In 2013 QoI-resistant strains of the rice blast fungus (MoO) emerged suddenly and spread in Hyogo Prefecture. To estimate factors associated with their spread and subsequent survival, the population structure of MoO strains was monitored from 2013 to 2017 and 2023 using DNA fingerprinting with Pot2. Most of the QoI-resistant isolates collected in 2013 were classified into haplotype HY1, irrespective of areas of collection in Hyogo Prefecture. This result suggests that the sudden emergence and spread of the QoI-resistant strains in 2013 were caused by almost the single haplotype HY1 probably through seed transmission. After discontinuance of the QoI fungicide application in 2014, however, the QoI-resistant strains decreased over the course of several years, suggesting that genetic alterations conferring the QoI resistance may have caused a decrease in fitness. Conversely, QoI-sensitive strains increased after 2015, but predominant haplotypes changed across years of collection. We suggest that it could be possible to re-use the QoI-fungicide if the disappearance of the resistant strains is confirmed by careful monitoring of QoI resistance throughout the prefecture, especially in and around fields for seed production.
Hemicriconemoides litchi is a sheathoid nematode of economic importance, yet its occurrence and ecological determinants in pomelo (Citrus maxima) orchards remain poorly understood. In this study, populations associated with pomelo in northern Vietnam were characterised using an integrative approach combining morphology, morphometrics, and molecular data, together with an assessment of their relationships with selected soil properties. Morphological observations of females agreed well with original description and subsequent reports, with minor morphometric variation falling within known intraspecific ranges. Molecular analysis of the D2–D3 expansion segments of 28S rDNA revealed very high sequence similarity (99.3–100
In June 2024, interveinal yellowing on leaves of melon (Cucumis melo L.) plants was observed in Shiga Prefecture, Japan. The deduced amino acid sequences for six open reading frames (ORFs) shared over 92.9
In the quorum sensing-active state, the phytopathogenic Ralstonia pseudosolanacearum strain OE1-1 activates the 347-amino acid LysR-type transcriptional regulator PhcA, which regulates PhcA-regulated genes responsible for its virulence. To elucidate the functional role of the PhcA C-terminus, the phcA-deletion strain was transformed with a truncated phcA encoding PhcA lacking only the 20 C-terminal amino acids or a frameshift-mutated phcA carrying a single adenine deletion at position 983. The frameshift-mutation but not truncation of PhcA C-terminus affected the regulation of PhcA-regulated genes, losing virulence. These results indicate that the frameshift-derived amino acid additions at the C-terminus impair PhcA’s regulatory function.
The increasing demand for environmentally sustainable disease management has stimulated interest in alternatives to chemical pesticides. Amino acids are ubiquitous plant metabolites that have been implicated in defense responses, but their role in disease suppression across pathogen types remains unclear. In this study, we evaluated the protective effects of exogenous amino acids against bacterial and fungal diseases in multiple crop systems. Foliar application of cysteine (Cys), lysine (Lys), and glutamate (Glu), individually or in combination, was tested against cabbage bacterial leaf spot caused by Pseudomonas cannabina pv. alisalensis (Pcal), wheat leaf rust caused by Puccinia recondita, and soybean rust caused by Phakopsora pachyrhizi. In cabbage, amino acid treatments reduced disease symptoms and bacterial populations, with mixtures showing enhanced effects. Mechanistically, amino acids decreased stomatal aperture width and limited bacterial entry, indicating a pre-entry mode of action. In wheat and soybean, amino acid treatments significantly reduced rust severity, primarily through inhibition of appressorium formation without affecting spore germination. These findings demonstrate that amino acids suppress both bacterial and rust diseases by targeting early infection processes. Notably, mixtures of amino acids consistently conferred stronger protection than individual treatments, suggesting additive or synergistic effects. Collectively, our results establish amino acids as potential pre-penetration barriers that interfere with pathogen entry across kingdoms and highlight their promise as sustainable tools for crop disease management.
In 2025, Lisianthus (Eustoma grandiflorum [Raf.] Shinn.) plants in Kagoshima Prefecture, Japan, exhibited wilting and black root rot. Dark brown–black lesions were observed on the roots, and progressing to severe decay. The fungus isolated from the diseased roots was identified as Berkeleyomyces rouxiae based on morphological characteristics and phylogenetic tree with four loci (rDNA-ITS, LSU, 60S and MCM7). Pathogenicity tests confirmed B. rouxiae is a causal agent. This is the first report of black root rot in Lisianthus caused by B. rouxiae in Japan.
The recent substantial reclassification of ramularioid fungi, agronomically important plant pathogens, highlights the need to reidentify historical isolates and reassess links between species identity and key biological traits. Here, we clarified the taxonomic placement of strain GR1, isolated from a Rumex weed in Japan and recorded as Ramularia pratensis, its original host association, and pathogenicity in problematic Rumex weeds using molecular analyses, morphological characters, and pathogenicity assays. The ITS sequence was identical to the ex-type of Teratoramularia rumicis, whereas the LSU sequence was identical to the ex-type of T. rumicicola. In a concatenated ITS–LSU phylogeny, GR1 clustered with the T. rumicicola ex-type, while the T. rumicis ex-type remained within the same assemblage but on a long branch. On-host morphology provided limited support for the treatment of GR1 as T. rumicicola. The host voucher specimen was morphologically consistent with Rumex japonicus, which developed the original symptoms after inoculation with the pathogen. GR1 caused disease symptoms on Rumex weed species and suppressed their growth. Based on currently available evidence, we treat GR1 as T. rumicicola but note that species boundaries between T. rumicicola and T. rumicis cannot be resolved unambiguously with the limited sampling and multilocus data for T. rumicis. This study provides a taxonomic reassessment of GR1 and supports further evaluation as a candidate for biological control of Rumex weeds.
Phytophthora infestans causes late blight of potato plants that can lead to decay of stored tubers, which are prone to secondary fungal or bacterial infections and subsequent decay. The bacteria responsible for this secondary decay have not been identified. In this study, we assessed whether the presence of endophytic bacteria promotes bacterial decay in tubers infected with Ph. infestans. We reproduced storage decay by inoculating tubers with Ph. infestans. Eleven bacteria isolated from these decayed tubers were then tested on tuber slices for their ability to cause decay; the isolates induced decay in tubers previously inoculated with Ph. infestans but not in control tubers that were not inoculated with Ph. infestans. To evaluate the impact of bacterial inoculation and Ph. infestans, we also weighed the exudate from decayed tissue. More exudate was produced by samples inoculated with both Ph. infestans and bacteria than those inoculated only with bacteria. Phylogenetic analysis based on 16S rRNA and rpoB sequences revealed that bacterial isolates were closely related to Paenibacillus polymyxa. Characteristics of three representative bacterial isolates were also consistent with those of Pa. polymyxa ATCC 842T. Real-time polymerase chain reactions confirmed that Pa. polymyxa proliferated in tubers infected with Ph. infestans, although tubers were not inoculated with the bacterium. Together, these findings indicate that the presence and proliferation of endophytic Pa. polymyxa contribute to storage decay in potato tubers infected by Ph. infestans.
Tomato curly top virus (ToCTV), a geminivirus first isolated from tomato in Japan, shares approximately 86
Rice blast, caused by Pyricularia oryzae, is a major constraint on rice production in Vietnam. To gain a high-resolution genomic understanding of the pathogen, we performed whole-genome resequencing of 31 P. oryzae isolates collected from major rice-growing regions. Using 9307 high-quality single-nucleotide polymorphisms (SNPs), we resolved four distinct genetic groups. This structure showed partial geographic correlation, revealing a unique Northern lineage and high genetic heterogeneity in the intensive Mekong Delta, where isolates were distributed across multiple groups. Population genetic analyses indicated strong subdivision and signals of balancing selection, as evidenced by positive Tajima’s D values across all groups (up to + 1.22). All isolates carried the MAT1-2 mating type, confirming a predominantly clonal reproductive mode. Effector gene profiling showed contrasting evolutionary patterns: AvrPi9 was completely conserved, while AvrPik exhibited high polymorphism, with the prevalent AvrPik-D allele and the adaptive AvrPik-D/F duplication detected in 11 of 31 isolates (35.48
In 2023, browning symptoms on leaves, stems, and flower buds were observed in cultivated vanilla plants in a greenhouse in Okinawa, Japan. The fungal isolate obtained from the symptomatic tissues was classified into the Fusarium fujikuroi species complex (FFSC) clade based on molecular and morphological analyses. Pathogenicity analysis revealed that inoculation of vanilla leaves with the isolate resulted in similar symptoms, and the same fungus was recovered. This study is the first to report an isolate belonging to the FFSC as a causal agent of Fusarium wilt in vanilla.
In August 2022, outbreaks of apple fruit rot occurred in orchards flooded by heavy rainfall in Aomori, Japan. An isolate of Phytophthora taken from diseased apple tissue was identified as P. pseudocitrophthora based on morphology and DNA sequences of 12 loci. This isolate formed radiate mycelia, grew at 10–35 °C on potato dextrose agar, and produced papillate or semipapillate sporangia on V8A in the soil extract. In the pathogenicity tests, inoculation of unwounded apple fruits with a zoospore suspension caused rot within 3 days. We propose that P. pseudocitrophthora is a novel causal agent of Phytophthora fruit rot on apples.
In the summer of 2023, sunflower plants in commercial plots in Calera de Víctor Rosales, Zacatecas, developed multiple flower heads and leaf buds, and younger leaves were long, deformed, and wide, suggesting phytoplasma infection. The 16S rDNA and SecY genes from phytoplasma were amplified using polymerase chain reaction and subjected to virtual restriction fragment length polymorphism analysis (iPhyClassifier). The phytoplasma identified in symptomatic plants (mother plants), and their seeds and emergent seedlings corresponded to the ‘Ca. P. trifolii’ strain, group 16SrVI-A. Seeds from symptomatic mother plants had a normal shape and color, but their length, width and mass were smaller than those of asymptomatic plants. In addition, germination was delayed, and resultant plants had developmental defects, including aborted flowers and retarded growth. This is the first report of a ‘Ca. P. trifolii’-related phytoplasma in sunflowers causing a new symptomatology in Mexico and confirms transmission of this phytoplasma through seeds and seedlings from diseased sunflower plants.
One of the genomic islands in Pseudomonas syringae pv. tabaci 6605 (GI-1Pta6605) has been identified as a pathogenicity island required for virulence because the deletion almost completely eliminated disease symptoms in inoculation tests at 4 × 105 CFU/ml. GI-1Pta6605 contains four cargo regions (CRs) named CR-1 to CR-4. The ∆CR-4 mutant did not produce tabtoxin like ∆GI-1 and disease symptoms did not develop in tobacco. However, it grew, although to a lesser extent than the wild-type strain. These results indicate that the tabtoxin biosynthetic gene cluster in GI-1 is required for virulence but not for establishment of compatibility.
Two Bremia lactucae isolates were obtained from infected lettuce (Lactuca sativa) plants in fields in Kagawa Prefecture. The two isolates exhibited distinct reaction phenotypes compared to those of races in Hyogo Prefecture previously characterized by the International Bremia Evaluation Board, suggesting the presence of unreported races in Japan. Some commercial lettuce cultivars with resistance genes supported minimal sporulation of an isolate, confirming their effectiveness for disease control. When wild L. serriola collected from three regions was inoculated with the other isolate, the isolate only sporulated on plants from Hiroshima Prefecture. L. sativa cotyledons inoculated with sporangia of the isolate from L. serriola also sporulated, providing evidence of cross-infection of L. sativa and L. serriola by B. lactucae in Japan. The presence of new B. lactucae races and the regional susceptibility of L. serriola to B. lactucae may be influenced by practices such as weed management and crop rotation, including paddy rice cultivation.
Sweet potato foot rot, first confirmed in Okinawa in 2018, is spreading to southern Kyushu and causing serious yield losses. A previous study showed that integrating soil treatment with trifloxystrobin wettable powder, seedling treatment with benomyl wettable powder, and foliar sprays with fluazinam and triflumizole wettable powders and basic copper sulfate is highly effective. Here we evaluated the efficacy of this integrated system and effects on yields using two new varieties resistant to foot rot and the main variety Chura-Koi-Beni in Okinawa. We evaluated three trifloxystrobin systems: system 1 (described above), a reduced-spray version of system 1 (system 2), and system 2 with copper sulfate applications (system 3). Disease incidence on Chura-Koi-Beni was lower in all three systems than in the conventional system, and yields were statistically similar to or greater than in the conventional. The new varieties also showed low levels of aboveground symptoms, indicating that combining them with the trifloxystrobin systems can further enhance disease suppression. Overall, the three trifloxystrobin-based systems in Okinawa Prefecture were effective against this disease; even the reduced spray (system 2) can be effective, and system 3 has the potential to achieve control equal to or greater than with system 2. In addition, combining resistant varieties can provide even better disease control.
Bacteria associated with lettuce leaf spot in Trinidad were isolated and their pathogenicity was confirmed. Based on the yellow mucoid and creamy white colonies and PCR amplification and sequencing of bacterial DNA, the pathogens were identified as Xanthomonas and Paracidovorax species. Whole-genome sequencing of Paracidovorax BLS4 and Xanthomonas BLS9 revealed two distinct bacterial species causing leaf spot of lettuce. BLS9 was identified as Xanthomonas hortorum pv. vitians and shared an average 98.37
The plant hormone, jasmonic acid (JA), is involved in plant defense and development. In this study, we investigated the role of the rice basic region/leucine zipper motif (bZIP) transcription factor, OsbZIP01, in the JA-regulated defense response against rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) in rice. JA did not induce the expression of OsbZIP01. OsbZIP01 did not interact with any JASMONATE ZIM-domain (JAZ) proteins that function as transcriptional repressors of the JA response. The loss-of-function mutant of OsbZIP01, osbzip01 exhibited JA-insensitive phenotypes. JA did not induce Xoo resistance in the osbzip01 mutant. Some JA-responsive defense-related genes, including the lignin biosynthesis gene OsPrx38, were not induced by JA in the osbzip01 mutants. JA-induced lignin accumulation did not occur in the osbzip01 mutants. These results indicated that OsbZIP01 acts as a positive regulator of the JA-mediated defense response against Xoo in rice.
In Kochi Prefecture, Japan, Passalora nattrassii, cause of eggplant leaf mold, is the most prevalent pathogen of eggplant because of its fungicide resistance. Sequencing analysis revealed amino acid substitutions including SdhB-H268C, SdhB-H268R, SdhB-I270V, SdhC-N83S, and SdhC-H149R. In efficacy trials of SDHI fungicides, isofetamid and pyraziflumid were effective against all five mutants except for SdhB-I270V and SdhB-H268C, respectively. Pyribencarb provided higher efficacy than azoxystrobin against QoI-resistant isolates with cytb-G143A. These results indicate that different mutations at the target sites are responsible for the different sensitivity patterns in P. nattrassii.
