Bacterial panicle blight (BPB) and sheath blight (SB) are major diseases of rice and few cultivars have shown a high level of resistance to these diseases. A recombinant inbred line (RIL) population developed from the U.S. cultivars Jupiter (moderately resistant) and Trenasse (susceptible) was investigated to identify loci associated with the partial disease resistance to BPB and SB. Disease phenotypes in BPB and SB, as well as the days-to-heading (DTH) trait, were evaluated in the field. DTH was correlated to BPB and SB diseases, while BPB was positively correlated to SB in the field trials with this RIL population. Genotyping was performed using Kompetitive Allele Specific PCR (KASP) assays and whole-genome sequence (WGS) analyses. Quantitative trait locus (QTL) mapping and bulk segregant analysis using a set of WGS data (QTL-seq) detected a major QTL on the upper arm of chromosome 3 for BPB, SB, and DTH traits within the 1.0–1.9 Mb position. Additional QTLs associated with BPB and SB were also identified from other chromosomes by the QTL-seq analysis. The QTLs identified in this study contain at least nine candidate genes that are predicted to have biological functions in defense or flowering. These findings provide an insight into the complex nature of the quantitative resistance to BPB and SB, which may also be closely linked to the flowering trait.

Bacterial panicle blight (BPB), caused by Burkholderia glumae, is one of the most severe seed-borne bacterial diseases of rice in the world, which can decrease rice production by ≤75%. Nevertheless, there are few effective measures to manage this disease. In an attempt to develop an alternative management tool for BPB, we isolated and characterized phages from soil and water that are effective to lyse several strains of B. glumae. After tests of host ranges, the phages NBP1-1, NBP4-7, and NBP4-8 were selected for further comprehensive characterization, all of which could lyse B. glumae BGLa14-8 (phage sensitive) but not B. glumae 336gr-1 (phage insensitive). This result indicates that the phages killing B. glumae cells have specific host ranges at the strain level within the bacterial species. In the greenhouse condition of this study, foliar application of the phage NBP4-7 reduced the severity of BPB caused by B. glumae BGLa14-8 ≤62% but did not cause any significant effect on the infection by B. glumae 336gr-1. Electron microscopy and whole-genome sequencing were also performed to characterize the three selected phages. Transmission electron microscopy revealed that the selected phages belong to the family Myoviridae. Furthermore, whole-genome sequence analysis indicated that the three phages belong to a same species and are closely related to the Burkholderia phage KL3, a member of the Myoviridae family.

In July 2023, panicle and leaf blight-like symptoms were observed from the rice (Oryza sativa) variety, PVL03, in research field plots in Louisiana (Rayne, LA 70578, USA; 30.21330⁰ N, 92.37309⁰ W). We observed that chlorosis started on the tips and spread throughout the whole leaf. We also observed panicle blight-like symptoms (grain discoloration of rice hulls) on infected rice plants at the heading stage, which ranged from dark brown to black. Disease incidences were approximately 70% in the observed plots. Five plants were sampled from five plots (one plant per plot). Leaf tissues including both symptomatic and healthy parts (~ 1 cm²) were surfaced sterilized and placed on CCNT medium, a semi-selective medium for the rice bacterial panicle blight pathogen Burkholderia glumae (Kawaradani et al., 2000), and on Luria-Bertani (LB) agar supplemented with cycloheximide (50 µg/ml) for non-selective isolation of bacteria. For the panicle samples, the surfaced sterilized rice kernels were dehulled and ground in sterile distilled H₂O using a sterile mortar and pestle. The homogenate was spread on the CCNT media and LB agar supplemented with nitrofurantoin (50 µg/ml) and cycloheximide (50 µg/ml). After ~72 h at 41⁰C, round, smooth and yellow-colored bacterial colonies were observed on both media. The two isolates, one from an infected rice leaf (LPL-1) and the other from the infected rice panicles (LPP-1), were initially identified as Pantoea ananatis based on PCR-amplified 16S rDNA sequences (Weisburg et al., 1991). The taxonomic identity of these two isolates was further confirmed through whole genome sequencing (NCBI Accession ID: PRJNA1092676), which was performed through a hybrid sequencing approach using Oxford Nanopore sequencer & Illumina NextSeq2000 system (Plasmidsaurus Inc., South San Francisco, CA, USA). To satisfy Koch's postulates, we inoculated six one-month-old rice plants (cv. Kitaake) with LPL-1 and LPP-1, respectively, by pricking the stems with a sterile toothpick touched to the overnight grown bacterial culture on LB agar (~ 5-8 x 10⁵ bacterial cells). This virulence assay was conducted twice, and rice plants inoculated with sterile distilled water were included as the negative control. By 27 days post inoculation (DPI), the inoculated plants developed symptoms on leaves and panicles, which were like the symptoms originally observed in the field, and additional symptoms such as shot holes and stem necrosis were also observed. From leaf and panicle samples of the artificially inoculated plants, we reisolated bacteria and confirmed the identity of the bacteria using the P. ananatis specific PCR primers PANA_1080 61F and PANA_1080 1009R (Asselin et al., 2016). To the best of our knowledge, this is the first report of bacterial panicle and leaf blight of rice caused by P. ananatis in Louisiana. Since P. ananatis is a recently emerging pathogen of rice worldwide, including the United States (Yu et. al., 2022; Lu et al., 2022; Luna et al., 2023), it is crucial to monitor the occurrence of this pathogen in other rice-growing areas as a potential threat to US rice production.

Rice (Oryza sativa) plants showing severe leaf and panicle blight symptoms were observed and collected from four field plots in Louisiana in summer 2023. As the observed symptoms looked like bacterial leaf and panicle blight caused by Pantoea ananatis (Bruno et al. 2025) or bacterial panicle blight caused by Burkholderia glumae and B. gladioli (Nandakumar et al. 2009), we presumptively attempted to isolate one of these bacterial pathogens as the causal agent. Bacteria were isolated from the symptomatic seeds, which were surface sterilized, dehulled and ground in sterile distilled water using a sterile mortar and pestle. The homogenate was spread on the CCNT medium (Kawaradani et al. 2000) and LB agar supplemented with nitrofurantoin (50 µg/ml) and cycloheximide (50 µg/ml). After 72 h incubation at 41⁰C, round, smooth and faint, yellow-colored bacterial colonies appeared on both CCNT and LB agar plates. Unexpectedly, all six bacterial isolates from rice samples were initially identified as Xanthomonas sacchari based on PCR-amplified 16S rDNA sequences using the primers fD1 (5'-CCGAATTCGTCGACAACAGAGTTTGATCCTGGCTCAG-3')/rD1 (3'-CCCGGGATCCAAGCTTAAGGAGGTGATCCAGCC-5') (Weisburg et al. 1991), regardless of their sampling locations. Whole genome sequencing analyses (NCBI Accession ID: PRJNA1223440) performed through a hybrid sequencing approach using Oxford Nanopore sequencer & Illumina NextSeq2000 system (Plasmidsaurus Inc., California, USA) further confirmed that all six strains belong to X. sacchari. To satisfy Koch's postulates, each of the six strains LXP-1780, LXP-1783, LXP-1790, LXP-1791, LXP-1792, and LXP-1793 was confirmed for its pathogenicity to rice through two inoculation methods, using one-month-old plants (cv. Kitaake) at tillering stage; 1) pricking the stems with a sterile toothpick touched to the overnight grown bacterial culture on LB agar (~ 5-8 x 10⁵ bacterial cells per tip) and 2) clipping the leaves with scissors dipped in the bacterial suspension containing ~1 × 10⁸ bacterial cells per mL of sterile distilled water. This virulence assay was conducted twice with three replications for each strain, and rice plants inoculated with sterile distilled water were included as the negative control. By twenty-seven days after inoculation (DAI), the inoculated plants developed symptoms on leaves and panicles, which were similar to the symptoms initially observed in the field. Besides blight symptoms and water-soaked lesions in the leaves, the most noticeable symptom observed was the blackening or darkening of the leaf tips, which appeared as dark spots or streaks. In panicles, panicle blight-like symptoms, such as grain discoloration and darkening of rice hulls, were observed. The bacteria were reisolated from each artificially inoculated plant and their identity were validated to be X. sacchari. To our knowledge, this is the first report of rice disease caused by X. sacchari in the United States. This finding strongly suggests the emergence of this disease as a new potential threat to U.S. rice industry. Furthermore, the strains of X. sacchari and their whole genome sequence information obtained from this study will serve as a foundation for future studies on this newly emerging disease.

The prevalence of antimicrobial resistance (AMR) in bacterial pathogens resulting from the intensive usage of antibiotics and antibiotic compounds is acknowledged as a significant global concern that impacts both human and animal health. In this study, we sequenced and analyzed the genomes of two emergent onion-pathogenic species of Burkholderia, B. cenocepacia CCRMBC56 and B. orbicola CCRMBC23, focusing on genes that are potentially associated with their high level of antibiotic and copper resistance. We also identified genes contributing to the copper resistance of B. cenocepacia CCRMBC56 through high-throughput analysis of mutated genes in random transposon mutant populations that were differentially enriched in a copper-containing medium. The results indicated that genes involved in DNA integration, recombination, and cation transport are important for the survival of B. cenocepacia CCRMBC56 in copper-stressed conditions. Furthermore, the fitness effect analysis identified additional genes crucial for copper resistance, which are involved in functions associated with the oxidative stress response, the ABC transporter complex, and the cell outer membrane. In the same analysis, genes related to penicillin binding, the TCA cycle, and FAD binding were found to hinder bacterial adaptation to copper toxicity. This study provides potential targets for reducing the copper resistance of B. cenocepacia and other copper-resistant bacterial pathogens.

One of the challenges in the practical application of plant growth-promoting bacteria (PGPB) is predicting their effectiveness under field conditions. Performance can vary due to environmental factors and the recruitment of genotype-specific microbiota through root exudates. In addition, the viability of PGPB during storage and delivery must be maintained to avoid inconsistent field performance. Lyophilization (freeze-drying) is a promising method for preserving bacterial cells; however, this process subjects bacterial cells to extreme thermal and osmotic stresses that can lead to irreversible cellular damage. In this study, the addition of crude soybean seed extract, with 10% glycine betaine and 5% cellobiose as cryoprotective agents, improved bacterial viability after freeze-drying with high recovery rates of 82–98% after preservation, which is essential to ensure the efficacy of beneficial soil bacteria used as biotic agents. To our knowledge, this is the first study to report optimal preservation conditions for beneficial soil bacteria shown to promote soybean growth, providing a basis for improving soybean yield through microbial applications.