatus (Haw.) Britt. and Rose] postharvest fruit rot was found at an agricultural products store in Itoman city, Okinawa Prefecture in 2006. The symptoms included depressed, water-soaked lesions with olive to black powdery spots coalescing into a soft rot. The causal fungus was identified as Bipolaris cactivora (Petrak) Alcorn. This is the first report of strawberry pear fruit rot caused by B. cactivora.     

Pythium rot of figmarigold (<Emphasis Type="Italic">Lampranthus spectabile</Emphasis>) caused by <Emphasis Type="Italic">Pythium aphanidermatum</Emphasis>

A new leaf rot disease was found on the leaves of figmarigold (Lampranthus spectabile). The causal organism, identified as Pythium aphanidermatum was found to cause the same symptoms after artificial inoculation and was then reisolated from the inoculated plants. We propose to name the disease Pythium rot of figmarigold.     

Isolation of pathogenicity- and gregatin-deficient mutants of <Emphasis Type="Italic">Phialophora gregata</Emphasis> f. sp. <Emphasis Type="Italic">adzukicola</Emphasis> through <Emphasis Type="Italic">Agrobacterium tumefaciens</Emphasis>-mediated transformation

Phialophora gregata f. sp. adzukicola, a causal agent of brown stem rot in adzuki beans, produces phytotoxic compounds: gregatins A, B, C, D, and E. Gregatins A, C, and D cause wilting and vascular browning in adzuki beans, which resemble the disease symptoms. Thus, gregatins are considered to be involved in pathogenicity. However, molecular analyses have not been conducted, and little is known about other pathogenic factors. We sought to isolate nonpathogenic and gregatin-deficient mutants through Agrobacterium tumefaciens-mediated transformation (ATMT) for cloning of pathogenicity-related genes. The co-cultivation of P. gregata and A. tumefaciens for 48 h at 20°C with 200 μM acetosyringone resulted in approximately 80 transformants per 10⁶ conidia. The presence of acetosyringone in the A. tumefaciens pre-cultivation period led to an increase in T-DNA copy number per genome. Of 420 and 110 transformants tested for their pathogenicity and productivity of gregatins, one nonpathogenic and three gregatin-deficient mutants were obtained, respectively. The nonpathogenic mutant produced gregatins, whereas the gregatin-deficient mutants had pathogenicity comparable to the wild-type strain. This is the first report of ATMT of P. gregata. Further analysis of these mutants will help reveal the nature of the pathogenicity of this fungus including the role of gregatin in pathogenesis.     

Influence of bacteria isolated from rice plants and rhizospheres on antibiotic production by the antagonistic bacterium <Emphasis Type="Italic">Serratia marcescens</Emphasis> strain B2

Serratia marcescens strain B2 is an antagonistic bacterium that produces the red-pigmented antibiotic prodigiosin and suppresses rice sheath blight caused by Rhizoctonia solani AG-1 IA. Rice sheath blight disease was suppressed when plants were inoculated with this bacterium an hour before pathogen inoculation but not when plants were treated 4 weeks before pathogen inoculation. In both cases the bacteria were detected in the rice rhizosphere 4 weeks after inoculation. Bacteria isolated from the rice plant and rhizosphere inhibited biosynthesis of prodigiosin in S. marcescens strain B2. We suggest that bacteria isolated from rice plants and rhizospheres mediate the suppression of antibiotic production of biological control agents and that such suppression is common under field conditions.