First Report of Pantoea agglomerans Causing Brown Apical Necrosis of Walnut in China

Analysis of key genes for the survival of Pantoea agglomerans under nutritional stress

The absolute amount of nutrients on plant leaves is usually low, and the growth of epiphytic bacteria is typically limited by nutrient content. Thus, is of great significance to study the survival mechanism of epiphytes under nutritional stress for plant disease control. In this paper, Pantoea agglomerans CHTF15 isolated from walnut leaves was used to detect the key genes for the survival of the bacterium under simulated nutrient stress in artificial medium. Genome sequencing was combined with transposon insertion sequencing (Tn-seq) for the detection technique. A total of 105 essential genes were screened from the whole genome. The genes were mainly related to the nucleotide metabolism, protein metabolism, biological oxidation and the gene repair of bacteria analyzed by gene ontology (GO) enrichment analysis. Volcano map analysis demonstrated that the functions of the 15 genes with the most significant differences were generally related to the synthesis of amino acids or proteins, the nucleotide metabolism and homologous recombination and repair. Competitive index analysis revealed that the deletion of the genes dksA and epmA regulating protein synthesis, the gene ribB involved in the nucleotide metabolism and the gene xerD involved in recombination repair induced a significant reduction in the survival ability of the corresponding mutants in the 0.10 % YEP medium and the walnut leaf surface. The results act as a foundation for further in-depth research on the infection process and the mechanisms of pathogenic bacteria.

Physiological and transcriptomic analyses of response of walnuts (Juglans regia) to Pantoea agglomerans infection

Introduction

Walnut blight is a serious bacterial disease that affects the yield and quality of walnuts. Pantoea agglomerans is one of the main causative agents of walnut blight. However, there have been few studies on the response of walnuts to P. agglomerans infection.

Methods

In this study, the soluble sugar, photosynthesis, antioxidant enzyme activities, and secondary metabolites were measured, and the transcriptomic analysis was performed to determine the response of walnut tissue cultures to P. agglomerans infection.

Results

After pathogen inoculation, the soluble sugar content decreased, and photosynthesis was inhibited. Antioxidant enzyme (superoxide dismutase and peroxidase) activities and secondary metabolites (phenol and flavonoid) contents increased, especially in the early stages of inoculation. Transcriptomic analysis revealed that the phenylpropanoid biosynthesis pathway is induced after infection, and pathogen infection promotes ABA and ethylene signal transduction and inhibits auxin signaling. In addition, SA and JA-related gene expression was altered after inoculation with P. agglomerans, and the FLS- and calcium-mediated disease resistance signaling pathways were activated. Furthermore, our results suggested an involvement of the R-protein RPM-mediated disease resistance pathway in the response of walnuts to bacterial infections.

Discussion

Our findings indicated that phenylpropanoid biosynthesis, hormone signal transduction, and plant-pathogen interaction have key roles in pathogenic inoculation, which provide insights into the molecular mechanisms in the response of walnuts to P. agglomerans infection.

Genomics assisted functional characterization of Bacillus velezensis E as a biocontrol and growth promoting bacterium for lily

Lily (Lilium spp.) is one of the most famous ornamental flowers globally. Lily basal rot (also known as root rot or stem rot) and lily gray mold have seriously affected the yield and quality of lily, resulting in huge economic losses. In this study, bacterial strain E was isolated from a continuous lily cropping field. Strain E displayed high control efficiency against lily basal rot and gray mold, caused by Fusarium oxysporum and Botrytis cinerea respectively, and promoted the occurrence of scale bulblets. Strain E displayed strong inhibitory effects against several other plant pathogenic fungi and two pathogenic bacteria in dual culture and disc diffusion assays, respectively. Whole genome sequencing revealed that strain E contained a 3,929,247 bp circular chromosome with 4,056 protein-coding genes and an average GC content of 47.32%. Strain E was classified as Bacillus velezensis using genome-based phylogenetic analysis and average nucleotide identity and digital DNA–DNA hybridization analyses. A total of 86 genes and 13 secondary metabolite biosynthetic gene clusters involved in antifungal and antibacterial activity, plant growth promotion, colonization, nutrient uptake and availability were identified in the genome of strain E. In vitro biochemical assays showed that strain E produced siderophores, proteases, cellulases, biofilms, antifungal and antibacterial substances, and exhibited organic phosphate solubilization and swimming and swarming motility, which were consistent with the results of the genome analysis. Colonization analysis showed that strain E could colonize the root of the lily, but not the leaf. Overall, these results demonstrate that B. velezensis strain E can be used as a potential biofertilizer and biocontrol agent for lily production.

Detection and Control of Pantoea agglomerans Causing Plum Bacterial Shot-Hole Disease by Loop-Mediated Isothermal Amplification Technique

Plum bacterial shot-hole caused by Pantoea agglomerans (P. agglomerans) is one of the primary bacterial diseases in plum tree planting areas, resulting in abnormal growth of plum trees and severe economic losses. Early diagnosis of P. agglomerans is crucial to effectively control plant diseases. In this study, loop-mediated isothermal amplification (LAMP) analysis for genome-specific gene sequences was developed for the specific detection of P. agglomerans. We designed the LAMP primers based on the gyrB gene of P. agglomerans. The best reaction system was 0.2 μmol·L-1 for outer primer F3/B3 and 1.6 μmol·L-1 for inner primer FIP/BIP. The LAMP reaction was optimal at 65°C for 60 min based on the color change and gel electrophoresis. This technology distinguished P. agglomerans from other control bacteria. The detection limit of the LAMP technology was 5 fg·μl-1 genomic DNA of P. agglomerans, which is 1,000 times that of the traditional PCR detection method. The LAMP technology could effectively detect the DNA of P. agglomerans from the infected leaves without symptoms after indoor inoculation. Furthermore, the LAMP technology was applied successfully to detect field samples, and the field control effect of 0.3% tetramycin after LAMP detection reached 82.51%, which was 7.90% higher than that of conventional control. The proposed LAMP detection technology in this study offers the advantages of ease of operation, visibility of results, rapidity, accuracy, and high sensitivity, making it suitable for the early diagnosis of plum bacteria shot-hole disease.

Pantoea agglomerans as a New Etiological Agent of a Bacterial Necrotic Disease of Mango Trees

Bacterial apical necrosis of mango trees, a disease elicited by Pseudomonas syringae pv. syringae, is a primary limiting factor of mango crop production in the Mediterranean region. In this study, a collection of bacterial isolates associated with necrotic symptoms in mango trees similar to those produced by bacterial apical necrosis disease were isolated over five consecutive years in orchards from the Canary Islands. The bacterial isolates were characterized and identified as Pantoea agglomerans. Pathogenicity tests conducted on onion bulbs and mango plants confirmed that P. agglomerans strains isolated from mango trees are a new etiological agent of a bacterial necrotic disease in the Canary Islands. Pathogenicity plasmids of the pPATH family have been previously reported in P. agglomerans. The majority of putatively pathogenic (n = 23) and pathogenic (n = 4) P. agglomerans strains isolated from mango trees harbored four plasmids, one of which was close in size to the 135-kb pPATH pathogenicity plasmid. The analysis of the presence of two major genes in pPATH plasmids (repA and hrpJ) was undertaken in P. agglomerans strains isolated from mango trees. The hrpJ gene was detected in the 140-kb plasmid of pathogenic P. agglomerans strains isolated from mango trees but it showed differences in nucleotide sequences compared with other pathogenic strains. In contrast, the repA gene was not detected in any of the putatively pathogenic and pathogenic P. agglomerans strains isolated from mango trees. Finally, genetic characterization and phylogenetic analysis using the hrpJ gene and the housekeeping genes gyrB and rpoB showed that almost all P. agglomerans strains that were putatively pathogenic and pathogenic on mango trees clustered together, forming a differentiated phylogroup with respect to the other pathogenic P. agglomerans strains described from other hosts.

Diseases and pests noxious to Pleurotus spp. mushroom crops

The Pleurotus genus is one of most extensively studied white-rot fungi due to its exceptional ligninolytic properties. It is an edible mushroom that possesses biological effects, as it contains important bioactive molecules. It is a rich source of nutrients, particularly proteins, minerals as well as vitamins B, C and D. In basidiomycete fungi, intensive cultivations of edible mushrooms can often be affected by some bacterial, mold and virus diseases that rather frequently cause dramatic production loss. These infections are facilitated by the particular conditions under which mushroom cultivation is commonly carried out such as warm temperatures, humidity, carbon dioxide (CO₂) levels and presence of pests. There is not much bibliographic information related to pests of mushrooms and their substrates. The updated review presents a practical checklist of diseases and pests of the Pleurotus genus, providing useful information that may help different users.

Pantoea hericii sp. nov., Isolated from the Fruiting Bodies of Hericium erinaceus

Three Gram-negative, facultatively anaerobic bacterial isolates were obtained from the fruiting bodies of the edible mushroom Hericium erinaceus showing symptoms of soft rot disease in Beijing, China. Sequences of partial 16S rRNA gene placed these isolates in the genus Pantoea. Multilocus sequence analysis based on the partial sequences of atpD, gyrB, infB and rpoB revealed P. eucalypti and P. anthophila as their closest phylogenetic relatives and indicated that these isolates constituted a possible novel species. DNA-DNA hybridization studies confirmed the classification of these isolates as a novel species and phenotypic tests allowed for differentiation from the closest phylogenetic neighbours. The name Pantoea hericii sp. nov. [Type strain LMG 28847(T) = CGMCC 1.15224(T) = JZB 2120024(T)] is proposed.

Pantoea pleuroti sp. nov., Isolated from the Fruiting Bodies of Pleurotus eryngii

Four Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from the fruiting bodies of the edible mushroom Pleurotus eryngii showing symptoms of bacterial blight disease in Beijing, China. Nearly complete 16S rRNA gene sequencing placed these isolates in the genus Pantoea. Multilocus sequence analysis based on the partial sequences of atpD, gyrB, infB and rpoB revealed Pantoea agglomerans as their closest phylogenetic relatives. DNA-DNA hybridization and phenotypic tests confirmed the classification of the new isolates as a novel species. The name Pantoea pleuroti sp. nov. [type strain KCTC 42084(T) = CGMCC 1.12894(T) = JZB 2120015(T)] is proposed.