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Analysis of Endophytic Bacteria Diversity and Community Composition in Soft Rot and Healthy Plant of Allium fistulosum in Tongxin of Ningxia
MAJuan, LAZhen, HUMingzhu, DAIJinxia
Chin Agric Sci Bull ›› 2026, Vol. 42 ›› Issue (2) : 191-197.
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Abbreviation (ISO4): Chin Agric Sci Bull
Editor in chief: Yulong YIN
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Analysis of Endophytic Bacteria Diversity and Community Composition in Soft Rot and Healthy Plant of Allium fistulosum in Tongxin of Ningxia
Allium fistulosum is one of the main characteristic economic crops in Tongxin, Ningxia, but the occurrence of soft rot disease affected the yield and quality of A. fistulosum. The analysis of the composition and diversity of endophytic bacterial communities related to the soft rot of A. fistulosum aims to provide a theoretical basis for understanding the mechanism of soft rot disease occurrence and determining the pathogenic bacteria. 16S rDNA high-throughput sequencing technology and traditional isolation methods were used to compare the commonalities and differences of endophytic bacterial communities in healthy and soft rot plants of A. fistulosum. A total of 1334 OTUs were obtained from healthy and diseased samples, and the richness and diversity of endophytic bacteria were lower in diseased samples than in healthy samples. There were significant differences in endophytic bacterial communities between the two samples, with Proteobacteria as the dominant phylum, and its relative abundance in diseased and healthy plants was 82.51% and 43.49%, respectively. At the genus level, unclassified Enterobacteriaceae was the dominant genus in diseased samples (46.59%), while Chryseobacterium (11.98%), Pseudomonas (7.10%), and Flavobacterium (5.01%) were dominant genera in healthy samples. The bacterial strains isolated from healthy and diseased samples belonged to 11 genera, including 4 genera endemic to healthy plants, 2 genera endemic to diseased plants, and 5 genera owned by both. Among them, Bacillus and Microbacterium were endemic genera to healthy plants with high isolation frequency, which may be related to disease resistance of healthy A. fistulosum; Klebsiella and Pseudomonas were common genera, and had a high isolation frequency in diseased plants. This study confirmed that the changes of endophytic bacterial diversity and community composition in A. fistulosum were closely related to the occurrence of soft rot disease, but the identification of pathogenic bacteria still requires screening and detection using multiple methods.
Allium fistulosum / soft rot disease / endophytic bacteria / 16S rDNA / high-throughput sequencing
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Bacterial diversity analyses often suffer from a bias due to sampling only from a limited number of hosts or narrow geographic locations. This was the case for the phytopathogenic species Dickeya solani, whose members were mainly isolated from a few hosts–potato and ornamentals–and from the same geographical area–Europe and Israel, which are connected by seed trade. Most D. solani members were clonal with the notable exception of the potato isolate RNS05.1.2A and two related strains that are clearly distinct from other D. solani genomes. To investigate if D. solani genomic diversity might be broadened by analysis of strains isolated from other environments, we analysed new strains isolated from ornamentals and from river water as well as strain CFBP 5647 isolated from tomato in the Caribbean island Guadeloupe. While water strains were clonal to RNS05.1.2A, the Caribbean tomato strain formed a third clade. The genomes of the three clades are highly syntenic; they shared almost 3900 protein families, and clade-specific genes were mainly included in genomic islands of extrachromosomal origin. Our study thus revealed both broader D. solani diversity with the characterisation of a third clade isolated in Latin America and a very high genomic conservation between clade members.
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During 2014 to 2015, a devastating bacterial soft rot on cucumber stems and leaves occurred in Shandong, Shanxi, Hebei, Henan, and Liaoning provinces of China, resulting in serious economic losses for cucumber production. The gummosis emerged on the surface of leaves, stems, petioles, and fruit of cucumber. The basal stem color was dark brown and the stem base turned to wet rot. Yellow spots and wet rot emerged at the edge of the infected cucumber leaves and gradually infected the leaf centers. In total, 45 bacterial strains were isolated from the infected tissues. On the basis of phenotypic properties of morphology, physiology, biochemistry, and 16S ribosomal RNA gene sequence analysis, the pathogen was identified as Pectobacterium carotovorum. Multilocus sequence analysis confirmed that the isolates were P. carotovorum subsp. brasiliense, and the pathogens fell in clade II. The pathogenicity of isolated bacteria strains was confirmed. The strains reisolated were the same as the original. The host range test confirmed that strains had a wide range of hosts. As far as we know, this is the first report of cucumber stem soft rot caused by P. carotovorum subsp. brasiliense in China as well as in the world, which has a significant economic impact on cucumber production.
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Klebsiella oxytoca C1036 (C1036) causes induced systemic resistance (ISR) activity against the soft-rot pathogen Pectobacterium carotovorum subsp. carotovorum SCC1 (SCC1). However, microbial metabolites from C1036 involved in ISR activity remain unknown. The present study was performed to identify an ISR-related metabolite produced by C1036.The supernatants of C1036 cultures grown on Luria-Bertani medium were subjected to solvent extraction, repeated column chromatography and preparative liquid chromatography for isolation of an ISR-related metabolite. High-resolution mass spectrometer analysis of the isolated metabolite indicated a C9H15O3N compound with a mass of 185.11. Low-resolution mass spectrometer analysis of the metabolite showed a molecular ion peak at 185 and its fragment ions at 84 and 56. Nuclear magnetic resonance spectrometer analyses characterised all protons and carbons of the isolated metabolite. Based on the data, the isolated metabolite was determined to be butyl 2-pyrrolidone-5-carboxylate (BPC). BPC at 12 mM significantly suppressed the disease symptoms in ISR bioassays against SCC1.This is the first report identifying BPC as an ISR-related metabolite produced by C1036. C1036 may play a role in promoting plant growth because it produces ISR-related metabolites against the plant pathogen SCC1.Copyright 2009 Society of Chemical Industry.
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Five Gram-reaction-negative, aerobic, motile with one to three polar flagella, rod-shaped bacterial strains, MAFF 212408T, MAFF 212409, MAFF 212410, MAFF 301498 and MAFF 730085, were isolated from diseased Welsh onion (Allium fistulosumL.) in Japan. Analysis of their 16S rRNA gene sequences showed that they belong to the genusPseudomonaswith the highest similarity toPseudomonas extremaustralis14-3T(99.86 %),Pseudomonas antarcticaCMS 35T(99.79 %) andPseudomonas poaeDSM 14936T(99.72%). The genomic DNA G+C content was 59.5 mol% and the major fatty acids (>5 %) were summed feature 3, C16 : 0, summed feature 8 and C12 : 02-OH. Multilocus sequence analysis using therpoD,gyrBandrpoBgene sequences and phylogenomic analysis based on the 90 core genes demonstrated that the strains are members of theP. fluorescenssubgroup, but are distant from all closely related species. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analysis confirmed low genomic relatedness to their closest relatives [below the recommended thresholds of 95 % (ANI) and 70 % (dDDH) for prokaryotic species delineation]. The strains were characterized by using API 20NE and Biolog GEN III tests, and inoculation tests in Welsh onion, showing that they are phenotypically differentiated from their closest relatives. Based on the genetic and phenotypic evidence, the strains should be classified as representing a novel species, for which the namePseudomonas kitaguniensissp. nov. is proposed. The type strain is MAFF 212408T(=ICMP 23530T).
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