Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears.

BACKGROUND: Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant. RESULTS: The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani. CONCLUSIONS: It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.

Genetic Diversity of Pseudomonas syringae pv. actinidiae Strains from Different Geographic Regions in China.

Pseudomonas syringae pv. actinidiae causes kiwifruit bacterial canker, with severe infection of the kiwifruit plant resulting in heavy economic losses. Little is known regarding the biodiversity and genetic variation of populations of P. syringae pv. actinidiae in China. A collection of 269 strains of P. syringae pv. actinidiae was identified from 300 isolates obtained from eight sampling sites in five provinces in China. The profiles of 50 strains of P. syringae pv. actinidiae and one strain of P. syringae pv. actinidifoliorum were characterized by Rep-, insertion sequences 50, and randomly amplified polymorphic DNA polymerase chain reaction (PCR). Discriminant analysis of principal coordinates, principal component analysis, and hierarchical cluster analysis were used to analyze the combined fingerprints of the different PCR assays. The results revealed that all isolates belonged to the Psa3 group, that strains of P. syringae pv. actinidiae from China have broad genetic variability that was related to source geographic region, and that Chinese strains can be readily differentiated from strains from France but are very similar to those from Italy. Multilocus sequence typing of 24 representative isolates using the concatenated sequences of five housekeeping genes (cts, gapA, gyrB, pfk, and rpoD) demonstrated that strain Jzhy2 from China formed an independent clade compared with the other biovars, which possessed the hopH1 effector gene but lacked the hopA1 effector gene. A constellation analysis based on the presence or absence of the four loci coding for phytotoxins and a cluster analysis based on the 11 effector genes showed that strains from China formed two distinct clades. All of the strains, including K3 isolated in 1997 from Jeju, Korea, lacked the cfl gene coding for coronatine. In contrast, the tox-argK gene cluster coding for phaseolotoxin was detected in K3 and in the biovar 1 strains (K3, Kw30, and Psa92), and produced a false-positive amplicon for the hopAM1-like gene in this study. To date, only one biovar (biovar 3) is represented by the strains of P. syringae pv. actinidiae from China, despite China being the center of origin for kiwifruit.