First Report of New Bacterial Leaf streak of Rice Caused by Pantoea ananatis in China

Rice (Oryza sativa L.) is the largest grain crop, accounting for about 40 % of the total grain production in China. In mid-July 2021, bacterial leaf streak-like disease emerged in rice varieties Chunyou584 and Yongyou2604 in Linyi city, Shandong Province, China. Disease incidences of the disease ranged from 80% to 90% in the surveyed fields. Infected rice leaves displayed dark green to yellowish-brown water-soaked thin streaks, and a large amount of beaded yellow oozes were observed on the lesions. After drying, there were gelatinous granules that were not easy to fall off and spread between leaf veins (Fig.S1A). According to the field symptoms of this disease, it was preliminarily suspected to be rice bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola (Xoc), which is a guaranteed disease in China. To isolate the causal agent, leaf discs (~1 cm2) of diseased leaves were collected from the margins of the lesions, surface sterilized and ground into pieces in sterile double distilled water. The 10-3, 10-4 and 10-5 dilutions were spread onto peptone sugar agar (PSA) and incubated at 28°C for 36 hours. Yellow mucous bacterial colonies were consistently obtained on PSA medium. To identify the pathogen, fragments of the 16S rDNA, leuS and rpoB were amplified and sequenced using the primers previously reported (Yu et al. 2021). Three strains (LY01, LY02 and LY03) showed identical colony morphology and LY01 was used for further analyses. Sequence analyses showed that the fragments of 16S rDNA (955 bp, GenBank accession number: OK261898), leuS (755 bp, GenBank accession number: OK298387) and rpoB (926 bp, GenBank accession number: OK298388) of strain LY01 shared 99.16%, 99.46% and 100% similarities with those of Pantoea ananatis TZ39 (GenBank accession numbers: CP081342.1 for 16S rDNA, MW981338.1 for leuS and MW981344.1 for rpoB), respectively, which suggest the pathogenic bacterial strain LY01 isolated is P. ananatis. In addition, the single colony of P. ananatis LY01 was shown as Fig. S2B. Furthermore, pathogenicity tests were also performed according to the following steps. Bacterial suspension at OD600=0.1 was inoculated into eight rice leaves of four healthy rice plants (Chunyou 584) at 25-33°C and 60%-80% relative humidity in the field using a clipping method (Yang et al. 2020) or spraying methods, and sterile distilled water was as negative control. The clipped leaves (Fig. S1B) and spray-inoculated leaves (Fig. S1C) showed dark green water-soaked streaks at 14 days after inoculation, respectively, which showed similar symptoms with those samples collected from the fields (Fig. S1A). On contrary, the control rice leaves remained healthy and symptomless (Fig. S2A). The bacterium was re-isolated in the inoculated rice leaves and the re-isolated bacterial isolates, which was confirmed by sequencing 16S rDNA, leuS and rpoB, incited the same symptoms as in fields, which fulfills Koch’s postulates. In the past decade, P. ananatis was reported to result in grain discoloration and leaf blight in China (Yan et al. 2010; Xue et al. 2020, Yu et al. 2021), which could result in 40% - 60% yield losses. To our best knowledge, this is the first report of the bacterial leaf streak-likely disease occurred in Shandong Province caused by P. ananatis, so we named it as Pantoea leaf streak of rice. Although P. ananatis was also reported in Zhejiang province and Jiangxi province, which caused leaf streak lesions on rice, the disease symptoms are completely different from those of Pantoea leaf streak of rice. To the best of our knowledge, this is the first report of Pantoea leaf streak of rice caused by P. ananatis. This study provides sloid evidence that Pantoea leaf streak of rice in Eastern China can be caused by the new pathogen, P. ananatis, rather than Xoc as traditionally assumed. Disease development and quarantine of the new Pantoea leaf streak of rice disease caused by P. ananatis on rice need more attention in the near future.

Nanoparticles in inhibiting Pantoea ananatis and to control maize white spot

ABSTRACT: Maize white spot (MWS) caused by Pantoea ananatis is one main maize leaf diseases, and nanoparticles (NPs) are an innovative approach for bacterial disease control. This research evaluated the toxicity of pure NPs and doped NPs with different elements in inhibiting bacterial growth and to control MWS. Pure NPs and ZnO NPs doped with silver (Ag), gold (Au), copper (Cu), iron (Fe), manganese (Mn), and nickel (Ni) at different concentrations were used to determine the toxicity for P. ananatis in vitro, evaluating the bacterial growth inhibition zone. To assess the control of MWS, in the preventive application, maize plants were sprayed with NPs of ZnO:0.1Cu, ZnO:0.05Fe, ZnO:0.2Mn and ZnO:0.7Ni at 10, 5 or 2.5 mg mL-1, and after 3 days, the plants were inoculated with bacterial suspension. To assess the curative application, plants were inoculated with the bacteria, and 3 days later sprayed with the NPs. The disease severity was assessed and the area under the disease-progress curve (AUDPC) was calculated. The doped ZnO NPs with different elements, and at different concentrations inhibited bacterial growth in vitro. NPs of ZnO:0.1Cu and ZnO:0.2Mn at 5 or 2.5 mg mL-1, in both applications reduced the severity of MWS, showing potential for use in the disease management.

Complete Genomic Data of Pantoea ananatis Strain TZ39 Associated with New Bacterial Blight of Rice in China

Pantoea ananatis is a phytopathogen infecting many economically important crops, including rice worldwide. Here, we report the complete genome of P. ananatis strain TZ39 identified as causative agent of a new bacterial blight of rice emerged in China in 2020. The assembled genome is consisted of one circular chromosome of 4, 483,976 bp, and two plasmids of 135,135, and 276,579 bp. This complete genome of the first Chinese pathogenic P. ananatis strain will provide new insights into the traits of pathogenicity on genomic level from China and worldwide.

Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion

Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the ‘alt’ gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.

First Report of New Bacterial Leaf Blight of Rice Caused by Pantoea ananatis in Southeast China

In autumn 2020, leaf blight was observed on rice (Oryza sativa L., variety Zhongzao39, Yongyou9, Yongyou12, Yongyou15, Yongyou18, Yongyou1540, Zhongzheyou8, Jiafengyou2, Xiangliangyou900 and Jiyou351) in the fields of 17 towns in Zhejiang and Jiangxi Provinces, China. The disease incidence was 45%-60%. Initially, water-soaked, linear, light brown lesions emerged in the upper blades of the leaves, and then spread down to leaf margins, which ultimately caused leaf curling and blight during the booting-harvest stage (Fig. S1). The disease symptoms were assumed to be caused by Xanthomonas oryzae pv. oryzae (Xoo), the pathogen of rice bacterial blight. 63 isolates were obtained from the collected diseased leaves as previously described (Hou et al. 2020). All isolates showed circular, smooth-margined, yellow colonies when cultured on peptone sugar agar (PSA) medium for 24h at 28℃. The cells were all gram-negative and rod-shaped with three to six peritrichous flagella; positive for catalase, indole, glucose fermentation and citrate utilization, while negative for oxidase, alkaline, phenylalanine deaminase, urease, and nitrate reductase reactions. 16S rRNA gene sequence analysis from the 6 isolates (FY43, JH31, JH99, TZ20, TZ39 and TZ68) revealed that the amplified fragments shared 98% similarity with Pantoea ananatis type strain LMG 2665T (GenBank JFZU01) (Table S3). To further verify P. ananatis identity of these isolates, fragments of three housekeeping genes including gyrB, leuS and rpoB from the 6 isolates were amplified and sequenced, which showed highest homology to LMG 2665T with a sequence similarity of 95%-100% (Table S3). Primers (Brady et al. 2008) and GenBank accession numbers of gene sequences from the 6 isolates are listed in Table S1 and Table S2. Phylogenetic analysis of gyrB, leuS and rpoB concatenated sequences indicated that the 6 isolates were clustered in a stable branch with P. ananatis (Fig. S2). Based on the above morphological, physiological, biochemical and molecular data, the isolates are identified as P. ananatis. For pathogenicity tests, bacterial suspension at 108 CFU/mL was inoculated into flag leaves of rice (cv. Zhongzao39) at the late booting stage using clipping method. Water was used as a negative control. The clipped leaves displayed water-soaked lesions at 3 to 5 days after inoculation (DAI); then the lesion spread downward and turned light brown. At about 14 DAI, blight was shown with similar symptoms to those samples collected from the rice field of Zhejiang and Jiangxi provinces (Fig. S1). In contrast, the control plants remained healthy and symptomless. The same P. ananatis was re-isolated in the inoculated rice plants, fulfilling Koch’s postulates. In the past decade, P. ananatis has been reported to cause grain discoloration in Hangzhou, China (Yan et al. 2010) and induce leaf blight as a companion of Enterobacter asburiae in Sichuan province, China (Xue et al. 2020). Nevertheless, to the best of our knowledge, this is the first report of P. ananatis as the causative agent of rice leaf blight in southeast China. This study raises the alarm that the emerging rice bacterial leaf blight in southeast China might be caused by a new pathogen P. ananatis, instead of Xoo as traditionally assumed. Further, the differences of occurrence, spread and control between two rice bacterial leaf blight diseases caused by P. ananatis and Xoo, respectively need to be determined in the future.

First Report of Pantoea ananatis causing leaf spot disease of maize in Ecuador

Maize (Zea mays) is the second most cultivated grain crop in Ecuador, with growing significance as a source of fodder and food. During the rainy season (November and December) of 2018 and 2019, a disease of maize that was not previously observed in Ecuador was found at commercial fields of Misqui Sara variety, at four parishes of canton Quito (Tumbaco, Pifo, Puembo, and Checa), province of Pichincha. Infected plants, at tassel initiation, displayed symptoms of localized chlorotic streaks on leaves that expanded with time, and around a month later turned necrotic. Severely affected plants wilted and died. Symptoms appeared in lower leaves first and were later observed in upper leaves as the disease progressed. Disease incidence was between 20 and 30% in the affected plantations, with around 30% of infected plants wilting and dying, resulting in 20-25% of yield losses. Upper leaves from ten symptomatic plants, five from Puembo and five from Checa, were collected randomly. Two 0.5 cm2 pieces of leaf from each plant were excised from the margins of the necrotic lesions, surface sterilized and macerated in 9 mL of sterile peptone water. The 10-3 dilutions were plated onto nutrient agar and incubated at 28°C for 24 hours. Yellow, mucoid colonies were isolated on nutrient agar. Three isolates from Puembo and two from Checa were selected for testing Koch´s postulates and further biochemical and molecular characterization. Isolates were Gram-negative rods, oxidase negative, catalase, indol and citrate positive. Fragments of the 16S, gyrB, and rpoB loci were amplified and sequenced using the 27F/1492R (Lane, D. J., 1991), UP-1/UP-2r (Yamamoto & Harayama, 1995), and rpoBCM81-F/rpoBCM32b-R (Brady, C., et al., 2008) primer pairs, respectively. All isolates presented identical sequences for the different loci, therefore only sequences from isolate FP191505 were deposited in GenBank (GenBank accession no. MW528428-MW528430). A search of homologous sequences using BLAST resulted in identities of 99.3, 99.7, and 100 % for 16S, gyrB, and rpoB, respectively, with sequences from Pantoea ananatis type specimen LGM 2665 (Brady, C., et al., 2008; Hauben, L., et al., 1998; GenBank accession nos NR_119362.1, EF988824.1 EF988996.1), indicating that our isolates belong to this species. Pathogenicity tests were performed by syringe infiltration of bacterial suspensions. Each one of the five characterized P. ananatis isolates was inoculated in four leaves (500 ul of 1 x 108 CFU mL-1 per leave) of three healthy maize plants. Negative control plants were infiltrated with sterile distilled water. Plants were incubated at 28-30°C and 60% relative humidity for 24 hours. Later, plants were maintained in a greenhouse with 27°C/21°C day/night temperatures and observed daily. After six weeks all bacteria-inoculated plants developed symptoms of chlorosis and necrosis while the control was symptomless. Bacteria were re-isolated from symptomatic leaves and identified as P. ananatis following the same methodologies used for the initial identification. To our knowledge, this is the first report of P. ananatis causing leaf spot of maize in Ecuador.